--- /srv/rebuilderd/tmp/rebuilderdymdU3D/inputs/r-bioc-phyloseq_1.56.0+dfsg-1_all.deb +++ /srv/rebuilderd/tmp/rebuilderdymdU3D/out/r-bioc-phyloseq_1.56.0+dfsg-1_all.deb ├── file list │ @@ -1,3 +1,3 @@ │ -rw-r--r-- 0 0 0 4 2026-08-10 15:23:36.000000 debian-binary │ --rw-r--r-- 0 0 0 2940 2026-08-10 15:23:36.000000 control.tar.xz │ --rw-r--r-- 0 0 0 2303488 2026-08-10 15:23:36.000000 data.tar.xz │ +-rw-r--r-- 0 0 0 2848 2026-08-10 15:23:36.000000 control.tar.xz │ +-rw-r--r-- 0 0 0 2259600 2026-08-10 15:23:36.000000 data.tar.xz ├── control.tar.xz │ ├── control.tar │ │ ├── file list │ │ │ @@ -1,3 +1,3 @@ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-10 15:23:36.000000 ./ │ │ │ --rw-r--r-- 0 root (0) root (0) 1233 2026-08-10 15:23:36.000000 ./control │ │ │ --rw-r--r-- 0 root (0) root (0) 6303 2026-08-10 15:23:36.000000 ./md5sums │ │ │ +-rw-r--r-- 0 root (0) root (0) 1039 2026-08-10 15:23:36.000000 ./control │ │ │ +-rw-r--r-- 0 root (0) root (0) 6219 2026-08-10 15:23:36.000000 ./md5sums │ │ ├── ./control │ │ │ @@ -1,14 +1,14 @@ │ │ │ Package: r-bioc-phyloseq │ │ │ Version: 1.56.0+dfsg-1 │ │ │ Architecture: all │ │ │ Maintainer: Debian R Packages Maintainers │ │ │ -Installed-Size: 3228 │ │ │ +Installed-Size: 3137 │ │ │ Depends: r-api-4.0, r-api-bioc-3.23, r-cran-ade4 (>= 1.7-4), r-cran-ape (>= 5.0), r-bioc-biobase (>= 2.36.2), r-bioc-biocgenerics (>= 0.22.0), r-bioc-biomformat (>= 1.0.0), r-bioc-biostrings (>= 2.40.0), r-cran-cluster (>= 2.0.4), r-cran-data.table (>= 1.10.4), r-cran-foreach (>= 1.4.3), r-cran-ggplot2 (>= 2.1.0), r-cran-igraph (>= 1.0.1), r-bioc-multtest (>= 2.28.0), r-cran-plyr (>= 1.8.3), r-cran-reshape2 (>= 1.4.1), r-cran-scales (>= 0.4.0), r-cran-vegan (>= 2.5), r-pkg-team-core-architecture │ │ │ -Suggests: r-bioc-biocstyle (>= 2.4), r-bioc-deseq2 (>= 1.16.1), r-bioc-genefilter (>= 1.58), r-cran-knitr (>= 1.16), r-cran-magrittr (>= 1.5), r-bioc-metagenomeseq (>= 1.14), r-cran-rmarkdown (>= 1.6), r-cran-testthat (>= 1.0.2) │ │ │ +Suggests: r-cran-magrittr (>= 1.5) │ │ │ Section: gnu-r │ │ │ Priority: optional │ │ │ Homepage: https://bioconductor.org/packages/phyloseq/ │ │ │ Description: GNU R handling and analysis of high-throughput microbiome census data │ │ │ The Bioconductor module phyloseq provides a set of classes and tools to │ │ │ facilitate the import, storage, analysis, and graphical display of │ │ │ microbiome census data. │ │ ├── ./md5sums │ │ │ ├── ./md5sums │ │ │ │┄ Files differ │ │ │ ├── line order │ │ │ │ @@ -4,15 +4,14 @@ │ │ │ │ usr/lib/R/site-library/phyloseq/Meta/Rd.rds │ │ │ │ usr/lib/R/site-library/phyloseq/Meta/data.rds │ │ │ │ usr/lib/R/site-library/phyloseq/Meta/features.rds │ │ │ │ usr/lib/R/site-library/phyloseq/Meta/hsearch.rds │ │ │ │ usr/lib/R/site-library/phyloseq/Meta/links.rds │ │ │ │ usr/lib/R/site-library/phyloseq/Meta/nsInfo.rds │ │ │ │ usr/lib/R/site-library/phyloseq/Meta/package.rds │ │ │ │ -usr/lib/R/site-library/phyloseq/Meta/vignette.rds │ │ │ │ usr/lib/R/site-library/phyloseq/NAMESPACE │ │ │ │ usr/lib/R/site-library/phyloseq/NEWS │ │ │ │ usr/lib/R/site-library/phyloseq/R/phyloseq │ │ │ │ usr/lib/R/site-library/phyloseq/R/phyloseq.rdb │ │ │ │ usr/lib/R/site-library/phyloseq/R/phyloseq.rdx │ │ │ │ usr/lib/R/site-library/phyloseq/README.md │ │ │ │ usr/lib/R/site-library/phyloseq/data/GlobalPatterns.RData ├── data.tar.xz │ ├── data.tar │ │ ├── file list │ │ │ @@ -11,31 +11,30 @@ │ │ │ -rw-r--r-- 0 root (0) root (0) 6523 2026-08-10 15:23:36.000000 ./usr/lib/R/site-library/phyloseq/Meta/Rd.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 286 2026-08-10 15:23:36.000000 ./usr/lib/R/site-library/phyloseq/Meta/data.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 123 2026-08-10 15:23:36.000000 ./usr/lib/R/site-library/phyloseq/Meta/features.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 6035 2026-08-10 15:23:36.000000 ./usr/lib/R/site-library/phyloseq/Meta/hsearch.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 3129 2026-08-10 15:23:36.000000 ./usr/lib/R/site-library/phyloseq/Meta/links.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 2479 2026-08-10 15:23:36.000000 ./usr/lib/R/site-library/phyloseq/Meta/nsInfo.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 2029 2026-08-10 15:23:36.000000 ./usr/lib/R/site-library/phyloseq/Meta/package.rds │ │ │ --rw-r--r-- 0 root (0) root (0) 314 2026-08-10 15:23:36.000000 ./usr/lib/R/site-library/phyloseq/Meta/vignette.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 7869 2026-08-10 15:23:36.000000 ./usr/lib/R/site-library/phyloseq/NAMESPACE │ │ │ -rw-r--r-- 0 root (0) root (0) 47261 2026-08-10 15:23:36.000000 ./usr/lib/R/site-library/phyloseq/NEWS │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-10 15:23:36.000000 ./usr/lib/R/site-library/phyloseq/R/ │ │ │ -rw-r--r-- 0 root (0) root (0) 1058 2026-08-10 15:23:36.000000 ./usr/lib/R/site-library/phyloseq/R/phyloseq │ │ │ --rw-r--r-- 0 root (0) root (0) 1089417 2026-08-10 15:23:36.000000 ./usr/lib/R/site-library/phyloseq/R/phyloseq.rdb │ │ │ --rw-r--r-- 0 root (0) root (0) 5621 2026-08-10 15:23:36.000000 ./usr/lib/R/site-library/phyloseq/R/phyloseq.rdx │ │ │ +-rw-r--r-- 0 root (0) root (0) 994405 2026-08-10 15:23:36.000000 ./usr/lib/R/site-library/phyloseq/R/phyloseq.rdb │ │ │ +-rw-r--r-- 0 root (0) root (0) 5550 2026-08-10 15:23:36.000000 ./usr/lib/R/site-library/phyloseq/R/phyloseq.rdx │ │ │ -rw-r--r-- 0 root (0) root (0) 2440 2026-08-10 15:23:36.000000 ./usr/lib/R/site-library/phyloseq/README.md │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-10 15:23:36.000000 ./usr/lib/R/site-library/phyloseq/data/ │ │ │ -rw-r--r-- 0 root (0) root (0) 435652 2026-08-10 15:23:36.000000 ./usr/lib/R/site-library/phyloseq/data/GlobalPatterns.RData │ │ │ -rw-r--r-- 0 root (0) root (0) 44 2026-08-10 15:23:36.000000 ./usr/lib/R/site-library/phyloseq/data/datalist │ │ │ -rw-r--r-- 0 root (0) root (0) 195260 2026-08-10 15:23:36.000000 ./usr/lib/R/site-library/phyloseq/data/enterotype.RData │ │ │ -rw-r--r-- 0 root (0) root (0) 1840 2026-08-10 15:23:36.000000 ./usr/lib/R/site-library/phyloseq/data/esophagus.RData │ │ │ -rw-r--r-- 0 root (0) root (0) 107392 2026-08-10 15:23:36.000000 ./usr/lib/R/site-library/phyloseq/data/soilrep.RData │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-10 15:23:36.000000 ./usr/lib/R/site-library/phyloseq/doc/ │ │ │ -rw-r--r-- 0 root (0) root (0) 2785 2026-08-10 15:23:36.000000 ./usr/lib/R/site-library/phyloseq/doc/Unweighted_UniFrac.RData │ │ │ --rw-r--r-- 0 root (0) root (0) 3219 2026-08-10 15:23:36.000000 ./usr/lib/R/site-library/phyloseq/doc/index.html │ │ │ +-rw-r--r-- 0 root (0) root (0) 2069 2026-08-10 15:23:36.000000 ./usr/lib/R/site-library/phyloseq/doc/index.html │ │ │ -rw-r--r-- 0 root (0) root (0) 1034 2026-08-10 15:23:36.000000 ./usr/lib/R/site-library/phyloseq/doc/phyloseq-FAQ.R │ │ │ -rw-r--r-- 0 root (0) root (0) 22815 2026-08-10 15:23:36.000000 ./usr/lib/R/site-library/phyloseq/doc/phyloseq-FAQ.Rmd │ │ │ -rw-r--r-- 0 root (0) root (0) 9621 2026-08-10 15:23:36.000000 ./usr/lib/R/site-library/phyloseq/doc/phyloseq-analysis.R │ │ │ -rw-r--r-- 0 root (0) root (0) 40398 2026-08-10 15:23:36.000000 ./usr/lib/R/site-library/phyloseq/doc/phyloseq-analysis.Rmd │ │ │ -rw-r--r-- 0 root (0) root (0) 4500 2026-08-10 15:23:36.000000 ./usr/lib/R/site-library/phyloseq/doc/phyloseq-basics.R │ │ │ -rw-r--r-- 0 root (0) root (0) 36964 2026-08-10 15:23:36.000000 ./usr/lib/R/site-library/phyloseq/doc/phyloseq-basics.Rmd │ │ │ -rw-r--r-- 0 root (0) root (0) 3220 2026-08-10 15:23:36.000000 ./usr/lib/R/site-library/phyloseq/doc/phyloseq-mixture-models.R │ │ │ @@ -69,17 +68,17 @@ │ │ │ -rw-r--r-- 0 root (0) root (0) 4991 2026-08-10 15:23:36.000000 ./usr/lib/R/site-library/phyloseq/extdata/study_816_split_library_seqs_and_mapping.tar.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 5191 2026-08-10 15:23:36.000000 ./usr/lib/R/site-library/phyloseq/extdata/study_816_split_library_seqs_and_mapping.zip │ │ │ -rw-r--r-- 0 root (0) root (0) 2438 2026-08-10 15:23:36.000000 ./usr/lib/R/site-library/phyloseq/extdata/study_gp.txt │ │ │ -rw-r--r-- 0 root (0) root (0) 12127 2026-08-10 15:23:36.000000 ./usr/lib/R/site-library/phyloseq/extdata/usearch.uc │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-10 15:23:36.000000 ./usr/lib/R/site-library/phyloseq/help/ │ │ │ -rw-r--r-- 0 root (0) root (0) 11844 2026-08-10 15:23:36.000000 ./usr/lib/R/site-library/phyloseq/help/AnIndex │ │ │ -rw-r--r-- 0 root (0) root (0) 2601 2026-08-10 15:23:36.000000 ./usr/lib/R/site-library/phyloseq/help/aliases.rds │ │ │ --rw-r--r-- 0 root (0) root (0) 1298 2026-08-10 15:23:36.000000 ./usr/lib/R/site-library/phyloseq/help/paths.rds │ │ │ --rw-r--r-- 0 root (0) root (0) 421908 2026-08-10 15:23:36.000000 ./usr/lib/R/site-library/phyloseq/help/phyloseq.rdb │ │ │ --rw-r--r-- 0 root (0) root (0) 3100 2026-08-10 15:23:36.000000 ./usr/lib/R/site-library/phyloseq/help/phyloseq.rdx │ │ │ +-rw-r--r-- 0 root (0) root (0) 1323 2026-08-10 15:23:36.000000 ./usr/lib/R/site-library/phyloseq/help/paths.rds │ │ │ +-rw-r--r-- 0 root (0) root (0) 425511 2026-08-10 15:23:36.000000 ./usr/lib/R/site-library/phyloseq/help/phyloseq.rdb │ │ │ +-rw-r--r-- 0 root (0) root (0) 3091 2026-08-10 15:23:36.000000 ./usr/lib/R/site-library/phyloseq/help/phyloseq.rdx │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-10 15:23:36.000000 ./usr/lib/R/site-library/phyloseq/html/ │ │ │ -rw-r--r-- 0 root (0) root (0) 31282 2026-08-10 15:23:36.000000 ./usr/lib/R/site-library/phyloseq/html/00Index.html │ │ │ -rw-r--r-- 0 root (0) root (0) 2133 2026-08-10 15:23:36.000000 ./usr/lib/R/site-library/phyloseq/html/R.css │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-10 15:23:36.000000 ./usr/lib/R/site-library/phyloseq/scripts/ │ │ │ -rw-r--r-- 0 root (0) root (0) 1869 2026-08-10 15:23:36.000000 ./usr/lib/R/site-library/phyloseq/scripts/installer.R │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-10 15:23:36.000000 ./usr/share/ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-10 15:23:36.000000 ./usr/share/doc/ │ │ ├── ./usr/lib/R/site-library/phyloseq/R/phyloseq.rdb │ │ │ ├── Rscript --vanilla - {} │ │ │ │ @@ -288,146 +288,14 @@ │ │ │ │ methods::S3Part(from) <- value │ │ │ │ from │ │ │ │ } │ │ │ │ }, simple = FALSE, by = structure("data.frame", package = "methods"), │ │ │ │ dataPart = FALSE, distance = 3)), versionKey = , │ │ │ │ sealed = FALSE) │ │ │ │ │ │ │ │ -.__C__NULL_OR_list (S4) = new("ClassUnionRepresentation", slots = list(), contains = list(), │ │ │ │ - virtual = TRUE, prototype = NULL, validity = NULL, access = list(), │ │ │ │ - className = structure("NULL_OR_list", package = "SparseArray"), │ │ │ │ - package = "SparseArray", subclasses = list("NULL" = new("SClassExtension", │ │ │ │ - subClass = structure("NULL", package = "methods"), superClass = structure("NULL_OR_list", package = "SparseArray"), │ │ │ │ - package = "SparseArray", coerce = function (from, strict = TRUE) │ │ │ │ - from, test = function (object) │ │ │ │ - TRUE, replace = function (from, to, value) │ │ │ │ - { │ │ │ │ - if (!is(value, "NULL_OR_list")) │ │ │ │ - stop(gettextf("the computation: 'as(object,\"%s\") <- value' is valid when object has class %s only if 'is(value, \"%s\")' is TRUE ('class(value)' was %s)\n", │ │ │ │ - "NULL_OR_list", dQuote("NULL"), "NULL_OR_list", │ │ │ │ - dQuote(class(value))), domain = NA) │ │ │ │ - value │ │ │ │ - }, simple = TRUE, by = character(0), dataPart = FALSE, │ │ │ │ - distance = 1), list = new("SClassExtension", subClass = structure("list", package = "methods"), │ │ │ │ - superClass = structure("NULL_OR_list", package = "SparseArray"), │ │ │ │ - package = "SparseArray", coerce = function (from, strict = TRUE) │ │ │ │ - from, test = function (object) │ │ │ │ - TRUE, replace = function (from, to, value) │ │ │ │ - { │ │ │ │ - if (!is(value, "NULL_OR_list")) │ │ │ │ - stop(gettextf("the computation: 'as(object,\"%s\") <- value' is valid when object has class %s only if 'is(value, \"%s\")' is TRUE ('class(value)' was %s)\n", │ │ │ │ - "NULL_OR_list", dQuote("list"), "NULL_OR_list", │ │ │ │ - dQuote(class(value))), domain = NA) │ │ │ │ - value │ │ │ │ - }, simple = TRUE, by = character(0), dataPart = FALSE, │ │ │ │ - distance = 1), .NULL = new("SClassExtension", subClass = structure(".NULL", package = "methods"), │ │ │ │ - superClass = structure("NULL_OR_list", package = "SparseArray"), │ │ │ │ - package = "methods", coerce = function (from, strict = TRUE) │ │ │ │ - { │ │ │ │ - from <- as(from, "NULL", strict = strict) │ │ │ │ - from │ │ │ │ - }, test = function (object) │ │ │ │ - TRUE, replace = function (from, to, value) │ │ │ │ - { │ │ │ │ - .value <- methods::as(from, "NULL", TRUE) │ │ │ │ - methods::as(.value, "NULL_OR_list") <- value │ │ │ │ - value <- .value │ │ │ │ - { │ │ │ │ - from@.xData <- value │ │ │ │ - from │ │ │ │ - } │ │ │ │ - }, simple = FALSE, by = structure("NULL", package = "methods"), │ │ │ │ - dataPart = FALSE, distance = 2), data.frame = new("SClassExtension", │ │ │ │ - subClass = structure("data.frame", package = "methods"), │ │ │ │ - superClass = structure("NULL_OR_list", package = "SparseArray"), │ │ │ │ - package = "methods", coerce = function (from, strict = TRUE) │ │ │ │ - { │ │ │ │ - if (strict) │ │ │ │ - from <- from@.Data │ │ │ │ - from │ │ │ │ - }, test = function (object) │ │ │ │ - TRUE, replace = function (from, to, value) │ │ │ │ - { │ │ │ │ - .value <- methods::as(from, "list", TRUE) │ │ │ │ - methods::as(.value, "NULL_OR_list") <- value │ │ │ │ - value <- .value │ │ │ │ - { │ │ │ │ - from@.Data <- methods::as(value, "list", strict = FALSE) │ │ │ │ - from │ │ │ │ - } │ │ │ │ - }, simple = TRUE, by = structure("list", package = "methods"), │ │ │ │ - dataPart = FALSE, distance = 2), namedList = new("SClassExtension", │ │ │ │ - subClass = structure("namedList", package = "methods"), │ │ │ │ - superClass = structure("NULL_OR_list", package = "SparseArray"), │ │ │ │ - package = "methods", coerce = function (from, strict = TRUE) │ │ │ │ - { │ │ │ │ - if (strict) │ │ │ │ - from <- from@.Data │ │ │ │ - from │ │ │ │ - }, test = function (object) │ │ │ │ - TRUE, replace = function (from, to, value) │ │ │ │ - { │ │ │ │ - .value <- methods::as(from, "list", TRUE) │ │ │ │ - methods::as(.value, "NULL_OR_list") <- value │ │ │ │ - value <- .value │ │ │ │ - { │ │ │ │ - from@.Data <- methods::as(value, "list", strict = FALSE) │ │ │ │ - from │ │ │ │ - } │ │ │ │ - }, simple = TRUE, by = structure("list", package = "methods"), │ │ │ │ - dataPart = FALSE, distance = 2), listOfMethods = new("SClassExtension", │ │ │ │ - subClass = structure("listOfMethods", package = "methods"), │ │ │ │ - superClass = structure("NULL_OR_list", package = "SparseArray"), │ │ │ │ - package = "methods", coerce = function (from, strict = TRUE) │ │ │ │ - { │ │ │ │ - if (strict) │ │ │ │ - from <- from@.Data │ │ │ │ - from │ │ │ │ - }, test = function (object) │ │ │ │ - TRUE, replace = function (from, to, value) │ │ │ │ - { │ │ │ │ - .value <- methods::as(from, "list", TRUE) │ │ │ │ - methods::as(.value, "NULL_OR_list") <- value │ │ │ │ - value <- .value │ │ │ │ - { │ │ │ │ - .value <- methods::as(from, "namedList", TRUE) │ │ │ │ - methods::as(.value, "list") <- value │ │ │ │ - value <- .value │ │ │ │ - { │ │ │ │ - for (what in c(".Data", "names")) methods::slot(from, │ │ │ │ - what) <- methods::slot(value, what) │ │ │ │ - from │ │ │ │ - } │ │ │ │ - } │ │ │ │ - }, simple = TRUE, by = structure("list", package = "methods"), │ │ │ │ - dataPart = FALSE, distance = 3), sample_data = new("SClassExtension", │ │ │ │ - subClass = structure("sample_data", package = "phyloseq"), │ │ │ │ - superClass = structure("NULL_OR_list", package = "SparseArray"), │ │ │ │ - package = "phyloseq", coerce = function (from, strict = TRUE) │ │ │ │ - { │ │ │ │ - from <- as(from, "data.frame", strict = strict) │ │ │ │ - { │ │ │ │ - if (strict) │ │ │ │ - from <- from@.Data │ │ │ │ - from │ │ │ │ - } │ │ │ │ - }, test = function (object) │ │ │ │ - TRUE, replace = function (from, to, value) │ │ │ │ - { │ │ │ │ - .value <- methods::as(from, "data.frame", TRUE) │ │ │ │ - methods::as(.value, "NULL_OR_list") <- value │ │ │ │ - value <- .value │ │ │ │ - { │ │ │ │ - methods::S3Part(from) <- value │ │ │ │ - from │ │ │ │ - } │ │ │ │ - }, simple = FALSE, by = structure("data.frame", package = "methods"), │ │ │ │ - dataPart = FALSE, distance = 3)), versionKey = , │ │ │ │ - sealed = FALSE) │ │ │ │ - │ │ │ │ .__C__XStringSetOrNULL (S4) = new("ClassUnionRepresentation", slots = list(), contains = list(), │ │ │ │ virtual = TRUE, prototype = NULL, validity = NULL, access = list(), │ │ │ │ className = structure("XStringSetOrNULL", package = "phyloseq"), │ │ │ │ package = "phyloseq", subclasses = list("NULL" = new("SClassExtension", │ │ │ │ subClass = structure("NULL", package = "methods"), superClass = structure("XStringSetOrNULL", package = "phyloseq"), │ │ │ │ package = "phyloseq", coerce = function (from, strict = TRUE) │ │ │ │ from, test = function (object) │ │ │ │ @@ -1056,274 +924,14 @@ │ │ │ │ methods::S3Part(from) <- value │ │ │ │ from │ │ │ │ } │ │ │ │ }, simple = FALSE, by = structure("data.frame", package = "methods"), │ │ │ │ dataPart = FALSE, distance = 3)), versionKey = , │ │ │ │ sealed = FALSE) │ │ │ │ │ │ │ │ -.__C__matrix_OR_array_OR_table_OR_numeric (S4) = new("ClassUnionRepresentation", slots = list(), contains = list(), │ │ │ │ - virtual = TRUE, prototype = structure(numeric(0), dim = 0L), │ │ │ │ - validity = NULL, access = list(), className = structure("matrix_OR_array_OR_table_OR_numeric", package = "MatrixGenerics"), │ │ │ │ - package = "MatrixGenerics", subclasses = list(array = new("SClassExtension", │ │ │ │ - subClass = structure("array", package = "methods"), superClass = structure("matrix_OR_array_OR_table_OR_numeric", package = "MatrixGenerics"), │ │ │ │ - package = "MatrixGenerics", coerce = function (from, │ │ │ │ - strict = TRUE) │ │ │ │ - from, test = function (object) │ │ │ │ - TRUE, replace = function (from, to, value) │ │ │ │ - { │ │ │ │ - if (!is(value, "matrix_OR_array_OR_table_OR_numeric")) │ │ │ │ - stop(gettextf("the computation: 'as(object,\"%s\") <- value' is valid when object has class %s only if 'is(value, \"%s\")' is TRUE ('class(value)' was %s)\n", │ │ │ │ - "matrix_OR_array_OR_table_OR_numeric", dQuote("array"), │ │ │ │ - "matrix_OR_array_OR_table_OR_numeric", dQuote(class(value))), │ │ │ │ - domain = NA) │ │ │ │ - value │ │ │ │ - }, simple = TRUE, by = character(0), dataPart = FALSE, │ │ │ │ - distance = 1), table = new("SClassExtension", subClass = structure("table", package = "methods"), │ │ │ │ - superClass = structure("matrix_OR_array_OR_table_OR_numeric", package = "MatrixGenerics"), │ │ │ │ - package = "MatrixGenerics", coerce = function (from, │ │ │ │ - strict = TRUE) │ │ │ │ - from, test = function (object) │ │ │ │ - TRUE, replace = function (from, to, value) │ │ │ │ - { │ │ │ │ - if (!is(value, "matrix_OR_array_OR_table_OR_numeric")) │ │ │ │ - stop(gettextf("the computation: 'as(object,\"%s\") <- value' is valid when object has class %s only if 'is(value, \"%s\")' is TRUE ('class(value)' was %s)\n", │ │ │ │ - "matrix_OR_array_OR_table_OR_numeric", dQuote("table"), │ │ │ │ - "matrix_OR_array_OR_table_OR_numeric", dQuote(class(value))), │ │ │ │ - domain = NA) │ │ │ │ - value │ │ │ │ - }, simple = TRUE, by = character(0), dataPart = FALSE, │ │ │ │ - distance = 1), numeric = new("SClassExtension", subClass = structure("numeric", package = "methods"), │ │ │ │ - superClass = structure("matrix_OR_array_OR_table_OR_numeric", package = "MatrixGenerics"), │ │ │ │ - package = "MatrixGenerics", coerce = function (from, │ │ │ │ - strict = TRUE) │ │ │ │ - from, test = function (object) │ │ │ │ - TRUE, replace = function (from, to, value) │ │ │ │ - { │ │ │ │ - if (!is(value, "matrix_OR_array_OR_table_OR_numeric")) │ │ │ │ - stop(gettextf("the computation: 'as(object,\"%s\") <- value' is valid when object has class %s only if 'is(value, \"%s\")' is TRUE ('class(value)' was %s)\n", │ │ │ │ - "matrix_OR_array_OR_table_OR_numeric", dQuote("numeric"), │ │ │ │ - "matrix_OR_array_OR_table_OR_numeric", dQuote(class(value))), │ │ │ │ - domain = NA) │ │ │ │ - value │ │ │ │ - }, simple = TRUE, by = character(0), dataPart = FALSE, │ │ │ │ - distance = 1), matrix = new("SClassExtension", subClass = structure("matrix", package = "methods"), │ │ │ │ - superClass = structure("matrix_OR_array_OR_table_OR_numeric", package = "MatrixGenerics"), │ │ │ │ - package = "methods", coerce = function (from, strict = TRUE) │ │ │ │ - { │ │ │ │ - from <- { │ │ │ │ - class(from) <- "array" │ │ │ │ - from │ │ │ │ - } │ │ │ │ - from │ │ │ │ - }, test = function (object) │ │ │ │ - TRUE, replace = function (from, to, value) │ │ │ │ - { │ │ │ │ - .value <- methods::as(from, "array", TRUE) │ │ │ │ - methods::as(.value, "matrix_OR_array_OR_table_OR_numeric") <- value │ │ │ │ - value <- .value │ │ │ │ - { │ │ │ │ - class(value) <- "matrix" │ │ │ │ - value │ │ │ │ - } │ │ │ │ - }, simple = TRUE, by = structure("array", package = "methods"), │ │ │ │ - dataPart = FALSE, distance = 2), summaryDefault = new("SClassExtension", │ │ │ │ - subClass = structure("summaryDefault", package = "methods"), │ │ │ │ - superClass = structure("matrix_OR_array_OR_table_OR_numeric", package = "MatrixGenerics"), │ │ │ │ - package = "methods", coerce = function (from, strict = TRUE) │ │ │ │ - { │ │ │ │ - from <- { │ │ │ │ - if (strict) │ │ │ │ - methods::S3Part(from, S3Class = "table") │ │ │ │ - else from │ │ │ │ - } │ │ │ │ - from │ │ │ │ - }, test = function (object) │ │ │ │ - TRUE, replace = function (from, to, value) │ │ │ │ - { │ │ │ │ - .value <- methods::as(from, "table", TRUE) │ │ │ │ - methods::as(.value, "matrix_OR_array_OR_table_OR_numeric") <- value │ │ │ │ - value <- .value │ │ │ │ - { │ │ │ │ - methods::S3Part(from) <- value │ │ │ │ - from │ │ │ │ - } │ │ │ │ - }, simple = TRUE, by = structure("table", package = "methods"), │ │ │ │ - dataPart = FALSE, distance = 2), integer = new("SClassExtension", │ │ │ │ - subClass = structure("integer", package = "methods"), │ │ │ │ - superClass = structure("matrix_OR_array_OR_table_OR_numeric", package = "MatrixGenerics"), │ │ │ │ - package = "methods", coerce = function (from, strict = TRUE) │ │ │ │ - { │ │ │ │ - from <- { │ │ │ │ - class(from) <- "numeric" │ │ │ │ - from │ │ │ │ - } │ │ │ │ - from │ │ │ │ - }, test = function (object) │ │ │ │ - TRUE, replace = function (from, to, value) │ │ │ │ - { │ │ │ │ - .value <- methods::as(from, "numeric", TRUE) │ │ │ │ - methods::as(.value, "matrix_OR_array_OR_table_OR_numeric") <- value │ │ │ │ - value <- .value │ │ │ │ - { │ │ │ │ - class(value) <- "integer" │ │ │ │ - value │ │ │ │ - } │ │ │ │ - }, simple = TRUE, by = structure("numeric", package = "methods"), │ │ │ │ - dataPart = FALSE, distance = 2), double = new("SClassExtension", │ │ │ │ - subClass = structure("double", package = "methods"), │ │ │ │ - superClass = structure("matrix_OR_array_OR_table_OR_numeric", package = "MatrixGenerics"), │ │ │ │ - package = "methods", coerce = function (from, strict = TRUE) │ │ │ │ - { │ │ │ │ - from <- { │ │ │ │ - class(from) <- "numeric" │ │ │ │ - from │ │ │ │ - } │ │ │ │ - from │ │ │ │ - }, test = function (object) │ │ │ │ - TRUE, replace = function (from, to, value) │ │ │ │ - { │ │ │ │ - .value <- methods::as(from, "numeric", TRUE) │ │ │ │ - methods::as(.value, "matrix_OR_array_OR_table_OR_numeric") <- value │ │ │ │ - value <- .value │ │ │ │ - { │ │ │ │ - class(value) <- "double" │ │ │ │ - value │ │ │ │ - } │ │ │ │ - }, simple = TRUE, by = structure("numeric", package = "methods"), │ │ │ │ - dataPart = FALSE, distance = 2), mts = new("SClassExtension", │ │ │ │ - subClass = structure("mts", package = "methods"), superClass = structure("matrix_OR_array_OR_table_OR_numeric", package = "MatrixGenerics"), │ │ │ │ - package = "methods", coerce = function (from, strict = TRUE) │ │ │ │ - { │ │ │ │ - from <- { │ │ │ │ - from <- { │ │ │ │ - .dm <- dim(from) │ │ │ │ - .dn <- dimnames(from) │ │ │ │ - attributes(from) <- NULL │ │ │ │ - dim(from) <- .dm │ │ │ │ - dimnames(from) <- .dn │ │ │ │ - from │ │ │ │ - } │ │ │ │ - { │ │ │ │ - class(from) <- "array" │ │ │ │ - from │ │ │ │ - } │ │ │ │ - } │ │ │ │ - from │ │ │ │ - }, test = function (object) │ │ │ │ - TRUE, replace = function (from, to, value) │ │ │ │ - { │ │ │ │ - .value <- methods::as(from, "array", TRUE) │ │ │ │ - methods::as(.value, "matrix_OR_array_OR_table_OR_numeric") <- value │ │ │ │ - value <- .value │ │ │ │ - { │ │ │ │ - .value <- methods::as(from, "matrix", TRUE) │ │ │ │ - methods::as(.value, "array") <- value │ │ │ │ - value <- .value │ │ │ │ - { │ │ │ │ - for (what in NULL) methods::slot(from, what) <- methods::slot(value, │ │ │ │ - what) │ │ │ │ - from │ │ │ │ - } │ │ │ │ - } │ │ │ │ - }, simple = TRUE, by = structure("array", package = "methods"), │ │ │ │ - dataPart = FALSE, distance = 3), factor = new("SClassExtension", │ │ │ │ - subClass = structure("factor", package = "methods"), │ │ │ │ - superClass = structure("matrix_OR_array_OR_table_OR_numeric", package = "MatrixGenerics"), │ │ │ │ - package = "methods", coerce = function (from, strict = TRUE) │ │ │ │ - { │ │ │ │ - from <- { │ │ │ │ - if (strict) │ │ │ │ - from <- from@.Data │ │ │ │ - { │ │ │ │ - class(from) <- "numeric" │ │ │ │ - from │ │ │ │ - } │ │ │ │ - } │ │ │ │ - from │ │ │ │ - }, test = function (object) │ │ │ │ - TRUE, replace = function (from, to, value) │ │ │ │ - { │ │ │ │ - .value <- methods::as(from, "numeric", TRUE) │ │ │ │ - methods::as(.value, "matrix_OR_array_OR_table_OR_numeric") <- value │ │ │ │ - value <- .value │ │ │ │ - { │ │ │ │ - .value <- methods::as(from, "integer", TRUE) │ │ │ │ - methods::as(.value, "numeric") <- value │ │ │ │ - value <- .value │ │ │ │ - { │ │ │ │ - from@.Data <- methods::as(value, "integer", │ │ │ │ - strict = FALSE) │ │ │ │ - from │ │ │ │ - } │ │ │ │ - } │ │ │ │ - }, simple = TRUE, by = structure("numeric", package = "methods"), │ │ │ │ - dataPart = FALSE, distance = 3), ordered = new("SClassExtension", │ │ │ │ - subClass = structure("ordered", package = "methods"), │ │ │ │ - superClass = structure("matrix_OR_array_OR_table_OR_numeric", package = "MatrixGenerics"), │ │ │ │ - package = "methods", coerce = function (from, strict = TRUE) │ │ │ │ - { │ │ │ │ - from <- { │ │ │ │ - from <- { │ │ │ │ - if (strict) │ │ │ │ - methods::S3Part(from, S3Class = "factor") │ │ │ │ - else from │ │ │ │ - } │ │ │ │ - { │ │ │ │ - if (strict) │ │ │ │ - from <- from@.Data │ │ │ │ - { │ │ │ │ - class(from) <- "numeric" │ │ │ │ - from │ │ │ │ - } │ │ │ │ - } │ │ │ │ - } │ │ │ │ - from │ │ │ │ - }, test = function (object) │ │ │ │ - TRUE, replace = function (from, to, value) │ │ │ │ - { │ │ │ │ - .value <- methods::as(from, "numeric", TRUE) │ │ │ │ - methods::as(.value, "matrix_OR_array_OR_table_OR_numeric") <- value │ │ │ │ - value <- .value │ │ │ │ - { │ │ │ │ - .value <- methods::as(from, "factor", TRUE) │ │ │ │ - methods::as(.value, "numeric") <- value │ │ │ │ - value <- .value │ │ │ │ - { │ │ │ │ - methods::S3Part(from) <- value │ │ │ │ - from │ │ │ │ - } │ │ │ │ - } │ │ │ │ - }, simple = TRUE, by = structure("numeric", package = "methods"), │ │ │ │ - dataPart = FALSE, distance = 4), taxonomyTable = new("SClassExtension", │ │ │ │ - subClass = structure("taxonomyTable", package = "phyloseq"), │ │ │ │ - superClass = structure("matrix_OR_array_OR_table_OR_numeric", package = "MatrixGenerics"), │ │ │ │ - package = "phyloseq", coerce = function (from, strict = TRUE) │ │ │ │ - { │ │ │ │ - from <- as(from, "matrix", strict = strict) │ │ │ │ - { │ │ │ │ - from <- { │ │ │ │ - class(from) <- "array" │ │ │ │ - from │ │ │ │ - } │ │ │ │ - from │ │ │ │ - } │ │ │ │ - }, test = function (object) │ │ │ │ - TRUE, replace = function (from, to, value) │ │ │ │ - { │ │ │ │ - .value <- methods::as(from, "matrix", TRUE) │ │ │ │ - methods::as(.value, "matrix_OR_array_OR_table_OR_numeric") <- value │ │ │ │ - value <- .value │ │ │ │ - { │ │ │ │ - from@.Data <- methods::as(value, "matrix", strict = FALSE) │ │ │ │ - from │ │ │ │ - } │ │ │ │ - }, simple = FALSE, by = structure("matrix", package = "methods"), │ │ │ │ - dataPart = FALSE, distance = 3)), versionKey = , │ │ │ │ - sealed = FALSE) │ │ │ │ - │ │ │ │ .__C__otu_table (S4) = new("classRepresentation", slots = list(.Data = structure("matrix", package = "methods"), │ │ │ │ taxa_are_rows = structure("logical", package = "methods")), │ │ │ │ contains = list(matrix = new("SClassExtension", subClass = structure("otu_table", package = "phyloseq"), │ │ │ │ superClass = structure("matrix", package = "methods"), │ │ │ │ package = "phyloseq", coerce = function (from, strict = TRUE) │ │ │ │ { │ │ │ │ .dm <- dim(from) │ │ │ │ @@ -1393,39 +1001,14 @@ │ │ │ │ methods::as(.value, "structure") <- value │ │ │ │ value <- .value │ │ │ │ { │ │ │ │ from@.Data <- methods::as(value, "matrix", strict = FALSE) │ │ │ │ from │ │ │ │ } │ │ │ │ }, simple = TRUE, by = structure("matrix", package = "methods"), │ │ │ │ - dataPart = FALSE, distance = 3), matrix_OR_array_OR_table_OR_numeric = new("SClassExtension", │ │ │ │ - subClass = structure("otu_table", package = "phyloseq"), │ │ │ │ - superClass = structure("matrix_OR_array_OR_table_OR_numeric", package = "MatrixGenerics"), │ │ │ │ - package = "phyloseq", coerce = function (from, strict = TRUE) │ │ │ │ - { │ │ │ │ - if (strict) │ │ │ │ - from <- from@.Data │ │ │ │ - { │ │ │ │ - from <- { │ │ │ │ - class(from) <- "array" │ │ │ │ - from │ │ │ │ - } │ │ │ │ - from │ │ │ │ - } │ │ │ │ - }, test = function (object) │ │ │ │ - TRUE, replace = function (from, to, value) │ │ │ │ - { │ │ │ │ - .value <- methods::as(from, "matrix", TRUE) │ │ │ │ - methods::as(.value, "matrix_OR_array_OR_table_OR_numeric") <- value │ │ │ │ - value <- .value │ │ │ │ - { │ │ │ │ - from@.Data <- methods::as(value, "matrix", strict = FALSE) │ │ │ │ - from │ │ │ │ - } │ │ │ │ - }, simple = TRUE, by = structure("matrix", package = "methods"), │ │ │ │ dataPart = FALSE, distance = 3), vector = new("SClassExtension", │ │ │ │ subClass = structure("otu_table", package = "phyloseq"), │ │ │ │ superClass = structure("vector", package = "methods"), │ │ │ │ package = "phyloseq", coerce = function (from, strict = TRUE) │ │ │ │ { │ │ │ │ from <- as(from, "matrix", strict = strict) │ │ │ │ { │ │ │ │ @@ -1813,40 +1396,14 @@ │ │ │ │ methods::as(.value, "list_OR_List") <- value │ │ │ │ value <- .value │ │ │ │ { │ │ │ │ methods::S3Part(from) <- value │ │ │ │ from │ │ │ │ } │ │ │ │ }, simple = TRUE, by = structure("data.frame", package = "methods"), │ │ │ │ - dataPart = FALSE, distance = 3), NULL_OR_list = new("SClassExtension", │ │ │ │ - subClass = structure("sample_data", package = "phyloseq"), │ │ │ │ - superClass = structure("NULL_OR_list", package = "SparseArray"), │ │ │ │ - package = "phyloseq", coerce = function (from, strict = TRUE) │ │ │ │ - { │ │ │ │ - from <- { │ │ │ │ - if (strict) │ │ │ │ - methods::S3Part(from, S3Class = "data.frame") │ │ │ │ - else from │ │ │ │ - } │ │ │ │ - { │ │ │ │ - if (strict) │ │ │ │ - from <- from@.Data │ │ │ │ - from │ │ │ │ - } │ │ │ │ - }, test = function (object) │ │ │ │ - TRUE, replace = function (from, to, value) │ │ │ │ - { │ │ │ │ - .value <- methods::as(from, "data.frame", TRUE) │ │ │ │ - methods::as(.value, "NULL_OR_list") <- value │ │ │ │ - value <- .value │ │ │ │ - { │ │ │ │ - methods::S3Part(from) <- value │ │ │ │ - from │ │ │ │ - } │ │ │ │ - }, simple = TRUE, by = structure("data.frame", package = "methods"), │ │ │ │ dataPart = FALSE, distance = 3), vector_OR_factor = new("SClassExtension", │ │ │ │ subClass = structure("sample_data", package = "phyloseq"), │ │ │ │ superClass = structure("vector_OR_factor", package = "S4Vectors"), │ │ │ │ package = "phyloseq", coerce = function (from, strict = TRUE) │ │ │ │ { │ │ │ │ from <- { │ │ │ │ if (strict) │ │ │ │ @@ -2033,39 +1590,14 @@ │ │ │ │ methods::as(.value, "structure") <- value │ │ │ │ value <- .value │ │ │ │ { │ │ │ │ from@.Data <- methods::as(value, "matrix", strict = FALSE) │ │ │ │ from │ │ │ │ } │ │ │ │ }, simple = TRUE, by = structure("matrix", package = "methods"), │ │ │ │ - dataPart = FALSE, distance = 3), matrix_OR_array_OR_table_OR_numeric = new("SClassExtension", │ │ │ │ - subClass = structure("taxonomyTable", package = "phyloseq"), │ │ │ │ - superClass = structure("matrix_OR_array_OR_table_OR_numeric", package = "MatrixGenerics"), │ │ │ │ - package = "phyloseq", coerce = function (from, strict = TRUE) │ │ │ │ - { │ │ │ │ - if (strict) │ │ │ │ - from <- from@.Data │ │ │ │ - { │ │ │ │ - from <- { │ │ │ │ - class(from) <- "array" │ │ │ │ - from │ │ │ │ - } │ │ │ │ - from │ │ │ │ - } │ │ │ │ - }, test = function (object) │ │ │ │ - TRUE, replace = function (from, to, value) │ │ │ │ - { │ │ │ │ - .value <- methods::as(from, "matrix", TRUE) │ │ │ │ - methods::as(.value, "matrix_OR_array_OR_table_OR_numeric") <- value │ │ │ │ - value <- .value │ │ │ │ - { │ │ │ │ - from@.Data <- methods::as(value, "matrix", strict = FALSE) │ │ │ │ - from │ │ │ │ - } │ │ │ │ - }, simple = TRUE, by = structure("matrix", package = "methods"), │ │ │ │ dataPart = FALSE, distance = 3), vector = new("SClassExtension", │ │ │ │ subClass = structure("taxonomyTable", package = "phyloseq"), │ │ │ │ superClass = structure("vector", package = "methods"), │ │ │ │ package = "phyloseq", coerce = function (from, strict = TRUE) │ │ │ │ { │ │ │ │ from <- as(from, "matrix", strict = strict) │ │ │ │ { │ │ │ │ @@ -3632,15 +3164,15 @@ │ │ │ │ "imports" = " Biostrings = c(.__C__QualityScaledRNAStringSet = ".__C__QualityScaledRNAStringSet"), " │ │ │ │ "imports" = " Biostrings = c(.__C__QualityScaledXStringSet = ".__C__QualityScaledXStringSet"), " │ │ │ │ "imports" = " Biostrings = c(.__C__RNAStringSet = ".__C__RNAStringSet"), " │ │ │ │ "imports" = " Biostrings = c(.__C__SolexaQuality = ".__C__SolexaQuality"), " │ │ │ │ "imports" = " Biostrings = c(.__C__XStringQuality = ".__C__XStringQuality"), " │ │ │ │ "imports" = " Biostrings = c(.__C__XStringSet = ".__C__XStringSet"))" │ │ │ │ "lazydata" = "" │ │ │ │ - "path" = ""/home/moeller/Salsa/r-bioc-phyloseq/debian/r-bioc-phyloseq/usr/lib/R/site-library/phyloseq"" │ │ │ │ + "path" = ""/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/debian/r-bioc-phyloseq/usr/lib/R/site-library/phyloseq"" │ │ │ │ "spec" = "c(name = "phyloseq", version = "1.56.0")" │ │ │ │ } │ │ │ │ │ │ │ │ .__S3MethodsTable__. (environment) = │ │ │ │ { │ │ │ │ } │ │ │ │ │ │ │ │ @@ -5169,31 +4701,14 @@ │ │ │ │ │ │ │ │ .__T__t:base (environment) = │ │ │ │ { │ │ │ │ "ANY" = "new("derivedDefaultMethod", .Data = function (x) " │ │ │ │ "ANY" = "UseMethod("t"), target = new("signature", .Data = "ANY", names = "x", " │ │ │ │ "ANY" = " package = "methods"), defined = new("signature", .Data = "ANY", " │ │ │ │ "ANY" = " names = "x", package = "methods"), generic = structure("t", package = "base"))" │ │ │ │ - "Array" = "new("MethodDefinition", .Data = function (x) " │ │ │ │ - "Array" = "{" │ │ │ │ - "Array" = " if (!isS4(x)) {" │ │ │ │ - "Array" = " x_class <- class(x)" │ │ │ │ - "Array" = " if (length(x_class) >= 2L) {" │ │ │ │ - "Array" = " class(x) <- tail(x_class, n = -1L)" │ │ │ │ - "Array" = " on.exit(class(x) <- x_class)" │ │ │ │ - "Array" = " return(base::t(x))" │ │ │ │ - "Array" = " }" │ │ │ │ - "Array" = " }" │ │ │ │ - "Array" = " if (length(dim(x)) != 2L) " │ │ │ │ - "Array" = " stop(wmsg("the ", class(x), " object to transpose ", " │ │ │ │ - "Array" = " "must have exactly 2 dimensions"))" │ │ │ │ - "Array" = " aperm(x)" │ │ │ │ - "Array" = "}, target = new("signature", .Data = "Array", names = "x", package = "S4Arrays"), " │ │ │ │ - "Array" = " defined = new("signature", .Data = "Array", names = "x", " │ │ │ │ - "Array" = " package = "S4Arrays"), generic = structure("t", package = "base"))" │ │ │ │ "CsparseMatrix" = "new("MethodDefinition", .Data = function (x) " │ │ │ │ "CsparseMatrix" = ".Call(R_sparse_transpose, x, FALSE), target = new("signature", " │ │ │ │ "CsparseMatrix" = " .Data = "CsparseMatrix", names = "x", package = "Matrix"), " │ │ │ │ "CsparseMatrix" = " defined = new("signature", .Data = "CsparseMatrix", names = "x", " │ │ │ │ "CsparseMatrix" = " package = "Matrix"), generic = structure("t", package = "base"))" │ │ │ │ "DataFrame" = "new("MethodDefinition", .Data = function (x) " │ │ │ │ "DataFrame" = "{" │ │ │ │ @@ -5201,31 +4716,14 @@ │ │ │ │ "DataFrame" = " if (!is.null(x_mcols)) " │ │ │ │ "DataFrame" = " mcols(x) <- NULL" │ │ │ │ "DataFrame" = " new2("TransposedDataFrame", data = x, elementMetadata = x_mcols, " │ │ │ │ "DataFrame" = " check = FALSE)" │ │ │ │ "DataFrame" = "}, target = new("signature", .Data = "DataFrame", names = "x", " │ │ │ │ "DataFrame" = " package = "S4Vectors"), defined = new("signature", .Data = "DataFrame", " │ │ │ │ "DataFrame" = " names = "x", package = "S4Vectors"), generic = structure("t", package = "base"))" │ │ │ │ - "DelayedArray" = "new("MethodDefinition", .Data = function (x) " │ │ │ │ - "DelayedArray" = "{" │ │ │ │ - "DelayedArray" = " if (!isS4(x)) {" │ │ │ │ - "DelayedArray" = " x_class <- class(x)" │ │ │ │ - "DelayedArray" = " if (length(x_class) >= 2L) {" │ │ │ │ - "DelayedArray" = " class(x) <- tail(x_class, n = -1L)" │ │ │ │ - "DelayedArray" = " on.exit(class(x) <- x_class)" │ │ │ │ - "DelayedArray" = " return(base::t(x))" │ │ │ │ - "DelayedArray" = " }" │ │ │ │ - "DelayedArray" = " }" │ │ │ │ - "DelayedArray" = " if (length(dim(x)) != 2L) " │ │ │ │ - "DelayedArray" = " stop(wmsg("the ", class(x), " object to transpose ", " │ │ │ │ - "DelayedArray" = " "must have exactly 2 dimensions"))" │ │ │ │ - "DelayedArray" = " aperm(x)" │ │ │ │ - "DelayedArray" = "}, target = new("signature", .Data = "DelayedArray", names = "x", " │ │ │ │ - "DelayedArray" = " package = "DelayedArray"), defined = new("signature", .Data = "DelayedArray", " │ │ │ │ - "DelayedArray" = " names = "x", package = "DelayedArray"), generic = structure("t", package = "base"))" │ │ │ │ "Hits" = "new("MethodDefinition", .Data = function (x) " │ │ │ │ "Hits" = "{" │ │ │ │ "Hits" = " if (is(x, "SortedByQueryHits")) {" │ │ │ │ "Hits" = " return(new_Hits(class(x), to(x), from(x), nRnode(x), " │ │ │ │ "Hits" = " nLnode(x), mcols(x, use.names = FALSE)))" │ │ │ │ "Hits" = " }" │ │ │ │ "Hits" = " BiocGenerics:::replaceSlots(x, from = to(x), to = from(x), " │ │ │ │ @@ -5236,48 +4734,28 @@ │ │ │ │ "HitsList" = "new("MethodDefinition", .Data = function (x) " │ │ │ │ "HitsList" = "{" │ │ │ │ "HitsList" = " x@elements <- lapply(as.list(x, use.names = FALSE), t)" │ │ │ │ "HitsList" = " x" │ │ │ │ "HitsList" = "}, target = new("signature", .Data = "HitsList", names = "x", " │ │ │ │ "HitsList" = " package = "S4Vectors"), defined = new("signature", .Data = "HitsList", " │ │ │ │ "HitsList" = " names = "x", package = "S4Vectors"), generic = structure("t", package = "base"))" │ │ │ │ - "NaMatrix" = "new("MethodDefinition", .Data = function (x) " │ │ │ │ - "NaMatrix" = "{" │ │ │ │ - "NaMatrix" = " check_svt_version(x)" │ │ │ │ - "NaMatrix" = " new_NaSVT <- SparseArray.Call("C_transpose_2D_SVT", x@dim, " │ │ │ │ - "NaMatrix" = " x@type, x@NaSVT)" │ │ │ │ - "NaMatrix" = " BiocGenerics:::replaceSlots(x, dim = rev(x@dim), dimnames = rev(x@dimnames), " │ │ │ │ - "NaMatrix" = " NaSVT = new_NaSVT, check = FALSE)" │ │ │ │ - "NaMatrix" = "}, target = new("signature", .Data = "NaMatrix", names = "x", " │ │ │ │ - "NaMatrix" = " package = "SparseArray"), defined = new("signature", .Data = "NaMatrix", " │ │ │ │ - "NaMatrix" = " names = "x", package = "SparseArray"), generic = structure("t", package = "base"))" │ │ │ │ "Pairs" = "new("MethodDefinition", .Data = function (x) " │ │ │ │ "Pairs" = "{" │ │ │ │ "Pairs" = " tx <- x" │ │ │ │ "Pairs" = " first(tx) <- second(x)" │ │ │ │ "Pairs" = " second(tx) <- first(x)" │ │ │ │ "Pairs" = " tx" │ │ │ │ "Pairs" = "}, target = new("signature", .Data = "Pairs", names = "x", package = "S4Vectors"), " │ │ │ │ "Pairs" = " defined = new("signature", .Data = "Pairs", names = "x", " │ │ │ │ "Pairs" = " package = "S4Vectors"), generic = structure("t", package = "base"))" │ │ │ │ "RsparseMatrix" = "new("MethodDefinition", .Data = function (x) " │ │ │ │ "RsparseMatrix" = ".Call(R_sparse_transpose, x, FALSE), target = new("signature", " │ │ │ │ "RsparseMatrix" = " .Data = "RsparseMatrix", names = "x", package = "Matrix"), " │ │ │ │ "RsparseMatrix" = " defined = new("signature", .Data = "RsparseMatrix", names = "x", " │ │ │ │ "RsparseMatrix" = " package = "Matrix"), generic = structure("t", package = "base"))" │ │ │ │ - "SVT_SparseMatrix" = "new("MethodDefinition", .Data = function (x) " │ │ │ │ - "SVT_SparseMatrix" = "{" │ │ │ │ - "SVT_SparseMatrix" = " check_svt_version(x)" │ │ │ │ - "SVT_SparseMatrix" = " new_SVT <- SparseArray.Call("C_transpose_2D_SVT", x@dim, " │ │ │ │ - "SVT_SparseMatrix" = " x@type, x@SVT)" │ │ │ │ - "SVT_SparseMatrix" = " BiocGenerics:::replaceSlots(x, dim = rev(x@dim), dimnames = rev(x@dimnames), " │ │ │ │ - "SVT_SparseMatrix" = " SVT = new_SVT, check = FALSE)" │ │ │ │ - "SVT_SparseMatrix" = "}, target = new("signature", .Data = "SVT_SparseMatrix", names = "x", " │ │ │ │ - "SVT_SparseMatrix" = " package = "SparseArray"), defined = new("signature", .Data = "SVT_SparseMatrix", " │ │ │ │ - "SVT_SparseMatrix" = " names = "x", package = "SparseArray"), generic = structure("t", package = "base"))" │ │ │ │ "TransposedDataFrame" = "new("MethodDefinition", .Data = function (x) " │ │ │ │ "TransposedDataFrame" = "{" │ │ │ │ "TransposedDataFrame" = " ans <- x@data" │ │ │ │ "TransposedDataFrame" = " mcols(ans) <- mcols(x, use.names = FALSE)" │ │ │ │ "TransposedDataFrame" = " ans" │ │ │ │ "TransposedDataFrame" = "}, target = new("signature", .Data = "TransposedDataFrame", names = "x", " │ │ │ │ "TransposedDataFrame" = " package = "S4Vectors"), defined = new("signature", .Data = "TransposedDataFrame", " │ │ ├── ./usr/lib/R/site-library/phyloseq/R/phyloseq.rdx │ │ │ ├── phyloseq.rdx-content │ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {} │ │ │ │ │ @@ -1,1552 +1,1531 @@ │ │ │ │ │ $variables │ │ │ │ │ $variables$.S3MethodsClasses │ │ │ │ │ [1] 1985 52 │ │ │ │ │ │ │ │ │ │ $variables$.__C__AssayData │ │ │ │ │ [1] 19336 3470 │ │ │ │ │ │ │ │ │ │ -$variables$.__C__NULL_OR_list │ │ │ │ │ -[1] 40116 2811 │ │ │ │ │ - │ │ │ │ │ $variables$.__C__XStringSetOrNULL │ │ │ │ │ -[1] 56360 4008 │ │ │ │ │ +[1] 36255 4007 │ │ │ │ │ │ │ │ │ │ $variables$.__C__data.frameOrNULL │ │ │ │ │ -[1] 60368 1874 │ │ │ │ │ +[1] 40262 1874 │ │ │ │ │ │ │ │ │ │ $variables$.__C__list_OR_List │ │ │ │ │ -[1] 62242 4161 │ │ │ │ │ - │ │ │ │ │ -$variables$.__C__matrix_OR_array_OR_table_OR_numeric │ │ │ │ │ -[1] 66403 4274 │ │ │ │ │ +[1] 42136 4161 │ │ │ │ │ │ │ │ │ │ $variables$.__C__otu_table │ │ │ │ │ -[1] 70677 3422 │ │ │ │ │ +[1] 46297 3306 │ │ │ │ │ │ │ │ │ │ $variables$.__C__otu_tableOrNULL │ │ │ │ │ -[1] 74099 1662 │ │ │ │ │ +[1] 49603 1660 │ │ │ │ │ │ │ │ │ │ $variables$.__C__phylo │ │ │ │ │ -[1] 75761 1400 │ │ │ │ │ +[1] 51263 1400 │ │ │ │ │ │ │ │ │ │ $variables$.__C__phyloOrNULL │ │ │ │ │ -[1] 77161 1656 │ │ │ │ │ +[1] 52663 1655 │ │ │ │ │ │ │ │ │ │ $variables$.__C__phyloseq │ │ │ │ │ -[1] 78817 1227 │ │ │ │ │ +[1] 54318 1227 │ │ │ │ │ │ │ │ │ │ $variables$.__C__sample_data │ │ │ │ │ -[1] 80044 3156 │ │ │ │ │ +[1] 55545 3059 │ │ │ │ │ │ │ │ │ │ $variables$.__C__sample_dataOrNULL │ │ │ │ │ -[1] 83200 1662 │ │ │ │ │ +[1] 58604 1660 │ │ │ │ │ │ │ │ │ │ $variables$.__C__taxonomyTable │ │ │ │ │ -[1] 84862 3365 │ │ │ │ │ +[1] 60264 3251 │ │ │ │ │ │ │ │ │ │ $variables$.__C__taxonomyTableOrNULL │ │ │ │ │ -[1] 88227 1666 │ │ │ │ │ +[1] 63515 1666 │ │ │ │ │ │ │ │ │ │ $variables$.__C__vector_OR_Vector │ │ │ │ │ -[1] 89893 6599 │ │ │ │ │ +[1] 65181 6599 │ │ │ │ │ │ │ │ │ │ $variables$.__C__vector_OR_factor │ │ │ │ │ -[1] 96492 5145 │ │ │ │ │ +[1] 71780 5145 │ │ │ │ │ │ │ │ │ │ $variables$.__NAMESPACE__. │ │ │ │ │ -[1] 108582 53 │ │ │ │ │ +[1] 83880 53 │ │ │ │ │ │ │ │ │ │ $variables$.__S3MethodsTable__. │ │ │ │ │ -[1] 108766 53 │ │ │ │ │ +[1] 84064 53 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__JSD:phyloseq` │ │ │ │ │ -[1] 115984 53 │ │ │ │ │ +[1] 91286 53 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__UniFrac:phyloseq` │ │ │ │ │ -[1] 120804 53 │ │ │ │ │ +[1] 96104 53 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__[:base` │ │ │ │ │ -[1] 185498 53 │ │ │ │ │ +[1] 147895 53 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__capscale.phyloseq:phyloseq` │ │ │ │ │ -[1] 191994 53 │ │ │ │ │ +[1] 154391 53 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__cca.phyloseq:phyloseq` │ │ │ │ │ -[1] 197631 53 │ │ │ │ │ +[1] 160028 53 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__coerce:methods` │ │ │ │ │ -[1] 499670 53 │ │ │ │ │ +[1] 417242 53 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__coerce<-:methods` │ │ │ │ │ -[1] 507614 54 │ │ │ │ │ +[1] 423839 54 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__distance:phyloseq` │ │ │ │ │ -[1] 517149 54 │ │ │ │ │ +[1] 433374 54 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__fix_phylo:phyloseq` │ │ │ │ │ -[1] 519476 54 │ │ │ │ │ +[1] 435702 54 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__genefilter_sample:phyloseq` │ │ │ │ │ -[1] 523121 54 │ │ │ │ │ +[1] 439346 54 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__get_sample:phyloseq` │ │ │ │ │ -[1] 525604 54 │ │ │ │ │ +[1] 441829 54 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__get_taxa:phyloseq` │ │ │ │ │ -[1] 528080 54 │ │ │ │ │ +[1] 444305 54 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__index_reorder:phyloseq` │ │ │ │ │ -[1] 534063 54 │ │ │ │ │ +[1] 450289 54 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__merge_phyloseq_pair:phyloseq` │ │ │ │ │ -[1] 547298 54 │ │ │ │ │ +[1] 463524 54 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__merge_samples:phyloseq` │ │ │ │ │ -[1] 557444 54 │ │ │ │ │ +[1] 473669 54 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__merge_taxa:phyloseq` │ │ │ │ │ -[1] 567146 54 │ │ │ │ │ +[1] 483371 54 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__mt:phyloseq` │ │ │ │ │ -[1] 576605 54 │ │ │ │ │ +[1] 492831 54 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__nsamples:phyloseq` │ │ │ │ │ -[1] 579120 54 │ │ │ │ │ +[1] 495346 54 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__ntaxa:phyloseq` │ │ │ │ │ -[1] 582086 54 │ │ │ │ │ +[1] 498313 54 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__otu_table:phyloseq` │ │ │ │ │ -[1] 585459 54 │ │ │ │ │ +[1] 501686 54 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__otu_table<-:phyloseq` │ │ │ │ │ -[1] 587939 54 │ │ │ │ │ +[1] 504166 54 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__phy_tree:phyloseq` │ │ │ │ │ -[1] 590138 54 │ │ │ │ │ +[1] 506356 54 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__phy_tree<-:phyloseq` │ │ │ │ │ -[1] 592506 54 │ │ │ │ │ +[1] 508724 54 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__plot_phyloseq:phyloseq` │ │ │ │ │ -[1] 595595 54 │ │ │ │ │ +[1] 511818 54 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__prune_samples:phyloseq` │ │ │ │ │ -[1] 601481 54 │ │ │ │ │ +[1] 517707 54 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__prune_taxa:phyloseq` │ │ │ │ │ -[1] 611106 54 │ │ │ │ │ +[1] 527332 54 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__refseq:phyloseq` │ │ │ │ │ -[1] 613323 54 │ │ │ │ │ +[1] 529540 54 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__sample_data:phyloseq` │ │ │ │ │ -[1] 616131 54 │ │ │ │ │ +[1] 532345 54 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__sample_names:phyloseq` │ │ │ │ │ -[1] 618659 54 │ │ │ │ │ +[1] 534874 54 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__sample_names<-:phyloseq` │ │ │ │ │ -[1] 622725 54 │ │ │ │ │ +[1] 538940 54 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__show:methods` │ │ │ │ │ -[1] 829936 54 │ │ │ │ │ +[1] 739442 54 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__t:base` │ │ │ │ │ -[1] 845906 54 │ │ │ │ │ +[1] 750906 54 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__tax_table:phyloseq` │ │ │ │ │ -[1] 849598 54 │ │ │ │ │ +[1] 754598 54 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__tax_table<-:phyloseq` │ │ │ │ │ -[1] 852360 54 │ │ │ │ │ +[1] 757357 54 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__taxa_are_rows:phyloseq` │ │ │ │ │ -[1] 854372 54 │ │ │ │ │ +[1] 759373 54 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__taxa_are_rows<-:phyloseq` │ │ │ │ │ -[1] 857076 54 │ │ │ │ │ +[1] 762072 54 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__taxa_names:phyloseq` │ │ │ │ │ -[1] 860140 54 │ │ │ │ │ +[1] 765136 54 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__taxa_names<-:phyloseq` │ │ │ │ │ -[1] 865164 54 │ │ │ │ │ +[1] 770160 54 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__vegdist:vegan` │ │ │ │ │ -[1] 887083 54 │ │ │ │ │ +[1] 792076 54 │ │ │ │ │ │ │ │ │ │ $variables$.__global__ │ │ │ │ │ -[1] 887137 291 │ │ │ │ │ +[1] 792130 291 │ │ │ │ │ │ │ │ │ │ $variables$.packageName │ │ │ │ │ -[1] 887428 53 │ │ │ │ │ +[1] 792421 53 │ │ │ │ │ │ │ │ │ │ $variables$.requireCachedGenerics │ │ │ │ │ -[1] 887481 100 │ │ │ │ │ +[1] 792474 100 │ │ │ │ │ │ │ │ │ │ $variables$DPCoA │ │ │ │ │ -[1] 887581 1224 │ │ │ │ │ +[1] 792574 1224 │ │ │ │ │ │ │ │ │ │ $variables$JSD │ │ │ │ │ -[1] 888805 430 │ │ │ │ │ +[1] 793798 429 │ │ │ │ │ │ │ │ │ │ $variables$RadialTheta │ │ │ │ │ -[1] 889235 734 │ │ │ │ │ +[1] 794227 734 │ │ │ │ │ │ │ │ │ │ $variables$UniFrac │ │ │ │ │ -[1] 889969 518 │ │ │ │ │ +[1] 794961 517 │ │ │ │ │ │ │ │ │ │ $variables$access │ │ │ │ │ -[1] 890487 925 │ │ │ │ │ +[1] 795478 925 │ │ │ │ │ │ │ │ │ │ $variables$build_tax_table │ │ │ │ │ -[1] 891412 1201 │ │ │ │ │ +[1] 796403 1201 │ │ │ │ │ │ │ │ │ │ $variables$capscale.phyloseq │ │ │ │ │ -[1] 892613 831 │ │ │ │ │ +[1] 797604 831 │ │ │ │ │ │ │ │ │ │ $variables$cca.phyloseq │ │ │ │ │ -[1] 893444 494 │ │ │ │ │ +[1] 798435 494 │ │ │ │ │ │ │ │ │ │ $variables$chunkReOrder │ │ │ │ │ -[1] 893938 828 │ │ │ │ │ +[1] 798929 828 │ │ │ │ │ │ │ │ │ │ $variables$decorana │ │ │ │ │ -[1] 894766 72 │ │ │ │ │ +[1] 799757 72 │ │ │ │ │ │ │ │ │ │ $variables$deprecated_phyloseq_function │ │ │ │ │ -[1] 894838 192 │ │ │ │ │ +[1] 799829 192 │ │ │ │ │ │ │ │ │ │ $variables$distance │ │ │ │ │ -[1] 895030 491 │ │ │ │ │ +[1] 800021 490 │ │ │ │ │ │ │ │ │ │ $variables$distanceMethodList │ │ │ │ │ -[1] 895521 347 │ │ │ │ │ +[1] 800511 347 │ │ │ │ │ │ │ │ │ │ $variables$dpcoa │ │ │ │ │ -[1] 895868 68 │ │ │ │ │ +[1] 800858 68 │ │ │ │ │ │ │ │ │ │ $variables$envHash2otu_table │ │ │ │ │ -[1] 895936 1288 │ │ │ │ │ +[1] 800926 1288 │ │ │ │ │ │ │ │ │ │ $variables$estimate_richness │ │ │ │ │ -[1] 897224 4352 │ │ │ │ │ +[1] 802214 4352 │ │ │ │ │ │ │ │ │ │ $variables$export_env_file │ │ │ │ │ -[1] 901576 1850 │ │ │ │ │ +[1] 806566 1850 │ │ │ │ │ │ │ │ │ │ $variables$export_mothur_dist │ │ │ │ │ -[1] 903426 2033 │ │ │ │ │ +[1] 808416 2033 │ │ │ │ │ │ │ │ │ │ $variables$extract_eigenvalue │ │ │ │ │ -[1] 905459 197 │ │ │ │ │ +[1] 810449 197 │ │ │ │ │ │ │ │ │ │ $variables$extract_eigenvalue.cca │ │ │ │ │ -[1] 905656 289 │ │ │ │ │ +[1] 810646 289 │ │ │ │ │ │ │ │ │ │ $variables$extract_eigenvalue.decorana │ │ │ │ │ -[1] 905945 190 │ │ │ │ │ +[1] 810935 190 │ │ │ │ │ │ │ │ │ │ $variables$extract_eigenvalue.default │ │ │ │ │ -[1] 906135 154 │ │ │ │ │ +[1] 811125 154 │ │ │ │ │ │ │ │ │ │ $variables$extract_eigenvalue.dpcoa │ │ │ │ │ -[1] 906289 189 │ │ │ │ │ +[1] 811279 189 │ │ │ │ │ │ │ │ │ │ $variables$extract_eigenvalue.pcoa │ │ │ │ │ -[1] 906478 228 │ │ │ │ │ +[1] 811468 228 │ │ │ │ │ │ │ │ │ │ $variables$extract_eigenvalue.rda │ │ │ │ │ -[1] 906706 289 │ │ │ │ │ +[1] 811696 289 │ │ │ │ │ │ │ │ │ │ $variables$f_comp_ps │ │ │ │ │ -[1] 906995 578 │ │ │ │ │ +[1] 811985 578 │ │ │ │ │ │ │ │ │ │ $variables$fastUniFrac │ │ │ │ │ -[1] 907573 5425 │ │ │ │ │ +[1] 812563 5425 │ │ │ │ │ │ │ │ │ │ $variables$filter_taxa │ │ │ │ │ -[1] 912998 884 │ │ │ │ │ +[1] 817988 884 │ │ │ │ │ │ │ │ │ │ $variables$filterfunSample │ │ │ │ │ -[1] 913882 293 │ │ │ │ │ +[1] 818872 293 │ │ │ │ │ │ │ │ │ │ $variables$filterfun_sample │ │ │ │ │ -[1] 914175 941 │ │ │ │ │ +[1] 819165 941 │ │ │ │ │ │ │ │ │ │ $variables$fix_phylo │ │ │ │ │ -[1] 915116 401 │ │ │ │ │ +[1] 820106 401 │ │ │ │ │ │ │ │ │ │ $variables$gapstat_ord │ │ │ │ │ -[1] 915517 691 │ │ │ │ │ +[1] 820507 691 │ │ │ │ │ │ │ │ │ │ $variables$genefilterSample │ │ │ │ │ -[1] 916208 294 │ │ │ │ │ +[1] 821198 294 │ │ │ │ │ │ │ │ │ │ $variables$genefilter_sample │ │ │ │ │ -[1] 916502 454 │ │ │ │ │ +[1] 821492 454 │ │ │ │ │ │ │ │ │ │ $variables$get.component.classes │ │ │ │ │ -[1] 916956 441 │ │ │ │ │ +[1] 821946 441 │ │ │ │ │ │ │ │ │ │ $variables$getSamples │ │ │ │ │ -[1] 917397 288 │ │ │ │ │ +[1] 822387 288 │ │ │ │ │ │ │ │ │ │ $variables$getSpecies │ │ │ │ │ -[1] 917685 286 │ │ │ │ │ +[1] 822675 286 │ │ │ │ │ │ │ │ │ │ $variables$getTaxa │ │ │ │ │ -[1] 917971 293 │ │ │ │ │ +[1] 822961 293 │ │ │ │ │ │ │ │ │ │ $variables$getVariable │ │ │ │ │ -[1] 918264 291 │ │ │ │ │ +[1] 823254 291 │ │ │ │ │ │ │ │ │ │ $variables$get_dpcoa_sites_coords │ │ │ │ │ -[1] 918555 802 │ │ │ │ │ +[1] 823545 802 │ │ │ │ │ │ │ │ │ │ $variables$get_dpcoa_species_coords │ │ │ │ │ -[1] 919357 802 │ │ │ │ │ +[1] 824347 802 │ │ │ │ │ │ │ │ │ │ $variables$get_sample │ │ │ │ │ -[1] 920159 430 │ │ │ │ │ +[1] 825149 430 │ │ │ │ │ │ │ │ │ │ $variables$get_taxa │ │ │ │ │ -[1] 920589 422 │ │ │ │ │ +[1] 825579 423 │ │ │ │ │ │ │ │ │ │ $variables$get_taxa_unique │ │ │ │ │ -[1] 921011 424 │ │ │ │ │ +[1] 826002 424 │ │ │ │ │ │ │ │ │ │ $variables$get_variable │ │ │ │ │ -[1] 921435 556 │ │ │ │ │ +[1] 826426 556 │ │ │ │ │ │ │ │ │ │ $variables$getslots.phyloseq │ │ │ │ │ -[1] 921991 264 │ │ │ │ │ +[1] 826982 264 │ │ │ │ │ │ │ │ │ │ $variables$howtolabnodes │ │ │ │ │ -[1] 922255 422 │ │ │ │ │ +[1] 827246 422 │ │ │ │ │ │ │ │ │ │ $variables$import │ │ │ │ │ -[1] 922677 1128 │ │ │ │ │ +[1] 827668 1128 │ │ │ │ │ │ │ │ │ │ $variables$import_RDP_cluster │ │ │ │ │ -[1] 923805 2545 │ │ │ │ │ +[1] 828796 2545 │ │ │ │ │ │ │ │ │ │ $variables$import_RDP_otu │ │ │ │ │ -[1] 926350 388 │ │ │ │ │ +[1] 831341 388 │ │ │ │ │ │ │ │ │ │ $variables$import_biom │ │ │ │ │ -[1] 926738 2756 │ │ │ │ │ +[1] 831729 2756 │ │ │ │ │ │ │ │ │ │ $variables$import_env_file │ │ │ │ │ -[1] 929494 570 │ │ │ │ │ +[1] 834485 570 │ │ │ │ │ │ │ │ │ │ $variables$import_mothur │ │ │ │ │ -[1] 930064 1212 │ │ │ │ │ +[1] 835055 1212 │ │ │ │ │ │ │ │ │ │ $variables$import_mothur_constaxonomy │ │ │ │ │ -[1] 931276 1267 │ │ │ │ │ +[1] 836267 1267 │ │ │ │ │ │ │ │ │ │ $variables$import_mothur_dist │ │ │ │ │ -[1] 932543 1545 │ │ │ │ │ +[1] 837534 1545 │ │ │ │ │ │ │ │ │ │ $variables$import_mothur_groups │ │ │ │ │ -[1] 934088 374 │ │ │ │ │ +[1] 839079 374 │ │ │ │ │ │ │ │ │ │ $variables$import_mothur_otu_table │ │ │ │ │ -[1] 934462 1910 │ │ │ │ │ +[1] 839453 1910 │ │ │ │ │ │ │ │ │ │ $variables$import_mothur_otulist │ │ │ │ │ -[1] 936372 1300 │ │ │ │ │ +[1] 841363 1300 │ │ │ │ │ │ │ │ │ │ $variables$import_mothur_shared │ │ │ │ │ -[1] 937672 1314 │ │ │ │ │ +[1] 842663 1314 │ │ │ │ │ │ │ │ │ │ $variables$import_pyrotagger_tab │ │ │ │ │ -[1] 938986 3731 │ │ │ │ │ +[1] 843977 3731 │ │ │ │ │ │ │ │ │ │ $variables$import_qiime │ │ │ │ │ -[1] 942717 2130 │ │ │ │ │ +[1] 847708 2130 │ │ │ │ │ │ │ │ │ │ $variables$import_qiime_otu_tax │ │ │ │ │ -[1] 944847 2088 │ │ │ │ │ +[1] 849838 2088 │ │ │ │ │ │ │ │ │ │ $variables$import_qiime_sampleData │ │ │ │ │ -[1] 946935 302 │ │ │ │ │ +[1] 851926 302 │ │ │ │ │ │ │ │ │ │ $variables$import_qiime_sample_data │ │ │ │ │ -[1] 947237 583 │ │ │ │ │ +[1] 852228 583 │ │ │ │ │ │ │ │ │ │ $variables$import_uparse │ │ │ │ │ -[1] 947820 2086 │ │ │ │ │ +[1] 852811 2086 │ │ │ │ │ │ │ │ │ │ $variables$import_usearch_uc │ │ │ │ │ -[1] 949906 1722 │ │ │ │ │ +[1] 854897 1722 │ │ │ │ │ │ │ │ │ │ $variables$index_reorder │ │ │ │ │ -[1] 951628 432 │ │ │ │ │ +[1] 856619 432 │ │ │ │ │ │ │ │ │ │ $variables$intersect_samples │ │ │ │ │ -[1] 952060 466 │ │ │ │ │ +[1] 857051 466 │ │ │ │ │ │ │ │ │ │ $variables$intersect_taxa │ │ │ │ │ -[1] 952526 462 │ │ │ │ │ +[1] 857517 462 │ │ │ │ │ │ │ │ │ │ $variables$is.component.class │ │ │ │ │ -[1] 952988 260 │ │ │ │ │ +[1] 857979 260 │ │ │ │ │ │ │ │ │ │ $variables$make_network │ │ │ │ │ -[1] 953248 2944 │ │ │ │ │ +[1] 858239 2944 │ │ │ │ │ │ │ │ │ │ $variables$manytextsize │ │ │ │ │ -[1] 956192 541 │ │ │ │ │ +[1] 861183 541 │ │ │ │ │ │ │ │ │ │ $variables$merge_phyloseq │ │ │ │ │ -[1] 956733 1322 │ │ │ │ │ +[1] 861724 1322 │ │ │ │ │ │ │ │ │ │ $variables$merge_phyloseq_pair │ │ │ │ │ -[1] 958055 429 │ │ │ │ │ +[1] 863046 429 │ │ │ │ │ │ │ │ │ │ $variables$merge_samples │ │ │ │ │ -[1] 958484 446 │ │ │ │ │ +[1] 863475 446 │ │ │ │ │ │ │ │ │ │ $variables$merge_species │ │ │ │ │ -[1] 958930 288 │ │ │ │ │ +[1] 863921 288 │ │ │ │ │ │ │ │ │ │ $variables$merge_taxa │ │ │ │ │ -[1] 959218 446 │ │ │ │ │ +[1] 864209 446 │ │ │ │ │ │ │ │ │ │ $variables$merge_taxa.indices.internal │ │ │ │ │ -[1] 959664 1599 │ │ │ │ │ +[1] 864655 1599 │ │ │ │ │ │ │ │ │ │ $variables$metaMDS │ │ │ │ │ -[1] 961263 71 │ │ │ │ │ +[1] 866254 71 │ │ │ │ │ │ │ │ │ │ $variables$microbio_me_qiime │ │ │ │ │ -[1] 961334 4307 │ │ │ │ │ +[1] 866325 4307 │ │ │ │ │ │ │ │ │ │ $variables$mt │ │ │ │ │ -[1] 965641 486 │ │ │ │ │ +[1] 870632 485 │ │ │ │ │ │ │ │ │ │ $variables$mt.phyloseq.internal │ │ │ │ │ -[1] 966127 548 │ │ │ │ │ +[1] 871117 548 │ │ │ │ │ │ │ │ │ │ $variables$nodeplotblank │ │ │ │ │ -[1] 966675 197 │ │ │ │ │ +[1] 871665 197 │ │ │ │ │ │ │ │ │ │ $variables$nodeplotboot │ │ │ │ │ -[1] 966872 2242 │ │ │ │ │ +[1] 871862 2242 │ │ │ │ │ │ │ │ │ │ $variables$nodeplotdefault │ │ │ │ │ -[1] 969114 619 │ │ │ │ │ +[1] 874104 619 │ │ │ │ │ │ │ │ │ │ $variables$nodesnotlabeled │ │ │ │ │ -[1] 969733 592 │ │ │ │ │ +[1] 874723 592 │ │ │ │ │ │ │ │ │ │ $variables$nsamples │ │ │ │ │ -[1] 970325 402 │ │ │ │ │ +[1] 875315 402 │ │ │ │ │ │ │ │ │ │ $variables$nspecies │ │ │ │ │ -[1] 970727 283 │ │ │ │ │ +[1] 875717 283 │ │ │ │ │ │ │ │ │ │ $variables$ntaxa │ │ │ │ │ -[1] 971010 400 │ │ │ │ │ +[1] 876000 400 │ │ │ │ │ │ │ │ │ │ $variables$ordinate │ │ │ │ │ -[1] 971410 3459 │ │ │ │ │ +[1] 876400 3459 │ │ │ │ │ │ │ │ │ │ $variables$originalUniFrac │ │ │ │ │ -[1] 974869 289 │ │ │ │ │ +[1] 879859 289 │ │ │ │ │ │ │ │ │ │ $variables$otuTable │ │ │ │ │ -[1] 975158 288 │ │ │ │ │ +[1] 880148 288 │ │ │ │ │ │ │ │ │ │ $variables$`otuTable<-` │ │ │ │ │ -[1] 975446 365 │ │ │ │ │ +[1] 880436 365 │ │ │ │ │ │ │ │ │ │ $variables$otu_table │ │ │ │ │ -[1] 975811 487 │ │ │ │ │ +[1] 880801 488 │ │ │ │ │ │ │ │ │ │ $variables$`otu_table<-` │ │ │ │ │ -[1] 976298 428 │ │ │ │ │ +[1] 881289 428 │ │ │ │ │ │ │ │ │ │ $variables$parse_taxonomy_default │ │ │ │ │ -[1] 976726 737 │ │ │ │ │ +[1] 881717 737 │ │ │ │ │ │ │ │ │ │ $variables$parse_taxonomy_greengenes │ │ │ │ │ -[1] 977463 1329 │ │ │ │ │ +[1] 882454 1329 │ │ │ │ │ │ │ │ │ │ $variables$parse_taxonomy_qiime │ │ │ │ │ -[1] 978792 342 │ │ │ │ │ +[1] 883783 342 │ │ │ │ │ │ │ │ │ │ $variables$pcoa │ │ │ │ │ -[1] 979134 68 │ │ │ │ │ +[1] 884125 68 │ │ │ │ │ │ │ │ │ │ $variables$phy_tree │ │ │ │ │ -[1] 979202 430 │ │ │ │ │ +[1] 884193 429 │ │ │ │ │ │ │ │ │ │ $variables$`phy_tree<-` │ │ │ │ │ -[1] 979632 428 │ │ │ │ │ +[1] 884622 427 │ │ │ │ │ │ │ │ │ │ $variables$phylo │ │ │ │ │ -[1] 980060 68 │ │ │ │ │ +[1] 885049 68 │ │ │ │ │ │ │ │ │ │ $variables$phyloseq │ │ │ │ │ -[1] 980128 2484 │ │ │ │ │ +[1] 885117 2484 │ │ │ │ │ │ │ │ │ │ $variables$phyloseq_JSD_pair │ │ │ │ │ -[1] 982612 776 │ │ │ │ │ +[1] 887601 776 │ │ │ │ │ │ │ │ │ │ $variables$phyloseq_to_deseq2 │ │ │ │ │ -[1] 983388 944 │ │ │ │ │ +[1] 888377 944 │ │ │ │ │ │ │ │ │ │ $variables$phyloseq_to_metagenomeSeq │ │ │ │ │ -[1] 984332 1774 │ │ │ │ │ +[1] 889321 1774 │ │ │ │ │ │ │ │ │ │ $variables$plot_bar │ │ │ │ │ -[1] 986106 1062 │ │ │ │ │ +[1] 891095 1062 │ │ │ │ │ │ │ │ │ │ $variables$plot_clusgap │ │ │ │ │ -[1] 987168 911 │ │ │ │ │ +[1] 892157 911 │ │ │ │ │ │ │ │ │ │ $variables$plot_heatmap │ │ │ │ │ -[1] 988079 6031 │ │ │ │ │ +[1] 893068 6031 │ │ │ │ │ │ │ │ │ │ $variables$plot_net │ │ │ │ │ -[1] 994110 6748 │ │ │ │ │ +[1] 899099 6748 │ │ │ │ │ │ │ │ │ │ $variables$plot_network │ │ │ │ │ -[1] 1000858 3292 │ │ │ │ │ +[1] 905847 3292 │ │ │ │ │ │ │ │ │ │ $variables$plot_ordination │ │ │ │ │ -[1] 1004150 10478 │ │ │ │ │ +[1] 909139 10478 │ │ │ │ │ │ │ │ │ │ $variables$plot_phyloseq │ │ │ │ │ -[1] 1014628 450 │ │ │ │ │ +[1] 919617 451 │ │ │ │ │ │ │ │ │ │ $variables$plot_richness │ │ │ │ │ -[1] 1015078 5453 │ │ │ │ │ +[1] 920068 5453 │ │ │ │ │ │ │ │ │ │ $variables$plot_richness_estimates │ │ │ │ │ -[1] 1020531 291 │ │ │ │ │ +[1] 925521 291 │ │ │ │ │ │ │ │ │ │ $variables$plot_scree │ │ │ │ │ -[1] 1020822 1465 │ │ │ │ │ +[1] 925812 1465 │ │ │ │ │ │ │ │ │ │ $variables$plot_taxa_bar │ │ │ │ │ -[1] 1022287 286 │ │ │ │ │ +[1] 927277 286 │ │ │ │ │ │ │ │ │ │ $variables$plot_tree │ │ │ │ │ -[1] 1022573 7428 │ │ │ │ │ +[1] 927563 7428 │ │ │ │ │ │ │ │ │ │ $variables$prune_samples │ │ │ │ │ -[1] 1030001 428 │ │ │ │ │ +[1] 934991 429 │ │ │ │ │ │ │ │ │ │ $variables$prune_species │ │ │ │ │ -[1] 1030429 288 │ │ │ │ │ +[1] 935420 288 │ │ │ │ │ │ │ │ │ │ $variables$prune_taxa │ │ │ │ │ -[1] 1030717 423 │ │ │ │ │ +[1] 935708 423 │ │ │ │ │ │ │ │ │ │ $variables$psmelt │ │ │ │ │ -[1] 1031140 4433 │ │ │ │ │ +[1] 936131 4433 │ │ │ │ │ │ │ │ │ │ $variables$rank.names │ │ │ │ │ -[1] 1035573 288 │ │ │ │ │ +[1] 940564 288 │ │ │ │ │ │ │ │ │ │ $variables$rank_names │ │ │ │ │ -[1] 1035861 295 │ │ │ │ │ +[1] 940852 295 │ │ │ │ │ │ │ │ │ │ $variables$rarefaction_subsample │ │ │ │ │ -[1] 1036156 1400 │ │ │ │ │ +[1] 941147 1400 │ │ │ │ │ │ │ │ │ │ $variables$rarefy_even_depth │ │ │ │ │ -[1] 1037556 3253 │ │ │ │ │ +[1] 942547 3253 │ │ │ │ │ │ │ │ │ │ $variables$read_tree │ │ │ │ │ -[1] 1040809 909 │ │ │ │ │ +[1] 945800 909 │ │ │ │ │ │ │ │ │ │ $variables$read_tree_greengenes │ │ │ │ │ -[1] 1041718 797 │ │ │ │ │ +[1] 946709 797 │ │ │ │ │ │ │ │ │ │ $variables$reconcile_categories │ │ │ │ │ -[1] 1042515 329 │ │ │ │ │ +[1] 947506 329 │ │ │ │ │ │ │ │ │ │ $variables$refseq │ │ │ │ │ -[1] 1042844 428 │ │ │ │ │ +[1] 947835 429 │ │ │ │ │ │ │ │ │ │ $variables$rm.na.phyloseq │ │ │ │ │ -[1] 1043272 722 │ │ │ │ │ +[1] 948264 722 │ │ │ │ │ │ │ │ │ │ $variables$rm_outlierf │ │ │ │ │ -[1] 1043994 541 │ │ │ │ │ +[1] 948986 541 │ │ │ │ │ │ │ │ │ │ $variables$rp.joint.fill │ │ │ │ │ -[1] 1044535 855 │ │ │ │ │ +[1] 949527 855 │ │ │ │ │ │ │ │ │ │ $variables$samData │ │ │ │ │ -[1] 1045390 289 │ │ │ │ │ +[1] 950382 289 │ │ │ │ │ │ │ │ │ │ $variables$sam_data │ │ │ │ │ -[1] 1045679 289 │ │ │ │ │ +[1] 950671 289 │ │ │ │ │ │ │ │ │ │ $variables$`sam_data<-` │ │ │ │ │ -[1] 1045968 368 │ │ │ │ │ +[1] 950960 368 │ │ │ │ │ │ │ │ │ │ $variables$sample.components │ │ │ │ │ -[1] 1046336 373 │ │ │ │ │ +[1] 951328 373 │ │ │ │ │ │ │ │ │ │ $variables$sample.names │ │ │ │ │ -[1] 1046709 290 │ │ │ │ │ +[1] 951701 290 │ │ │ │ │ │ │ │ │ │ $variables$sample.variables │ │ │ │ │ -[1] 1046999 292 │ │ │ │ │ +[1] 951991 292 │ │ │ │ │ │ │ │ │ │ $variables$sampleData │ │ │ │ │ -[1] 1047291 289 │ │ │ │ │ +[1] 952283 289 │ │ │ │ │ │ │ │ │ │ $variables$`sampleData<-` │ │ │ │ │ -[1] 1047580 368 │ │ │ │ │ +[1] 952572 368 │ │ │ │ │ │ │ │ │ │ $variables$sampleNames │ │ │ │ │ -[1] 1047948 290 │ │ │ │ │ +[1] 952940 290 │ │ │ │ │ │ │ │ │ │ $variables$sampleSums │ │ │ │ │ -[1] 1048238 289 │ │ │ │ │ +[1] 953230 289 │ │ │ │ │ │ │ │ │ │ $variables$sample_data │ │ │ │ │ -[1] 1048527 437 │ │ │ │ │ +[1] 953519 435 │ │ │ │ │ │ │ │ │ │ $variables$`sample_data<-` │ │ │ │ │ -[1] 1048964 515 │ │ │ │ │ +[1] 953954 515 │ │ │ │ │ │ │ │ │ │ $variables$sample_names │ │ │ │ │ -[1] 1049479 404 │ │ │ │ │ +[1] 954469 405 │ │ │ │ │ │ │ │ │ │ $variables$`sample_names<-` │ │ │ │ │ -[1] 1049883 629 │ │ │ │ │ +[1] 954874 629 │ │ │ │ │ │ │ │ │ │ $variables$sample_sums │ │ │ │ │ -[1] 1050512 382 │ │ │ │ │ +[1] 955503 382 │ │ │ │ │ │ │ │ │ │ $variables$sample_variables │ │ │ │ │ -[1] 1050894 296 │ │ │ │ │ +[1] 955885 296 │ │ │ │ │ │ │ │ │ │ $variables$scores.dpcoa │ │ │ │ │ -[1] 1051190 685 │ │ │ │ │ +[1] 956181 685 │ │ │ │ │ │ │ │ │ │ $variables$scores.pcoa │ │ │ │ │ -[1] 1051875 1282 │ │ │ │ │ +[1] 956866 1282 │ │ │ │ │ │ │ │ │ │ $variables$select_mothur_cutoff │ │ │ │ │ -[1] 1053157 813 │ │ │ │ │ +[1] 958148 813 │ │ │ │ │ │ │ │ │ │ $variables$show_mothur_cutoffs │ │ │ │ │ -[1] 1053970 340 │ │ │ │ │ +[1] 958961 340 │ │ │ │ │ │ │ │ │ │ $variables$show_mothur_list_cutoffs │ │ │ │ │ -[1] 1054310 298 │ │ │ │ │ +[1] 959301 298 │ │ │ │ │ │ │ │ │ │ $variables$species.names │ │ │ │ │ -[1] 1054608 288 │ │ │ │ │ +[1] 959599 288 │ │ │ │ │ │ │ │ │ │ $variables$speciesAreRows │ │ │ │ │ -[1] 1054896 291 │ │ │ │ │ +[1] 959887 291 │ │ │ │ │ │ │ │ │ │ $variables$`speciesAreRows<-` │ │ │ │ │ -[1] 1055187 370 │ │ │ │ │ +[1] 960178 370 │ │ │ │ │ │ │ │ │ │ $variables$speciesSums │ │ │ │ │ -[1] 1055557 288 │ │ │ │ │ +[1] 960548 288 │ │ │ │ │ │ │ │ │ │ $variables$speciesarerows │ │ │ │ │ -[1] 1055845 291 │ │ │ │ │ +[1] 960836 291 │ │ │ │ │ │ │ │ │ │ $variables$splat.phyloseq.objects │ │ │ │ │ -[1] 1056136 1147 │ │ │ │ │ +[1] 961127 1147 │ │ │ │ │ │ │ │ │ │ $variables$subset_ord_plot │ │ │ │ │ -[1] 1057283 1870 │ │ │ │ │ +[1] 962274 1870 │ │ │ │ │ │ │ │ │ │ $variables$subset_samples │ │ │ │ │ -[1] 1059153 745 │ │ │ │ │ +[1] 964144 745 │ │ │ │ │ │ │ │ │ │ $variables$subset_species │ │ │ │ │ -[1] 1059898 289 │ │ │ │ │ +[1] 964889 289 │ │ │ │ │ │ │ │ │ │ $variables$subset_taxa │ │ │ │ │ -[1] 1060187 867 │ │ │ │ │ +[1] 965178 867 │ │ │ │ │ │ │ │ │ │ $variables$t │ │ │ │ │ -[1] 1061054 417 │ │ │ │ │ +[1] 966045 416 │ │ │ │ │ │ │ │ │ │ $variables$taxTab │ │ │ │ │ -[1] 1061471 287 │ │ │ │ │ +[1] 966461 287 │ │ │ │ │ │ │ │ │ │ $variables$`taxTab<-` │ │ │ │ │ -[1] 1061758 365 │ │ │ │ │ +[1] 966748 365 │ │ │ │ │ │ │ │ │ │ $variables$tax_glom │ │ │ │ │ -[1] 1062123 2271 │ │ │ │ │ +[1] 967113 2271 │ │ │ │ │ │ │ │ │ │ $variables$tax_table │ │ │ │ │ -[1] 1064394 434 │ │ │ │ │ +[1] 969384 433 │ │ │ │ │ │ │ │ │ │ $variables$`tax_table<-` │ │ │ │ │ -[1] 1064828 428 │ │ │ │ │ +[1] 969817 427 │ │ │ │ │ │ │ │ │ │ $variables$taxa.components │ │ │ │ │ -[1] 1065256 418 │ │ │ │ │ +[1] 970244 418 │ │ │ │ │ │ │ │ │ │ $variables$taxa_are_rows │ │ │ │ │ -[1] 1065674 407 │ │ │ │ │ +[1] 970662 407 │ │ │ │ │ │ │ │ │ │ $variables$`taxa_are_rows<-` │ │ │ │ │ -[1] 1066081 465 │ │ │ │ │ +[1] 971069 465 │ │ │ │ │ │ │ │ │ │ $variables$taxa_names │ │ │ │ │ -[1] 1066546 405 │ │ │ │ │ +[1] 971534 405 │ │ │ │ │ │ │ │ │ │ $variables$`taxa_names<-` │ │ │ │ │ -[1] 1066951 627 │ │ │ │ │ +[1] 971939 627 │ │ │ │ │ │ │ │ │ │ $variables$taxa_sums │ │ │ │ │ -[1] 1067578 382 │ │ │ │ │ +[1] 972566 382 │ │ │ │ │ │ │ │ │ │ $variables$taxaplot │ │ │ │ │ -[1] 1067960 286 │ │ │ │ │ +[1] 972948 286 │ │ │ │ │ │ │ │ │ │ $variables$taxglom │ │ │ │ │ -[1] 1068246 287 │ │ │ │ │ +[1] 973234 287 │ │ │ │ │ │ │ │ │ │ $variables$taxtab │ │ │ │ │ -[1] 1068533 287 │ │ │ │ │ +[1] 973521 287 │ │ │ │ │ │ │ │ │ │ $variables$threshrank │ │ │ │ │ -[1] 1068820 698 │ │ │ │ │ +[1] 973808 698 │ │ │ │ │ │ │ │ │ │ $variables$threshrankfun │ │ │ │ │ -[1] 1069518 342 │ │ │ │ │ +[1] 974506 342 │ │ │ │ │ │ │ │ │ │ $variables$tip_glom │ │ │ │ │ -[1] 1069860 1000 │ │ │ │ │ +[1] 974848 1000 │ │ │ │ │ │ │ │ │ │ $variables$tipglom │ │ │ │ │ -[1] 1070860 287 │ │ │ │ │ +[1] 975848 287 │ │ │ │ │ │ │ │ │ │ $variables$topf │ │ │ │ │ -[1] 1071147 720 │ │ │ │ │ +[1] 976135 720 │ │ │ │ │ │ │ │ │ │ $variables$topk │ │ │ │ │ -[1] 1071867 540 │ │ │ │ │ +[1] 976855 540 │ │ │ │ │ │ │ │ │ │ $variables$topp │ │ │ │ │ -[1] 1072407 606 │ │ │ │ │ +[1] 977395 606 │ │ │ │ │ │ │ │ │ │ $variables$transformSampleCounts │ │ │ │ │ -[1] 1073013 1697 │ │ │ │ │ +[1] 978001 1697 │ │ │ │ │ │ │ │ │ │ $variables$transform_sample_counts │ │ │ │ │ -[1] 1074710 1697 │ │ │ │ │ +[1] 979698 1697 │ │ │ │ │ │ │ │ │ │ $variables$tre │ │ │ │ │ -[1] 1076407 284 │ │ │ │ │ +[1] 981395 284 │ │ │ │ │ │ │ │ │ │ $variables$`tre<-` │ │ │ │ │ -[1] 1076691 366 │ │ │ │ │ +[1] 981679 366 │ │ │ │ │ │ │ │ │ │ $variables$tree_layout │ │ │ │ │ -[1] 1077057 3162 │ │ │ │ │ +[1] 982045 3162 │ │ │ │ │ │ │ │ │ │ $variables$validTaxonomyTable │ │ │ │ │ -[1] 1080219 706 │ │ │ │ │ +[1] 985207 706 │ │ │ │ │ │ │ │ │ │ $variables$validotu_table │ │ │ │ │ -[1] 1080925 722 │ │ │ │ │ +[1] 985913 722 │ │ │ │ │ │ │ │ │ │ $variables$validphyloseq │ │ │ │ │ -[1] 1081647 960 │ │ │ │ │ +[1] 986635 960 │ │ │ │ │ │ │ │ │ │ $variables$validsample_data │ │ │ │ │ -[1] 1082607 385 │ │ │ │ │ +[1] 987595 385 │ │ │ │ │ │ │ │ │ │ $variables$veganifyOTU │ │ │ │ │ -[1] 1082992 415 │ │ │ │ │ +[1] 987980 415 │ │ │ │ │ │ │ │ │ │ $variables$vegdist │ │ │ │ │ -[1] 1083407 6010 │ │ │ │ │ +[1] 988395 6010 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $references │ │ │ │ │ $references$`env::1` │ │ │ │ │ [1] 1063 922 │ │ │ │ │ │ │ │ │ │ $references$`env::10` │ │ │ │ │ [1] 31543 143 │ │ │ │ │ │ │ │ │ │ $references$`env::100` │ │ │ │ │ -[1] 259125 1316 │ │ │ │ │ +[1] 228090 1316 │ │ │ │ │ │ │ │ │ │ $references$`env::101` │ │ │ │ │ -[1] 260441 1316 │ │ │ │ │ +[1] 322473 93067 │ │ │ │ │ │ │ │ │ │ $references$`env::102` │ │ │ │ │ -[1] 261757 1316 │ │ │ │ │ +[1] 415540 622 │ │ │ │ │ │ │ │ │ │ $references$`env::103` │ │ │ │ │ -[1] 263073 1317 │ │ │ │ │ +[1] 422979 860 │ │ │ │ │ │ │ │ │ │ $references$`env::104` │ │ │ │ │ -[1] 264390 1317 │ │ │ │ │ +[1] 422729 250 │ │ │ │ │ │ │ │ │ │ $references$`env::105` │ │ │ │ │ -[1] 265707 1316 │ │ │ │ │ +[1] 417295 2717 │ │ │ │ │ │ │ │ │ │ $references$`env::106` │ │ │ │ │ -[1] 382495 115472 │ │ │ │ │ +[1] 420012 2717 │ │ │ │ │ │ │ │ │ │ $references$`env::107` │ │ │ │ │ -[1] 497967 622 │ │ │ │ │ +[1] 430303 3071 │ │ │ │ │ │ │ │ │ │ $references$`env::108` │ │ │ │ │ -[1] 506753 861 │ │ │ │ │ +[1] 430035 268 │ │ │ │ │ │ │ │ │ │ $references$`env::109` │ │ │ │ │ -[1] 506503 250 │ │ │ │ │ +[1] 423893 3071 │ │ │ │ │ │ │ │ │ │ $references$`env::11` │ │ │ │ │ [1] 22806 8737 │ │ │ │ │ │ │ │ │ │ $references$`env::110` │ │ │ │ │ -[1] 499723 3390 │ │ │ │ │ +[1] 426964 3071 │ │ │ │ │ │ │ │ │ │ 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$references$`env::91` │ │ │ │ │ -[1] 247278 1316 │ │ │ │ │ +[1] 216242 1316 │ │ │ │ │ │ │ │ │ │ $references$`env::92` │ │ │ │ │ -[1] 248594 1316 │ │ │ │ │ +[1] 217558 1316 │ │ │ │ │ │ │ │ │ │ $references$`env::93` │ │ │ │ │ -[1] 249910 1316 │ │ │ │ │ +[1] 218874 1317 │ │ │ │ │ │ │ │ │ │ $references$`env::94` │ │ │ │ │ -[1] 251226 1317 │ │ │ │ │ +[1] 220191 1317 │ │ │ │ │ │ │ │ │ │ $references$`env::95` │ │ │ │ │ -[1] 252543 1317 │ │ │ │ │ +[1] 221508 1316 │ │ │ │ │ │ │ │ │ │ $references$`env::96` │ │ │ │ │ -[1] 253860 1316 │ │ │ │ │ +[1] 222824 1316 │ │ │ │ │ │ │ │ │ │ $references$`env::97` │ │ │ │ │ -[1] 255176 1316 │ │ │ │ │ +[1] 224140 1317 │ │ │ │ │ │ │ │ │ │ $references$`env::98` │ │ │ │ │ -[1] 256492 1316 │ │ │ │ │ +[1] 225457 1316 │ │ │ │ │ │ │ │ │ │ $references$`env::99` │ │ │ │ │ -[1] 257808 1317 │ │ │ │ │ +[1] 226773 1317 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $compressed │ │ │ │ │ [1] TRUE │ │ ├── ./usr/lib/R/site-library/phyloseq/doc/index.html │ │ │ @@ -10,47 +10,24 @@ │ │ │ │ │ │
│ │ │
│ │ │ [Up] │ │ │ [Top] │ │ │
│ │ │

Vignettes from package 'phyloseq'

│ │ │ - │ │ │ -│ │ │ -│ │ │ -│ │ │ -│ │ │ -│ │ │ -│ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
phyloseq::phyloseq Frequently Asked Questions (FAQ)source
phyloseq::analysis vignettesource
phyloseq::phyloseq basics vignettesource
phyloseq::phyloseq and DESeq2 on Colorectal Cancer Datasource
│ │ │ +The package contains no vignette meta-information. │ │ │

Other files in the doc directory

│ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ + │ │ │ │ │ │ + │ │ │ │ │ │ + │ │ │ │ │ │ + │ │ │
Unweighted_UniFrac.RData
phyloseq-FAQ.R
phyloseq-FAQ.Rmd
phyloseq-analysis.R
phyloseq-analysis.Rmd
phyloseq-basics.R
phyloseq-basics.Rmd
phyloseq-mixture-models.R
phyloseq-mixture-models.Rmd
│ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,14 +1,15 @@ │ │ │ │ ************ VViiggnneetttteess aanndd ootthheerr ddooccuummeennttaattiioonn[[[[RR llooggoo]]]] ************ │ │ │ │ =============================================================================== │ │ │ │ _[_[_U_p_]_]_[_[_T_o_p_]_] │ │ │ │ ********** VViiggnneetttteess ffrroomm ppaacckkaaggee ''pphhyylloosseeqq'' ********** │ │ │ │ -_p_h_y_l_o_s_e_q_:_: phyloseq Frequently Asked Questions (FAQ) _s_o_u_r_c_e │ │ │ │ -_p_h_y_l_o_s_e_q_:_: analysis vignette _s_o_u_r_c_e │ │ │ │ -_p_h_y_l_o_s_e_q_:_: phyloseq basics vignette _s_o_u_r_c_e │ │ │ │ -_p_h_y_l_o_s_e_q_:_: phyloseq and DESeq2 on Colorectal Cancer Data _s_o_u_r_c_e │ │ │ │ +The package contains no vignette meta-information. │ │ │ │ ********** OOtthheerr ffiilleess iinn tthhee ddoocc ddiirreeccttoorryy ********** │ │ │ │ _U_n_w_e_i_g_h_t_e_d___U_n_i_F_r_a_c_._R_D_a_t_a │ │ │ │ _p_h_y_l_o_s_e_q_-_F_A_Q_._R │ │ │ │ + _p_h_y_l_o_s_e_q_-_F_A_Q_._R_m_d │ │ │ │ _p_h_y_l_o_s_e_q_-_a_n_a_l_y_s_i_s_._R │ │ │ │ + _p_h_y_l_o_s_e_q_-_a_n_a_l_y_s_i_s_._R_m_d │ │ │ │ _p_h_y_l_o_s_e_q_-_b_a_s_i_c_s_._R │ │ │ │ + _p_h_y_l_o_s_e_q_-_b_a_s_i_c_s_._R_m_d │ │ │ │ _p_h_y_l_o_s_e_q_-_m_i_x_t_u_r_e_-_m_o_d_e_l_s_._R │ │ │ │ + _p_h_y_l_o_s_e_q_-_m_i_x_t_u_r_e_-_m_o_d_e_l_s_._R_m_d │ │ ├── ./usr/lib/R/site-library/phyloseq/help/paths.rds │ │ │ ├── paths.rds-content │ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {} │ │ │ │ │ @@ -1,134 +1,134 @@ │ │ │ │ │ - [1] "/home/moeller/Salsa/r-bioc-phyloseq/man/DPCoA.Rd" │ │ │ │ │ - [2] "/home/moeller/Salsa/r-bioc-phyloseq/man/JSD.Rd" │ │ │ │ │ - [3] "/home/moeller/Salsa/r-bioc-phyloseq/man/UniFrac-methods.Rd" │ │ │ │ │ - [4] "/home/moeller/Salsa/r-bioc-phyloseq/man/access.Rd" │ │ │ │ │ - [5] "/home/moeller/Salsa/r-bioc-phyloseq/man/assign-otu_table.Rd" │ │ │ │ │ - [6] "/home/moeller/Salsa/r-bioc-phyloseq/man/assign-phy_tree.Rd" │ │ │ │ │ - [7] "/home/moeller/Salsa/r-bioc-phyloseq/man/assign-sample_data.Rd" │ │ │ │ │ - [8] "/home/moeller/Salsa/r-bioc-phyloseq/man/assign-sample_names.Rd" │ │ │ │ │ - [9] "/home/moeller/Salsa/r-bioc-phyloseq/man/assign-tax_table.Rd" │ │ │ │ │ - [10] "/home/moeller/Salsa/r-bioc-phyloseq/man/assign-taxa_are_rows.Rd" │ │ │ │ │ - [11] "/home/moeller/Salsa/r-bioc-phyloseq/man/assign-taxa_names.Rd" │ │ │ │ │ - [12] "/home/moeller/Salsa/r-bioc-phyloseq/man/build_tax_table.Rd" │ │ │ │ │ - [13] "/home/moeller/Salsa/r-bioc-phyloseq/man/capscale-phyloseq-methods.Rd" │ │ │ │ │ - [14] "/home/moeller/Salsa/r-bioc-phyloseq/man/cca-rda-phyloseq-methods.Rd" │ │ │ │ │ - [15] "/home/moeller/Salsa/r-bioc-phyloseq/man/chunkReOrder.Rd" │ │ │ │ │ - [16] "/home/moeller/Salsa/r-bioc-phyloseq/man/data-GlobalPatterns.Rd" │ │ │ │ │ - [17] "/home/moeller/Salsa/r-bioc-phyloseq/man/data-enterotype.Rd" │ │ │ │ │ - [18] "/home/moeller/Salsa/r-bioc-phyloseq/man/data-esophagus.Rd" │ │ │ │ │ - [19] "/home/moeller/Salsa/r-bioc-phyloseq/man/data-soilrep.Rd" │ │ │ │ │ - [20] "/home/moeller/Salsa/r-bioc-phyloseq/man/decorana.Rd" │ │ │ │ │ - [21] "/home/moeller/Salsa/r-bioc-phyloseq/man/dist-class.Rd" │ │ │ │ │ - [22] "/home/moeller/Salsa/r-bioc-phyloseq/man/distance.Rd" │ │ │ │ │ - [23] "/home/moeller/Salsa/r-bioc-phyloseq/man/distanceMethodList.Rd" │ │ │ │ │ - [24] "/home/moeller/Salsa/r-bioc-phyloseq/man/envHash2otu_table.Rd" │ │ │ │ │ - [25] "/home/moeller/Salsa/r-bioc-phyloseq/man/estimate_richness.Rd" │ │ │ │ │ - [26] "/home/moeller/Salsa/r-bioc-phyloseq/man/export_env_file.Rd" │ │ │ │ │ - [27] "/home/moeller/Salsa/r-bioc-phyloseq/man/export_mothur_dist.Rd" │ │ │ │ │ - [28] "/home/moeller/Salsa/r-bioc-phyloseq/man/extract-methods.Rd" │ │ │ │ │ - [29] "/home/moeller/Salsa/r-bioc-phyloseq/man/filter_taxa.Rd" │ │ │ │ │ - [30] "/home/moeller/Salsa/r-bioc-phyloseq/man/filterfun_sample.Rd" │ │ │ │ │ - [31] "/home/moeller/Salsa/r-bioc-phyloseq/man/fix_phylo.Rd" │ │ │ │ │ - [32] "/home/moeller/Salsa/r-bioc-phyloseq/man/gapstat_ord.Rd" │ │ │ │ │ - [33] "/home/moeller/Salsa/r-bioc-phyloseq/man/genefilter_sample-methods.Rd" │ │ │ │ │ - [34] "/home/moeller/Salsa/r-bioc-phyloseq/man/get.component.classes.Rd" │ │ │ │ │ - [35] "/home/moeller/Salsa/r-bioc-phyloseq/man/get_sample-methods.Rd" │ │ │ │ │ - [36] "/home/moeller/Salsa/r-bioc-phyloseq/man/get_taxa-methods.Rd" │ │ │ │ │ - [37] "/home/moeller/Salsa/r-bioc-phyloseq/man/get_taxa_unique.Rd" │ │ │ │ │ - [38] "/home/moeller/Salsa/r-bioc-phyloseq/man/get_variable.Rd" │ │ │ │ │ - [39] "/home/moeller/Salsa/r-bioc-phyloseq/man/getslots.phyloseq.Rd" │ │ │ │ │ - [40] "/home/moeller/Salsa/r-bioc-phyloseq/man/import.Rd" │ │ │ │ │ - [41] "/home/moeller/Salsa/r-bioc-phyloseq/man/import_RDP_cluster.Rd" │ │ │ │ │ - [42] "/home/moeller/Salsa/r-bioc-phyloseq/man/import_RDP_otu.Rd" │ │ │ │ │ - [43] "/home/moeller/Salsa/r-bioc-phyloseq/man/import_biom.Rd" │ │ │ │ │ - [44] "/home/moeller/Salsa/r-bioc-phyloseq/man/import_env_file.Rd" │ │ │ │ │ - [45] "/home/moeller/Salsa/r-bioc-phyloseq/man/import_mothur.Rd" │ │ │ │ │ - [46] "/home/moeller/Salsa/r-bioc-phyloseq/man/import_mothur_constaxonomy.Rd" │ │ │ │ │ - [47] "/home/moeller/Salsa/r-bioc-phyloseq/man/import_mothur_dist.Rd" │ │ │ │ │ - [48] "/home/moeller/Salsa/r-bioc-phyloseq/man/import_mothur_groups.Rd" │ │ │ │ │ - [49] "/home/moeller/Salsa/r-bioc-phyloseq/man/import_mothur_otu_table.Rd" │ │ │ │ │ - [50] "/home/moeller/Salsa/r-bioc-phyloseq/man/import_mothur_otulist.Rd" │ │ │ │ │ - [51] "/home/moeller/Salsa/r-bioc-phyloseq/man/import_mothur_shared.Rd" │ │ │ │ │ - [52] "/home/moeller/Salsa/r-bioc-phyloseq/man/import_pyrotagger_tab.Rd" │ │ │ │ │ - [53] "/home/moeller/Salsa/r-bioc-phyloseq/man/import_qiime.Rd" │ │ │ │ │ - [54] "/home/moeller/Salsa/r-bioc-phyloseq/man/import_qiime_otu_tax.Rd" │ │ │ │ │ - [55] "/home/moeller/Salsa/r-bioc-phyloseq/man/import_qiime_sample_data.Rd" │ │ │ │ │ - [56] "/home/moeller/Salsa/r-bioc-phyloseq/man/import_uparse.Rd" │ │ │ │ │ - [57] "/home/moeller/Salsa/r-bioc-phyloseq/man/import_usearch_uc.Rd" │ │ │ │ │ - [58] "/home/moeller/Salsa/r-bioc-phyloseq/man/index_reorder.Rd" │ │ │ │ │ - [59] "/home/moeller/Salsa/r-bioc-phyloseq/man/intersect_taxa.Rd" │ │ │ │ │ - [60] "/home/moeller/Salsa/r-bioc-phyloseq/man/make_network.Rd" │ │ │ │ │ - [61] "/home/moeller/Salsa/r-bioc-phyloseq/man/merge_phyloseq.Rd" │ │ │ │ │ - [62] "/home/moeller/Salsa/r-bioc-phyloseq/man/merge_phyloseq_pair-methods.Rd" │ │ │ │ │ - [63] "/home/moeller/Salsa/r-bioc-phyloseq/man/merge_samples-methods.Rd" │ │ │ │ │ - [64] "/home/moeller/Salsa/r-bioc-phyloseq/man/merge_taxa-methods.Rd" │ │ │ │ │ - [65] "/home/moeller/Salsa/r-bioc-phyloseq/man/metaMDS.Rd" │ │ │ │ │ - [66] "/home/moeller/Salsa/r-bioc-phyloseq/man/microbio_me_qiime.Rd" │ │ │ │ │ - [67] "/home/moeller/Salsa/r-bioc-phyloseq/man/mt-methods.Rd" │ │ │ │ │ - [68] "/home/moeller/Salsa/r-bioc-phyloseq/man/nodeplotblank.Rd" │ │ │ │ │ - [69] "/home/moeller/Salsa/r-bioc-phyloseq/man/nodeplotboot.Rd" │ │ │ │ │ - [70] "/home/moeller/Salsa/r-bioc-phyloseq/man/nodeplotdefault.Rd" │ │ │ │ │ - [71] "/home/moeller/Salsa/r-bioc-phyloseq/man/nsamples-methods.Rd" │ │ │ │ │ - [72] "/home/moeller/Salsa/r-bioc-phyloseq/man/ntaxa-methods.Rd" │ │ │ │ │ - [73] "/home/moeller/Salsa/r-bioc-phyloseq/man/ordinate.Rd" │ │ │ │ │ - [74] "/home/moeller/Salsa/r-bioc-phyloseq/man/otu_table-class.Rd" │ │ │ │ │ - [75] "/home/moeller/Salsa/r-bioc-phyloseq/man/otu_table-methods.Rd" │ │ │ │ │ - [76] "/home/moeller/Salsa/r-bioc-phyloseq/man/parseTaxonomy-functions.Rd" │ │ │ │ │ - [77] "/home/moeller/Salsa/r-bioc-phyloseq/man/pcoa.Rd" │ │ │ │ │ - [78] "/home/moeller/Salsa/r-bioc-phyloseq/man/phy_tree-methods.Rd" │ │ │ │ │ - [79] "/home/moeller/Salsa/r-bioc-phyloseq/man/phylo-class.Rd" │ │ │ │ │ - [80] "/home/moeller/Salsa/r-bioc-phyloseq/man/phylo.Rd" │ │ │ │ │ - [81] "/home/moeller/Salsa/r-bioc-phyloseq/man/phyloseq-class.Rd" │ │ │ │ │ - [82] 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[95] "/home/moeller/Salsa/r-bioc-phyloseq/man/plot_scree.Rd" │ │ │ │ │ - [96] "/home/moeller/Salsa/r-bioc-phyloseq/man/plot_tree.Rd" │ │ │ │ │ - [97] "/home/moeller/Salsa/r-bioc-phyloseq/man/prune_samples-methods.Rd" │ │ │ │ │ - [98] "/home/moeller/Salsa/r-bioc-phyloseq/man/prune_taxa-methods.Rd" │ │ │ │ │ - [99] "/home/moeller/Salsa/r-bioc-phyloseq/man/psmelt.Rd" │ │ │ │ │ -[100] "/home/moeller/Salsa/r-bioc-phyloseq/man/rank_names.Rd" │ │ │ │ │ -[101] "/home/moeller/Salsa/r-bioc-phyloseq/man/rarefy_even_depth.Rd" │ │ │ │ │ -[102] "/home/moeller/Salsa/r-bioc-phyloseq/man/read_tree.Rd" │ │ │ │ │ -[103] "/home/moeller/Salsa/r-bioc-phyloseq/man/read_tree_greengenes.Rd" │ │ │ │ │ -[104] "/home/moeller/Salsa/r-bioc-phyloseq/man/reconcile_categories.Rd" │ │ │ │ │ -[105] "/home/moeller/Salsa/r-bioc-phyloseq/man/refseq-methods.Rd" │ │ │ │ │ -[106] "/home/moeller/Salsa/r-bioc-phyloseq/man/rm_outlierf.Rd" │ │ │ │ │ -[107] "/home/moeller/Salsa/r-bioc-phyloseq/man/sample_data-class.Rd" │ │ │ │ │ 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"/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/plot_network.Rd" │ │ │ │ │ + [92] "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/plot_ordination.Rd" │ │ │ │ │ + [93] "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/plot_phyloseq-methods.Rd" │ │ │ │ │ + [94] "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/plot_richness.Rd" │ │ │ │ │ + [95] "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/plot_scree.Rd" │ │ │ │ │ + [96] "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/plot_tree.Rd" │ │ │ │ │ + [97] "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/prune_samples-methods.Rd" │ │ │ │ │ + [98] "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/prune_taxa-methods.Rd" │ │ │ │ │ + [99] "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/psmelt.Rd" │ │ │ │ │ +[100] "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/rank_names.Rd" │ │ │ │ │ +[101] "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/rarefy_even_depth.Rd" │ │ │ │ │ +[102] "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/read_tree.Rd" │ │ │ │ │ +[103] "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/read_tree_greengenes.Rd" │ │ │ │ │ +[104] "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/reconcile_categories.Rd" │ │ │ │ │ +[105] "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/refseq-methods.Rd" │ │ │ │ │ +[106] "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/rm_outlierf.Rd" │ │ │ │ │ +[107] "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/sample_data-class.Rd" │ │ │ │ │ +[108] "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/sample_data-methods.Rd" │ │ │ │ │ +[109] "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/sample_names-methods.Rd" │ │ │ │ │ +[110] "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/sample_sums.Rd" │ │ │ │ │ +[111] "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/sample_variables.Rd" │ │ │ │ │ +[112] "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/show-methods.Rd" │ │ │ │ │ +[113] "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/show_mothur_cutoffs.Rd" │ │ │ │ │ +[114] "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/splat.phyloseq.objects.Rd" │ │ │ │ │ +[115] "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/subset_ord_plot.Rd" │ │ │ │ │ +[116] "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/subset_samples-methods.Rd" │ │ │ │ │ +[117] "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/subset_taxa-methods.Rd" │ │ │ │ │ +[118] "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/tax_glom.Rd" │ │ │ │ │ +[119] "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/tax_table-methods.Rd" │ │ │ │ │ +[120] "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/taxa_are_rows-methods.Rd" │ │ │ │ │ +[121] "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/taxa_names-methods.Rd" │ │ │ │ │ +[122] "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/taxa_sums.Rd" │ │ │ │ │ +[123] "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/taxonomyTable-class.Rd" │ │ │ │ │ +[124] "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/threshrank.Rd" │ │ │ │ │ +[125] "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/threshrankfun.Rd" │ │ │ │ │ +[126] "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/tip_glom.Rd" │ │ │ │ │ +[127] "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/topf.Rd" │ │ │ │ │ +[128] "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/topk.Rd" │ │ │ │ │ +[129] "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/topp.Rd" │ │ │ │ │ +[130] "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/transformcounts.Rd" │ │ │ │ │ +[131] "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/transpose-methods.Rd" │ │ │ │ │ +[132] "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/tree_layout.Rd" │ │ │ │ │ attr(,"first") │ │ │ │ │ -[1] 41 │ │ │ │ │ +[1] 58 │ │ ├── ./usr/lib/R/site-library/phyloseq/help/phyloseq.rdb │ │ │ ├── Rscript --vanilla - {} │ │ │ │ @@ -106,15 +106,15 @@ │ │ │ │ structure("#\n", Rd_tag = "RCODE"), structure("#\n", Rd_tag = "RCODE"), │ │ │ │ structure("# # # # # # GlobalPatterns\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(GlobalPatterns)\n", Rd_tag = "RCODE"), │ │ │ │ structure("# subset GP to top-150 taxa (to save computation time in example)\n", Rd_tag = "RCODE"), │ │ │ │ structure("keepTaxa <- names(sort(taxa_sums(GlobalPatterns), TRUE)[1:150])\n", Rd_tag = "RCODE"), │ │ │ │ structure("GP <- prune_taxa(keepTaxa, GlobalPatterns)\n", Rd_tag = "RCODE"), │ │ │ │ structure("# Perform DPCoA\n", Rd_tag = "RCODE"), structure("GP.dpcoa <- DPCoA(GP)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("plot_ordination(GP, GP.dpcoa, color=\"SampleType\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/DPCoA.Rd", class = "Rd", meta = list( │ │ │ │ + structure("plot_ordination(GP, GP.dpcoa, color=\"SampleType\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/DPCoA.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ JSD (list) = structure(list(structure(list(structure("Calculate the Jensen-Shannon Divergence (distance)", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("JSD", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("JSD", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("internal", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This is a phyloseq-specific implementation of the Jensen-Shannon Divergence\n", Rd_tag = "TEXT"), │ │ │ │ @@ -168,15 +168,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("# library(doParallel) # Do this and next line only if you have multi-cores\n", Rd_tag = "RCODE"), │ │ │ │ structure("# registerDoParallel(cores=6)\n", Rd_tag = "RCODE"), │ │ │ │ structure("# data(enterotype)\n", Rd_tag = "RCODE"), │ │ │ │ structure("# # ent.jsd <- JSD(enterotype, TRUE) # internal only\n", Rd_tag = "RCODE"), │ │ │ │ structure("# ent.jsd <- distance(enterotype, \"jsd\", parallel=TRUE)\n", Rd_tag = "RCODE"), │ │ │ │ structure("# ent.PCoA <- ordinate(enterotype, \"PCoA\", ent.jsd) # Perform principle coordinate analysis\n", Rd_tag = "RCODE"), │ │ │ │ structure("# p <- plot_ordination(enterotype, ent.PCoA, color=\"Enterotype\", shape=\"SeqTech\") \n", Rd_tag = "RCODE"), │ │ │ │ - structure("# (p <- p + geom_point(size=5, alpha=0.5))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/JSD.Rd", class = "Rd", meta = list( │ │ │ │ + structure("# (p <- p + geom_point(size=5, alpha=0.5))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/JSD.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ UniFrac-methods (list) = structure(list(structure(list(structure("Calculate weighted or unweighted (Fast) UniFrac distance for all sample pairs.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("UniFrac", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("UniFrac", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("UniFrac,phyloseq-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function calculates the (Fast) UniFrac distance for all sample-pairs\n", Rd_tag = "TEXT"), │ │ │ │ @@ -379,15 +379,15 @@ │ │ │ │ structure("# registerDoParallel(cl)\n", Rd_tag = "RCODE"), │ │ │ │ structure("# UniFrac(esophagus, TRUE)\n", Rd_tag = "RCODE"), │ │ │ │ structure("# # Force to sequential backed:\n", Rd_tag = "RCODE"), │ │ │ │ structure("# registerDoSEQ()\n", Rd_tag = "RCODE"), structure("# # For multicore-like functionality (will probably not work on windows),\n", Rd_tag = "RCODE"), │ │ │ │ structure("# # register the backend like this:\n", Rd_tag = "RCODE"), │ │ │ │ structure("# registerDoParallel(cores=3)\n", Rd_tag = "RCODE"), │ │ │ │ structure("# UniFrac(esophagus, TRUE)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("################################################################################\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/UniFrac-methods.Rd", class = "Rd", meta = list( │ │ │ │ + structure("################################################################################\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/UniFrac-methods.Rd", class = "Rd", meta = list( │ │ │ │ docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ access (list) = structure(list(structure(list(structure("Universal slot accessor function for phyloseq-class.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("access", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("access", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function is used internally by many accessors and in \n", Rd_tag = "TEXT"), │ │ │ │ structure("many functions/methods that need to access a particular type of component data.\n", Rd_tag = "TEXT"), │ │ │ │ @@ -438,15 +438,15 @@ │ │ │ │ structure("## data(GlobalPatterns)\n", Rd_tag = "RCODE"), │ │ │ │ structure("## access(GlobalPatterns, \"tax_table\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("## access(GlobalPatterns, \"phy_tree\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("## access(otu_table(GlobalPatterns), \"otu_table\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("## # Should return NULL:\n", Rd_tag = "RCODE"), │ │ │ │ structure("## access(otu_table(GlobalPatterns), \"sample_data\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("## access(otuTree(GlobalPatterns), \"sample_data\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("## access(otuSam(GlobalPatterns), \"phy_tree\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/access.Rd", class = "Rd", meta = list( │ │ │ │ + structure("## access(otuSam(GlobalPatterns), \"phy_tree\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/access.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ assign-otu_table (list) = structure(list(structure(list(structure("Assign a new OTU Table to ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("x", Rd_tag = "RCODE")), Rd_tag = "\\code")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("otu_table<-", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("otu_table<-", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("assign-otu_table", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -484,15 +484,15 @@ │ │ │ │ structure("# ex2b <- GlobalPatterns\n", Rd_tag = "RCODE"), │ │ │ │ structure("# OTU <- otu_table(GlobalPatterns)[1:100, ]\n", Rd_tag = "RCODE"), │ │ │ │ structure("# otu_table(ex2b) <- OTU\n", Rd_tag = "RCODE"), │ │ │ │ structure("# identical(ex2a, ex2b)\n", Rd_tag = "RCODE"), │ │ │ │ structure("# print(ex2b)\n", Rd_tag = "RCODE"), structure("# # Relace otu_table by implying the component in context.\n", Rd_tag = "RCODE"), │ │ │ │ structure("# ex2c <- GlobalPatterns\n", Rd_tag = "RCODE"), │ │ │ │ structure("# otu_table(ex2c) <- ex2b\n", Rd_tag = "RCODE"), │ │ │ │ - structure("# identical(ex2a, ex2c)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/assign-otu_table.Rd", class = "Rd", meta = list( │ │ │ │ + structure("# identical(ex2a, ex2c)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/assign-otu_table.Rd", class = "Rd", meta = list( │ │ │ │ docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ assign-phy_tree (list) = structure(list(structure(list(structure("Assign a (new) phylogenetic tree to ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("x", Rd_tag = "RCODE")), Rd_tag = "\\code")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("phy_tree<-", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("phy_tree<-", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("assign-phy_tree", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -520,15 +520,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("#\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(\"esophagus\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("# An example of pruning to just the first 20 taxa in esophagus\n", Rd_tag = "RCODE"), │ │ │ │ structure("ex2a <- prune_taxa(taxa_names(esophagus)[1:20], esophagus)\n", Rd_tag = "RCODE"), │ │ │ │ structure("# The following 3 lines produces an ex2b that is equal to ex2a\n", Rd_tag = "RCODE"), │ │ │ │ structure("ex2b <- ex2a\n", Rd_tag = "RCODE"), structure("phy_tree(ex2b) <- phy_tree(esophagus)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("identical(ex2a, ex2b)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/assign-phy_tree.Rd", class = "Rd", meta = list( │ │ │ │ + structure("identical(ex2a, ex2b)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/assign-phy_tree.Rd", class = "Rd", meta = list( │ │ │ │ docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ assign-sample_data (list) = structure(list(structure(list(structure("Assign (new) sample_data to ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("x", Rd_tag = "RCODE")), Rd_tag = "\\code")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("sample_data<-", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("sample_data<-", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("assign-sample_data", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -598,15 +598,15 @@ │ │ │ │ structure(list(structure(list(structure("sample_data-class", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" object without error.", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("No return. This is an assignment statement.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure(" data(soilrep)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" soilrep\n", Rd_tag = "RCODE"), structure(" head(sample_data(soilrep))\n", Rd_tag = "RCODE"), │ │ │ │ structure(" sample_data(soilrep)$Time <- as.integer(substr(sample_data(soilrep)$Sample, 1, 1))\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" head(sample_data(soilrep))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/assign-sample_data.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" head(sample_data(soilrep))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/assign-sample_data.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ assign-sample_names (list) = structure(list(structure(list(structure("Replace OTU identifier names", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("sample_names<-", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("sample_names<-", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("assign-sample_names", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("sample_names<-,ANY,ANY-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -651,15 +651,15 @@ │ │ │ │ structure("# plot_tree(esophagus, color=\"sample_names\", ladderize=\"left\") \n", Rd_tag = "RCODE"), │ │ │ │ structure("## non-characters are first coerced to characters.\n", Rd_tag = "RCODE"), │ │ │ │ structure("sample_names(esophagus) <- 1:nsamples(esophagus)\n", Rd_tag = "RCODE"), │ │ │ │ structure("sample_names(esophagus)\n", Rd_tag = "RCODE"), │ │ │ │ structure("# plot_tree(esophagus, color=\"sample_names\", ladderize=\"left\") \n", Rd_tag = "RCODE"), │ │ │ │ structure("## Cannot assign non-unique or differently-lengthed name vectors. Error.\n", Rd_tag = "RCODE"), │ │ │ │ structure("# sample_names(esophagus) <- sample(c(TRUE, FALSE), nsamples(esophagus), TRUE)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("# sample_names(esophagus) <- sample(sample_names(esophagus), nsamples(esophagus)-1, FALSE)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/assign-sample_names.Rd", class = "Rd", meta = list( │ │ │ │ + structure("# sample_names(esophagus) <- sample(sample_names(esophagus), nsamples(esophagus)-1, FALSE)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/assign-sample_names.Rd", class = "Rd", meta = list( │ │ │ │ docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ assign-tax_table (list) = structure(list(structure(list(structure("Assign a (new) Taxonomy Table to ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("x", Rd_tag = "RCODE")), Rd_tag = "\\code")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("tax_table<-", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("tax_table<-", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("assign-tax_table", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -717,15 +717,15 @@ │ │ │ │ structure("# identical(ex2a, ex2b)\n", Rd_tag = "RCODE"), │ │ │ │ structure("# print(ex2b)\n", Rd_tag = "RCODE"), structure("# # 2 examples adding a tax_table component from phyloseq or matrix classes\n", Rd_tag = "RCODE"), │ │ │ │ structure("# ex2c <- phyloseq(otu_table(ex2b), sample_data(ex2b), phy_tree(ex2b))\n", Rd_tag = "RCODE"), │ │ │ │ structure("# tax_table(ex2c) <- ex2b\n", Rd_tag = "RCODE"), │ │ │ │ structure("# identical(ex2a, ex2c)\n", Rd_tag = "RCODE"), │ │ │ │ structure("# ex2c <- phyloseq(otu_table(ex2b), sample_data(ex2b), phy_tree(ex2b))\n", Rd_tag = "RCODE"), │ │ │ │ structure("# tax_table(ex2c) <- as(tax_table(ex2b), \"matrix\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("# identical(ex2a, ex2c)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/assign-tax_table.Rd", class = "Rd", meta = list( │ │ │ │ + structure("# identical(ex2a, ex2c)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/assign-tax_table.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ assign-taxa_are_rows (list) = structure(list(structure(list(structure("Manually change taxa_are_rows through assignment.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("taxa_are_rows<-", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("taxa_are_rows<-", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("assign-taxa_are_rows", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("taxa_are_rows<-,otu_table,logical-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -752,15 +752,15 @@ │ │ │ │ list(structure("A logical of length equal to 1. If ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("length(value) > 1", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(", \n", Rd_tag = "TEXT"), structure("the additional elements will be ignored. Only the first element is assigned\n", Rd_tag = "TEXT"), │ │ │ │ structure("to the taxa_are_rows slot.", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure(" data(esophagus)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" taxa_are_rows(esophagus)\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" taxa_are_rows(otu_table(esophagus))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/assign-taxa_are_rows.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" taxa_are_rows(otu_table(esophagus))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/assign-taxa_are_rows.Rd", class = "Rd", meta = list( │ │ │ │ docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ assign-taxa_names (list) = structure(list(structure(list(structure("Replace OTU identifier names", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("taxa_names<-", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("taxa_names<-", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("assign-taxa_names", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("taxa_names<-,ANY,ANY-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -812,15 +812,15 @@ │ │ │ │ structure("# plot_tree(esophagus, label.tips=\"taxa_names\", ladderize=\"left\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("## non-characters are first coerced to characters.\n", Rd_tag = "RCODE"), │ │ │ │ structure("taxa_names(esophagus) <- 1:ntaxa(esophagus)\n", Rd_tag = "RCODE"), │ │ │ │ structure("taxa_names(esophagus)\n", Rd_tag = "RCODE"), │ │ │ │ structure("# plot_tree(esophagus, label.tips=\"taxa_names\", ladderize=\"left\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("## Cannot assign non-unique or differently-lengthed name vectors. Error.\n", Rd_tag = "RCODE"), │ │ │ │ structure("# taxa_names(esophagus) <- sample(c(TRUE, FALSE), ntaxa(esophagus), TRUE)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("# taxa_names(esophagus) <- sample(taxa_names(esophagus), ntaxa(esophagus)-5, FALSE)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/assign-taxa_names.Rd", class = "Rd", meta = list( │ │ │ │ + structure("# taxa_names(esophagus) <- sample(taxa_names(esophagus), ntaxa(esophagus)-5, FALSE)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/assign-taxa_names.Rd", class = "Rd", meta = list( │ │ │ │ docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ build_tax_table (list) = structure(list(structure(list(structure("Build a ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("tax_table", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" from a named possibly-jagged list", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("build_tax_table", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("build_tax_table", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -864,15 +864,15 @@ │ │ │ │ structure(" parse_taxonomy_default(taxvec1)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" parse_taxonomy_greengenes(taxvec1)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" taxvec2 = c(\"Root;k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Staphylococcaceae\")\n", Rd_tag = "RCODE"), │ │ │ │ structure(" parse_taxonomy_qiime(taxvec2)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" taxlist1 = list(OTU1=parse_taxonomy_greengenes(taxvec1), OTU2=parse_taxonomy_qiime(taxvec2))\n", Rd_tag = "RCODE"), │ │ │ │ structure(" taxlist2 = list(OTU1=parse_taxonomy_default(taxvec1), OTU2=parse_taxonomy_qiime(taxvec2))\n", Rd_tag = "RCODE"), │ │ │ │ structure(" build_tax_table(taxlist1)\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" build_tax_table(taxlist2)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/build_tax_table.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" build_tax_table(taxlist2)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/build_tax_table.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ capscale-phyloseq-methods (list) = structure(list(structure(list(structure("Constrained Analysis of Principal Coordinates, ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("capscale", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("vegan", Rd_tag = "TEXT"))), Rd_tag = "\\code"), │ │ │ │ structure(".", Rd_tag = "TEXT")), Rd_tag = "\\title"), structure(list( │ │ │ │ structure("capscale.phyloseq", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("capscale.phyloseq", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -957,15 +957,15 @@ │ │ │ │ structure("capscale", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("vegan", Rd_tag = "TEXT"))), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("# See other examples at\n", Rd_tag = "RCODE"), │ │ │ │ structure("# http://joey711.github.io/phyloseq/plot_ordination-examples\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(GlobalPatterns)\n", Rd_tag = "RCODE"), │ │ │ │ structure("GP = prune_taxa(names(sort(taxa_sums(GlobalPatterns), TRUE)[1:50]), GlobalPatterns)\n", Rd_tag = "RCODE"), │ │ │ │ structure("ordcap = ordinate(GP, \"CAP\", \"bray\", ~SampleType)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("plot_ordination(GP, ordcap, \"samples\", color=\"SampleType\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/capscale-phyloseq-methods.Rd", class = "Rd", meta = list( │ │ │ │ + structure("plot_ordination(GP, ordcap, \"samples\", color=\"SampleType\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/capscale-phyloseq-methods.Rd", class = "Rd", meta = list( │ │ │ │ docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ cca-rda-phyloseq-methods (list) = structure(list(structure(list(structure("Constrained Correspondence Analysis and Redundancy Analysis.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("cca.phyloseq", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("cca.phyloseq", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("rda.phyloseq", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("cca.phyloseq,phyloseq,formula-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -1038,15 +1038,15 @@ │ │ │ │ structure(list(structure("plot_ordination", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(",\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("rda", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("vegan", Rd_tag = "TEXT"))), Rd_tag = "\\code"), │ │ │ │ structure(", ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("cca", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("vegan", Rd_tag = "TEXT"))), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("#\n", Rd_tag = "RCODE"), │ │ │ │ - structure("# cca.phyloseq(physeq, formula, method, ...)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/cca-rda-phyloseq-methods.Rd", class = "Rd", meta = list( │ │ │ │ + structure("# cca.phyloseq(physeq, formula, method, ...)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/cca-rda-phyloseq-methods.Rd", class = "Rd", meta = list( │ │ │ │ docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ chunkReOrder (list) = structure(list(structure(list(structure("Chunk re-order a vector so that specified newstart is first.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("chunkReOrder", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("chunkReOrder", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("internal", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Different than relevel.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -1066,15 +1066,15 @@ │ │ │ │ structure("# # This is also the default\n", Rd_tag = "RCODE"), │ │ │ │ structure("# all(chunkReOrder(10:25) == 10:25)\n", Rd_tag = "RCODE"), │ │ │ │ structure("# # An example with characters\n", Rd_tag = "RCODE"), │ │ │ │ structure("# chunkReOrder(LETTERS, \"G\") \n", Rd_tag = "RCODE"), │ │ │ │ structure("# chunkReOrder(LETTERS, \"B\") \n", Rd_tag = "RCODE"), │ │ │ │ structure("# chunkReOrder(LETTERS, \"Z\") \n", Rd_tag = "RCODE"), │ │ │ │ structure("# # What about when `newstart` is not in `x`? Return x as-is, throw warning.\n", Rd_tag = "RCODE"), │ │ │ │ - structure("# chunkReOrder(LETTERS, \"g\") \n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/chunkReOrder.Rd", class = "Rd", meta = list( │ │ │ │ + structure("# chunkReOrder(LETTERS, \"g\") \n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/chunkReOrder.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ data-GlobalPatterns (list) = structure(list(structure(list(structure("(Data) Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample (2011)", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("data-GlobalPatterns", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("data-GlobalPatterns", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("GlobalPatterns", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("data", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ @@ -1105,15 +1105,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\references"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("The examples on the phyloseq wiki page for ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("plot_ordination", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" show \n", Rd_tag = "TEXT"), structure(" many more examples:\n", Rd_tag = "TEXT"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(list(structure("https://github.com/joey711/phyloseq/wiki/plot_ordination", Rd_tag = "VERB")), Rd_tag = "\\url"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(GlobalPatterns)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("plot_richness(GlobalPatterns, x=\"SampleType\", measures=c(\"Observed\", \"Chao1\", \"Shannon\"))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/data-GlobalPatterns.Rd", class = "Rd", meta = list( │ │ │ │ + structure("plot_richness(GlobalPatterns, x=\"SampleType\", measures=c(\"Observed\", \"Chao1\", \"Shannon\"))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/data-GlobalPatterns.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ data-enterotype (list) = structure(list(structure(list(structure("(Data) Enterotypes of the human gut microbiome (2011)", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("data-enterotype", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("data-enterotype", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("enterotype", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("data", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ @@ -1140,15 +1140,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(list(structure("http://www.nature.com/doifinder/10.1038/nature09944", Rd_tag = "VERB")), Rd_tag = "\\url"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("See supplemental information for subject data. \n", Rd_tag = "TEXT"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("OTU-clustered data was downloaded from the publicly-accessible:\n", Rd_tag = "TEXT"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(list(structure("http://www.bork.embl.de/Docu/Arumugam_et_al_2011/downloads.html", Rd_tag = "VERB")), Rd_tag = "\\url"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\references"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(enterotype)\n", Rd_tag = "RCODE"), │ │ │ │ structure("ig <- make_network(enterotype, \"samples\", max.dist=0.3)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("plot_network(ig, enterotype, color=\"SeqTech\", shape=\"Enterotype\", line_weight=0.3, label=NULL)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/data-enterotype.Rd", class = "Rd", meta = list( │ │ │ │ + structure("plot_network(ig, enterotype, color=\"SeqTech\", shape=\"Enterotype\", line_weight=0.3, label=NULL)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/data-enterotype.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ data-esophagus (list) = structure(list(structure(list(structure("(Data) Small example dataset from a human esophageal community (2004)", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("data-esophagus", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("data-esophagus", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("esophagus", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("data", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ @@ -1184,15 +1184,15 @@ │ │ │ │ structure("UniFrac(esophagus, weighted=TRUE)\n", Rd_tag = "RCODE"), │ │ │ │ structure("# How to re-create the esophagus dataset using import_mothur function\n", Rd_tag = "RCODE"), │ │ │ │ structure("mothlist <- system.file(\"extdata\", \"esophagus.fn.list.gz\", package=\"phyloseq\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("mothgroup <- system.file(\"extdata\", \"esophagus.good.groups.gz\", package=\"phyloseq\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("mothtree <- system.file(\"extdata\", \"esophagus.tree.gz\", package=\"phyloseq\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("show_mothur_cutoffs(mothlist)\n", Rd_tag = "RCODE"), │ │ │ │ structure("cutoff <- \"0.10\"\n", Rd_tag = "RCODE"), │ │ │ │ - structure("esophman <- import_mothur(mothlist, mothgroup, mothtree, cutoff)\t\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/data-esophagus.Rd", class = "Rd", meta = list( │ │ │ │ + structure("esophman <- import_mothur(mothlist, mothgroup, mothtree, cutoff)\t\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/data-esophagus.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ data-soilrep (list) = structure(list(structure(list(structure("(Data) Reproducibility of soil microbiome data (2011)", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("data-soilrep", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("data-soilrep", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("soilrep", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("data", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ @@ -1268,15 +1268,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("# Load the data\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(soilrep)\n", Rd_tag = "RCODE"), structure("################################################################################\n", Rd_tag = "RCODE"), │ │ │ │ structure("# Alpha diversity (richness) example. Accept null hypothesis: \n", Rd_tag = "RCODE"), │ │ │ │ structure("# No convincing difference in species richness between warmed/unwarmed soils.\n", Rd_tag = "RCODE"), │ │ │ │ structure("################################################################################\n", Rd_tag = "RCODE"), │ │ │ │ structure("# Graphically compare richness between the different treatments.\n", Rd_tag = "RCODE"), │ │ │ │ structure("man.col <- c(WC=\"red\", WU=\"brown\", UC=\"blue\", UU=\"darkgreen\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("plot_richness(soilrep, x=\"Treatment\", color=\"Treatment\", measures=c(\"Observed\", \"Chao1\", \"Shannon\"))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/data-soilrep.Rd", class = "Rd", meta = list( │ │ │ │ + structure("plot_richness(soilrep, x=\"Treatment\", color=\"Treatment\", measures=c(\"Observed\", \"Chao1\", \"Shannon\"))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/data-soilrep.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ decorana (list) = structure(list(structure(list(structure("S3 class placeholder definition (list) for decorana", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("decorana", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("decorana", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("internal", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("The ape package does export a version of its ", Rd_tag = "TEXT"), │ │ │ │ @@ -1293,30 +1293,30 @@ │ │ │ │ structure("judiciously and within phyloseq.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("decorana\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("An object of class ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("decorana", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" of length 0.\n", Rd_tag = "TEXT")), Rd_tag = "\\format"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("decorana", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("vegan", Rd_tag = "TEXT"))), Rd_tag = "\\code"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/decorana.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/decorana.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ dist-class (list) = structure(list(structure(list(structure("An S4 placeholder for the ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("dist", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("stats", Rd_tag = "TEXT"))), Rd_tag = "\\code"), │ │ │ │ structure(" class.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("dist-class", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("dist-class", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("See ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("dist", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("stats", Rd_tag = "TEXT"))), Rd_tag = "\\code"), │ │ │ │ structure(" for details\n", Rd_tag = "TEXT"), structure("about this type of a distance matrix object.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("dist", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("stats", Rd_tag = "TEXT"))), Rd_tag = "\\code"), │ │ │ │ structure(", ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("setOldClass", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/dist-class.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/dist-class.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ distance (list) = structure(list(structure(list(structure("Calculate distance, dissimilarity", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("distance", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("distance", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("distance,phyloseq,ANY-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("distance,otu_table,character-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -1466,15 +1466,15 @@ │ │ │ │ structure("distance(esophagus, \"wunifrac\") # weighted UniFrac\n", Rd_tag = "RCODE"), │ │ │ │ structure("distance(esophagus, \"jaccard\", binary = TRUE) # vegdist jaccard\n", Rd_tag = "RCODE"), │ │ │ │ structure("distance(esophagus, \"gower\") # vegdist option \"gower\"\n", Rd_tag = "RCODE"), │ │ │ │ structure("distance(esophagus, \"g\") # designdist method option \"g\"\n", Rd_tag = "RCODE"), │ │ │ │ structure("distance(esophagus, \"minkowski\") # invokes a method from the base dist() function.\n", Rd_tag = "RCODE"), │ │ │ │ structure("distance(esophagus, \"(A+B-2*J)/(A+B)\") # designdist custom distance\n", Rd_tag = "RCODE"), │ │ │ │ structure("distanceMethodList\n", Rd_tag = "RCODE"), │ │ │ │ - structure("help(\"distance\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/distance.Rd", class = "Rd", meta = list( │ │ │ │ + structure("help(\"distance\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/distance.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ distanceMethodList (list) = structure(list(structure(list(structure("List of distance method keys supported in ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("distance", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("phyloseq", Rd_tag = "TEXT"))), Rd_tag = "\\code")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("distanceMethodList", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("distanceMethodList", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("datasets", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ @@ -1627,15 +1627,15 @@ │ │ │ │ structure(list(list(structure(list(structure("ANY", Rd_tag = "RCODE")), Rd_tag = "\\code")), │ │ │ │ list(structure(list(structure(list(structure("designdist", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("vegan", Rd_tag = "TEXT"))), Rd_tag = "\\code"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\describe"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\format"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("distance", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("phyloseq", Rd_tag = "TEXT"))), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ - structure(list(structure("\n", Rd_tag = "RCODE"), structure("distanceMethodList\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/distanceMethodList.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("\n", Rd_tag = "RCODE"), structure("distanceMethodList\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/distanceMethodList.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ envHash2otu_table (list) = structure(list(structure(list(structure("Convert a sequence-sample hash (like ENV file) into an OTU table.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("envHash2otu_table", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("envHash2otu_table", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("internal", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Parses an ENV-file into a sparse matrix of species-by-sample, where\n", Rd_tag = "TEXT"), │ │ │ │ @@ -1674,15 +1674,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("#\n", Rd_tag = "RCODE"), │ │ │ │ structure("## fakeSeqNameVec <- paste(\"seq_\", 1:8, sep=\"\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("## fakeSamNameVec <- c(rep(\"A\", 4), rep(\"B\", 4))\n", Rd_tag = "RCODE"), │ │ │ │ structure("## fakeSeqAbunVec <- sample(1:50, 8, TRUE)\n", Rd_tag = "RCODE"), │ │ │ │ structure("## test <- cbind(fakeSeqNameVec, fakeSamNameVec, fakeSeqAbunVec)\n", Rd_tag = "RCODE"), │ │ │ │ structure("## testotu <- envHash2otu_table( test )\n", Rd_tag = "RCODE"), │ │ │ │ structure("## test <- cbind(fakeSeqNameVec, fakeSamNameVec)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("## testotu <- envHash2otu_table( test )\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/envHash2otu_table.Rd", class = "Rd", meta = list( │ │ │ │ + structure("## testotu <- envHash2otu_table( test )\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/envHash2otu_table.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ estimate_richness (list) = structure(list(structure(list(structure("Summarize alpha diversity", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("estimate_richness", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("estimate_richness", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Performs a number of standard alpha diversity estimates, \n", Rd_tag = "TEXT"), │ │ │ │ structure("and returns the results as a ", Rd_tag = "TEXT"), │ │ │ │ @@ -1743,15 +1743,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("## There are many more interesting examples at the phyloseq online tutorials.\n", Rd_tag = "RCODE"), │ │ │ │ structure("## http://joey711.github.com/phyloseq/plot_richness-examples\n", Rd_tag = "RCODE"), │ │ │ │ structure(" data(\"esophagus\")\n", Rd_tag = "RCODE"), │ │ │ │ structure(" # Default is all available measures\n", Rd_tag = "RCODE"), │ │ │ │ structure(" estimate_richness(esophagus)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" # Specify just one:\n", Rd_tag = "RCODE"), │ │ │ │ structure(" estimate_richness(esophagus, measures=\"Observed\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" # Specify a few:\n", Rd_tag = "RCODE"), structure(" estimate_richness(esophagus, measures=c(\"Observed\", \"InvSimpson\", \"Shannon\", \"Chao1\"))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/estimate_richness.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" # Specify a few:\n", Rd_tag = "RCODE"), structure(" estimate_richness(esophagus, measures=c(\"Observed\", \"InvSimpson\", \"Shannon\", \"Chao1\"))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/estimate_richness.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ export_env_file (list) = structure(list(structure(list(structure("Export environment (ENV) file for UniFrac Server.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("export_env_file", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("export_env_file", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Creates the environment table that is needed for the original UniFrac\n", Rd_tag = "TEXT"), │ │ │ │ structure("algorithm. Useful for cross-checking, or if want to use UniFrac server.\n", Rd_tag = "TEXT"), │ │ │ │ @@ -1785,15 +1785,15 @@ │ │ │ │ structure(list(list(structure("return", Rd_tag = "TEXT")), │ │ │ │ list(structure("(Optional). Should the ENV table be returned to the R workspace?\n", Rd_tag = "TEXT"), │ │ │ │ structure("Default is ", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure("FALSE", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(".", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("# # Load example data\n", Rd_tag = "RCODE"), │ │ │ │ - structure("# data(esophagus)\n", Rd_tag = "RCODE"), structure("# export_env_file(esophagus, \"~/Desktop/esophagus.txt\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/export_env_file.Rd", class = "Rd", meta = list( │ │ │ │ + structure("# data(esophagus)\n", Rd_tag = "RCODE"), structure("# export_env_file(esophagus, \"~/Desktop/esophagus.txt\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/export_env_file.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ export_mothur_dist (list) = structure(list(structure(list(structure("Export a distance object as ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(".names", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" and ", Rd_tag = "TEXT"), structure(list(structure(".dist", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" files for mothur", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("export_mothur_dist", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ @@ -1844,15 +1844,15 @@ │ │ │ │ structure("mothur", Rd_tag = "TEXT")), Rd_tag = "\\emph"), │ │ │ │ structure(" output. This an important extra step prior to\n", Rd_tag = "TEXT"), │ │ │ │ structure(" importing the OTUs with the ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("import_mothur_otulist()", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" function.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("#\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(esophagus) \n", Rd_tag = "RCODE"), structure("myDistObject <- as.dist(ape::cophenetic.phylo(phy_tree(esophagus)))\n", Rd_tag = "RCODE"), │ │ │ │ - structure("export_mothur_dist(myDistObject)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/export_mothur_dist.Rd", class = "Rd", meta = list( │ │ │ │ + structure("export_mothur_dist(myDistObject)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/export_mothur_dist.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extract-methods (list) = structure(list(structure(list(structure("Method extensions to extraction operator for phyloseq objects.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("[,otu_table,ANY,ANY,ANY-method", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("[,otu_table,ANY,ANY,ANY-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("[,sample_data,ANY,ANY,ANY-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("[,taxonomyTable,ANY,ANY,ANY-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -1915,15 +1915,15 @@ │ │ │ │ structure(list(structure("drop", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" argument.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("Extract", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("base", Rd_tag = "TEXT"))), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(esophagus)\n", Rd_tag = "RCODE"), │ │ │ │ structure("nrow(otu_table(esophagus))\n", Rd_tag = "RCODE"), │ │ │ │ - structure("nrow(otu_table(esophagus)[1:5, ])\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/extract-methods.Rd", class = "Rd", meta = list( │ │ │ │ + structure("nrow(otu_table(esophagus)[1:5, ])\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/extract-methods.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ filter_taxa (list) = structure(list(structure(list(structure("Filter taxa based on across-sample OTU abundance criteria", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("filter_taxa", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("filter_taxa", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function is directly analogous to the\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("genefilter", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("genefilter", Rd_tag = "TEXT"))), Rd_tag = "\\code"), │ │ │ │ @@ -1985,15 +1985,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure(" data(\"enterotype\")\n", Rd_tag = "RCODE"), │ │ │ │ structure(" require(\"genefilter\")\n", Rd_tag = "RCODE"), │ │ │ │ structure(" flist <- filterfun(kOverA(5, 2e-05))\n", Rd_tag = "RCODE"), │ │ │ │ structure(" ent.logi <- filter_taxa(enterotype, flist)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" ent.trim <- filter_taxa(enterotype, flist, TRUE)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" identical(ent.trim, prune_taxa(ent.logi, enterotype)) \n", Rd_tag = "RCODE"), │ │ │ │ structure(" identical(sum(ent.logi), ntaxa(ent.trim))\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" filter_taxa(enterotype, flist, TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/filter_taxa.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" filter_taxa(enterotype, flist, TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/filter_taxa.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ filterfun_sample (list) = structure(list(structure(list(structure("A sample-wise filter function builder\n", Rd_tag = "TEXT"), │ │ │ │ structure("analogous to ", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("filterfun", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("genefilter", Rd_tag = "TEXT"))), Rd_tag = "\\code"), │ │ │ │ structure(".", Rd_tag = "TEXT")), Rd_tag = "\\title"), structure(list( │ │ │ │ structure("filterfun_sample", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ @@ -2017,29 +2017,29 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("# Use simulated abundance matrix\n", Rd_tag = "RCODE"), │ │ │ │ structure("set.seed(711)\n", Rd_tag = "RCODE"), structure("testOTU <- otu_table(matrix(sample(1:50, 25, replace=TRUE), 5, 5), taxa_are_rows=FALSE)\n", Rd_tag = "RCODE"), │ │ │ │ structure("f1 <- filterfun_sample(topk(2))\n", Rd_tag = "RCODE"), │ │ │ │ structure("wh1 <- genefilter_sample(testOTU, f1, A=2)\n", Rd_tag = "RCODE"), │ │ │ │ structure("wh2 <- c(TRUE, TRUE, TRUE, FALSE, FALSE)\n", Rd_tag = "RCODE"), │ │ │ │ structure("prune_taxa(wh1, testOTU)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("prune_taxa(wh2, testOTU)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/filterfun_sample.Rd", class = "Rd", meta = list( │ │ │ │ + structure("prune_taxa(wh2, testOTU)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/filterfun_sample.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ fix_phylo (list) = structure(list(structure(list(structure("Method for fixing problems with phylo-class trees in phyloseq", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("fix_phylo", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("fix_phylo", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("fix_phylo,phylo-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("internal", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("For now this only entails replacing each missing (", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("NA", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(") branch-length\n", Rd_tag = "TEXT"), structure("value with 0.0.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("fix_phylo(tree)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure(list(list( │ │ │ │ structure("fix_phylo", Rd_tag = "TEXT")), list(structure("phylo", Rd_tag = "TEXT"))), Rd_tag = "\\S4method"), │ │ │ │ - structure("(tree)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/fix_phylo.Rd", class = "Rd", meta = list( │ │ │ │ + structure("(tree)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/fix_phylo.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ gapstat_ord (list) = structure(list(structure(list(structure("Estimate the gap statistic on an ordination result", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("gapstat_ord", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("gapstat_ord", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This is a wrapper for the ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("clusGap", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("cluster", Rd_tag = "TEXT"))), Rd_tag = "\\code"), │ │ │ │ @@ -2128,15 +2128,15 @@ │ │ │ │ structure(" documentation for more details.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(\"soilrep\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("sord = ordinate(soilrep, \"PCoA\", \"bray\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("# Evaluate axes with scree plot\n", Rd_tag = "RCODE"), │ │ │ │ structure("plot_scree(sord)\n", Rd_tag = "RCODE"), structure("# Gap Statistic\n", Rd_tag = "RCODE"), │ │ │ │ structure("gs = gapstat_ord(sord, axes=1:3, verbose=FALSE)\n", Rd_tag = "RCODE"), │ │ │ │ structure("# plot_ordination(soilrep, sord, color=\"Treatment\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("plot_clusgap(gs)\n", Rd_tag = "RCODE"), structure("print(gs, method=\"Tibs2001SEmax\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/gapstat_ord.Rd", class = "Rd", meta = list( │ │ │ │ + structure("plot_clusgap(gs)\n", Rd_tag = "RCODE"), structure("print(gs, method=\"Tibs2001SEmax\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/gapstat_ord.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ genefilter_sample-methods (list) = structure(list(structure(list(structure("Filter OTUs with arbitrary function, sample-wise.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("genefilter_sample", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("genefilter_sample", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("genefilter_sample,matrix-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("genefilter_sample,otu_table-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -2217,28 +2217,28 @@ │ │ │ │ structure("## f1 <- filterfun_sample(topk(2))\n", Rd_tag = "RCODE"), │ │ │ │ structure("## wh1 <- genefilter_sample(testOTU, f1, A=2)\n", Rd_tag = "RCODE"), │ │ │ │ structure("## wh2 <- c(TRUE, TRUE, TRUE, FALSE, FALSE)\n", Rd_tag = "RCODE"), │ │ │ │ structure("## prune_taxa(wh1, testOTU)\n", Rd_tag = "RCODE"), │ │ │ │ structure("## prune_taxa(wh2, testOTU)\n", Rd_tag = "RCODE"), │ │ │ │ structure("## \n", Rd_tag = "RCODE"), structure("## tax_table1 <- tax_table(matrix(\"abc\", 5, 5))\n", Rd_tag = "RCODE"), │ │ │ │ structure("## prune_taxa(wh1, tax_table1)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("## prune_taxa(wh2, tax_table1)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/genefilter_sample-methods.Rd", class = "Rd", meta = list( │ │ │ │ + structure("## prune_taxa(wh2, tax_table1)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/genefilter_sample-methods.Rd", class = "Rd", meta = list( │ │ │ │ docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ get.component.classes (list) = structure(list(structure(list(structure("Show the component objects classes and slot names.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("get.component.classes", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("get.component.classes", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("internal", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("There are no arguments to this function. It returns a named character\n", Rd_tag = "TEXT"), │ │ │ │ structure("when called, which can then be used for tests of component data types, etc.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("get.component.classes()\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("a character vector of the component objects classes, where each \n", Rd_tag = "TEXT"), │ │ │ │ structure("element is named by the corresponding slot name in the phyloseq-class.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("#\n", Rd_tag = "RCODE"), │ │ │ │ - structure("#get.component.classes()\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/get.component.classes.Rd", class = "Rd", meta = list( │ │ │ │ + structure("#get.component.classes()\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/get.component.classes.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ get_sample-methods (list) = structure(list(structure(list(structure("Returns all abundance values for species ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("i", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(".", Rd_tag = "TEXT")), Rd_tag = "\\title"), structure(list( │ │ │ │ structure("get_sample", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("get_sample", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -2275,15 +2275,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("taxa_names", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("sample_names", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(esophagus)\n", Rd_tag = "RCODE"), │ │ │ │ structure("taxa_names(esophagus)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("get_sample(esophagus, \"59_5_19\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/get_sample-methods.Rd", class = "Rd", meta = list( │ │ │ │ + structure("get_sample(esophagus, \"59_5_19\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/get_sample-methods.Rd", class = "Rd", meta = list( │ │ │ │ docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ get_taxa-methods (list) = structure(list(structure(list(structure("Returns all abundance values of sample ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("i", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(".", Rd_tag = "TEXT")), Rd_tag = "\\title"), structure(list( │ │ │ │ structure("get_taxa", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("get_taxa", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -2321,15 +2321,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("taxa_names", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("sample_names", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(esophagus)\n", Rd_tag = "RCODE"), │ │ │ │ structure("sample_names(esophagus)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("get_taxa(esophagus, \"B\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/get_taxa-methods.Rd", class = "Rd", meta = list( │ │ │ │ + structure("get_taxa(esophagus, \"B\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/get_taxa-methods.Rd", class = "Rd", meta = list( │ │ │ │ docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ get_taxa_unique (list) = structure(list(structure(list(structure("Get a unique vector of the observed taxa at a particular taxonomic rank", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("get_taxa_unique", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("get_taxa_unique", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This is a simple accessor function to make it more convenient to determine\n", Rd_tag = "TEXT"), │ │ │ │ structure("the different taxa present for a particular taxonomic rank\n", Rd_tag = "TEXT"), │ │ │ │ @@ -2369,15 +2369,15 @@ │ │ │ │ structure(list(structure(list(structure("taxa_names", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("sample_names", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(enterotype)\n", Rd_tag = "RCODE"), │ │ │ │ structure("get_taxa_unique(enterotype)\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(GlobalPatterns)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("get_taxa_unique(GlobalPatterns, \"Family\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/get_taxa_unique.Rd", class = "Rd", meta = list( │ │ │ │ + structure("get_taxa_unique(GlobalPatterns, \"Family\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/get_taxa_unique.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ get_variable (list) = structure(list(structure(list(structure("Get the values for a particular variable in sample_data", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("get_variable", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("get_variable", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This is a simple accessor function for streamlining access\n", Rd_tag = "TEXT"), │ │ │ │ structure("to values/vectors/factors/etc contained in the sample_data.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -2406,15 +2406,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("sample_variables", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("# Load the GlobalPatterns dataset into the workspace environment\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(GlobalPatterns)\n", Rd_tag = "RCODE"), │ │ │ │ structure("# Look at the different values for SampleType \n", Rd_tag = "RCODE"), │ │ │ │ - structure("get_variable(GlobalPatterns, \"SampleType\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/get_variable.Rd", class = "Rd", meta = list( │ │ │ │ + structure("get_variable(GlobalPatterns, \"SampleType\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/get_variable.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ getslots.phyloseq (list) = structure(list(structure(list(structure("Return the non-empty slot names of a phyloseq object.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getslots.phyloseq", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getslots.phyloseq", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Like ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("getSlots", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ @@ -2440,15 +2440,15 @@ │ │ │ │ structure("the ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("phyloseq-class", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(".\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("merge_phyloseq\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("#\n", Rd_tag = "RCODE"), │ │ │ │ structure(" data(GlobalPatterns)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" getslots.phyloseq(GlobalPatterns)\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" data(esophagus)\n", Rd_tag = "RCODE"), structure(" getslots.phyloseq(esophagus)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/getslots.phyloseq.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" data(esophagus)\n", Rd_tag = "RCODE"), structure(" getslots.phyloseq(esophagus)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/getslots.phyloseq.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ hideOutput (NULL) = NULL │ │ │ │ │ │ │ │ import (list) = structure(list(structure(list(structure("Universal import method (wrapper) for phyloseq-package", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("import", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("import", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -2518,15 +2518,15 @@ │ │ │ │ structure(list(structure(list(structure("import_qiime", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure("For RDP pipeline, see:\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("import_RDP_cluster", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("import_RDP_otu", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ - structure(list(structure("\n", Rd_tag = "RCODE"), structure(" ## See documentation of a specific import function\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/import.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("\n", Rd_tag = "RCODE"), structure(" ## See documentation of a specific import function\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/import.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ import_RDP_cluster (list) = structure(list(structure(list(structure("Import RDP cluster file and return otu_table (abundance table).", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("import_RDP_cluster", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("import_RDP_cluster", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("The RDP cluster pipeline (specifically, the output of the complete linkage clustering step)\n", Rd_tag = "TEXT"), │ │ │ │ structure("has no formal documentation for the ", Rd_tag = "TEXT"), │ │ │ │ @@ -2571,15 +2571,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("An ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("otu_table", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" object parsed from the ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("\".clust\"", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" file.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure("http://pyro.cme.msu.edu/index.jsp", Rd_tag = "VERB")), Rd_tag = "\\url"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\references")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/import_RDP_cluster.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\references")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/import_RDP_cluster.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ import_RDP_otu (list) = structure(list(structure(list(structure("Import new RDP OTU-table format", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("import_RDP_otu", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("import_RDP_otu", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Recently updated tools on RDP Pyro site make it easier to import Pyrosequencing output \n", Rd_tag = "TEXT"), │ │ │ │ structure("into R. The modified tool ``Cluster To R Formatter'' can take a cluster file \n", Rd_tag = "TEXT"), │ │ │ │ @@ -2607,15 +2607,15 @@ │ │ │ │ structure(list(structure("http://pyro.cme.msu.edu/index.jsp", Rd_tag = "VERB")), Rd_tag = "\\url"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("otufile <- system.file(\"extdata\", \"rformat_dist_0.03.txt.gz\", package=\"phyloseq\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("### the gzipped file is automatically recognized, and read using R-connections\n", Rd_tag = "RCODE"), │ │ │ │ structure("ex_otu <- import_RDP_otu(otufile)\n", Rd_tag = "RCODE"), │ │ │ │ structure("class(ex_otu)\n", Rd_tag = "RCODE"), structure("ntaxa(ex_otu)\n", Rd_tag = "RCODE"), │ │ │ │ structure("nsamples(ex_otu)\n", Rd_tag = "RCODE"), structure("sample_sums(ex_otu)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("head(t(ex_otu))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/import_RDP_otu.Rd", class = "Rd", meta = list( │ │ │ │ + structure("head(t(ex_otu))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/import_RDP_otu.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ import_biom (list) = structure(list(structure(list(structure("Import phyloseq data from biom-format file", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("import_biom", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("import_biom", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("New versions of QIIME produce a more-comprehensive and formally-defined\n", Rd_tag = "TEXT"), │ │ │ │ structure("JSON file format, called biom file format:\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -2824,15 +2824,15 @@ │ │ │ │ structure("import_biom(rich_dense_biom, parseFunction=parse_taxonomy_greengenes)\n", Rd_tag = "RCODE"), │ │ │ │ structure("# An included example of a sparse dense biom file\n", Rd_tag = "RCODE"), │ │ │ │ structure("rich_sparse_biom <- system.file(\"extdata\", \"rich_sparse_otu_table.biom\", package=\"phyloseq\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("import_biom(rich_sparse_biom, parseFunction=parse_taxonomy_greengenes)\n", Rd_tag = "RCODE"), │ │ │ │ structure("# # # Example code for importing large file with parallel backend\n", Rd_tag = "RCODE"), │ │ │ │ structure("# library(\"doParallel\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("# registerDoParallel(cores=6)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("# import_biom(\"my/file/path/file.biom\", parseFunction=parse_taxonomy_greengenes, parallel=TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/import_biom.Rd", class = "Rd", meta = list( │ │ │ │ + structure("# import_biom(\"my/file/path/file.biom\", parseFunction=parse_taxonomy_greengenes, parallel=TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/import_biom.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ import_env_file (list) = structure(list(structure(list(structure("Read a UniFrac-formatted ENV file.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("import_env_file", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("import_env_file", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Convenience wrapper function to read the environment-file, as formatted for \n", Rd_tag = "TEXT"), │ │ │ │ structure("input to the UniFrac server (", Rd_tag = "TEXT"), │ │ │ │ @@ -2875,15 +2875,15 @@ │ │ │ │ structure("http://bmf2.colorado.edu/unifrac/", Rd_tag = "VERB")), Rd_tag = "\\url"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\references"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("import", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("tip_glom", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ - structure(list(structure("\n", Rd_tag = "RCODE"), structure("# import_env_file(myEnvFile, myTree)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/import_env_file.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("\n", Rd_tag = "RCODE"), structure("# import_env_file(myEnvFile, myTree)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/import_env_file.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ import_mothur (list) = structure(list(structure(list(structure("General function for importing mothur data files into phyloseq.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("import_mothur", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("import_mothur", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Technically all parameters are optional,\n", Rd_tag = "TEXT"), │ │ │ │ structure("but if you don't provide any file connections, then nothing will be returned.\n", Rd_tag = "TEXT"), │ │ │ │ @@ -3044,15 +3044,15 @@ │ │ │ │ structure("# # Returns just a tree\n", Rd_tag = "RCODE"), │ │ │ │ structure("# import_mothur(mothur_list_file, mothur_tree_file=mothur_tree_file)\n", Rd_tag = "RCODE"), │ │ │ │ structure("# # Returns just an otu_table\n", Rd_tag = "RCODE"), │ │ │ │ structure("# import_mothur(mothur_list_file, mothur_group_file=mothur_group_file)\n", Rd_tag = "RCODE"), │ │ │ │ structure("# # Returns an error\n", Rd_tag = "RCODE"), │ │ │ │ structure("# import_mothur(mothur_list_file)\n", Rd_tag = "RCODE"), │ │ │ │ structure("# # Should return an \"OMG, you must provide the list file\" error\n", Rd_tag = "RCODE"), │ │ │ │ - structure("# import_mothur()\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/import_mothur.Rd", class = "Rd", meta = list( │ │ │ │ + structure("# import_mothur()\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/import_mothur.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ import_mothur_constaxonomy (list) = structure(list(structure(list(structure("Import mothur constaxonomy file and return a taxonomyTable", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("import_mothur_constaxonomy", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("import_mothur_constaxonomy", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("internal", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Import mothur constaxonomy file and return a taxonomyTable\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -3086,15 +3086,15 @@ │ │ │ │ structure(" object.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("import_mothur", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("tax_table", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("phyloseq", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/import_mothur_constaxonomy.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/import_mothur_constaxonomy.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ import_mothur_dist (list) = structure(list(structure(list(structure("Import mothur-formatted distance file", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("import_mothur_dist", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("import_mothur_dist", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("The mothur application will produce a file containing the pairwise distances\n", Rd_tag = "TEXT"), │ │ │ │ structure("between all sequences in a dataset. This distance matrix can be the basis for\n", Rd_tag = "TEXT"), │ │ │ │ @@ -3112,15 +3112,15 @@ │ │ │ │ structure(list(structure("import_mothur", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("# # Take a look at the dataset shown here as an example:\n", Rd_tag = "RCODE"), │ │ │ │ structure("# # \"http://www.mothur.org/wiki/Esophageal_community_analysis\"\n", Rd_tag = "RCODE"), │ │ │ │ structure("# # find the file ending with extension \".dist\", download to your system\n", Rd_tag = "RCODE"), │ │ │ │ structure("# # The location of your file may vary\n", Rd_tag = "RCODE"), │ │ │ │ structure("# mothur_dist_file <- \"~/Downloads/mothur/Esophagus/esophagus.dist\"\n", Rd_tag = "RCODE"), │ │ │ │ - structure("# myNewDistObject <- import_mothur_dist(mothur_dist_file)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/import_mothur_dist.Rd", class = "Rd", meta = list( │ │ │ │ + structure("# myNewDistObject <- import_mothur_dist(mothur_dist_file)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/import_mothur_dist.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ import_mothur_groups (list) = structure(list(structure(list(structure("Parse mothur group file into a simple hash table.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("import_mothur_groups", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("import_mothur_groups", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("internal", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("The data.frame object\n", Rd_tag = "TEXT"), │ │ │ │ @@ -3147,15 +3147,15 @@ │ │ │ │ structure("is recorded. See \n", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("http://www.mothur.org/wiki/Make.group", Rd_tag = "RCODE")), Rd_tag = "\\code"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("A data.frame that is effectively a hash table between sequence names\n", Rd_tag = "TEXT"), │ │ │ │ structure(" and their sample source.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("import_mothur", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/import_mothur_groups.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/import_mothur_groups.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ import_mothur_otu_table (list) = structure(list(structure(list(structure("Import mothur list and group files and return an otu_table", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("import_mothur_otu_table", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("import_mothur_otu_table", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("internal", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Import mothur list and group files and return an otu_table\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -3204,15 +3204,15 @@ │ │ │ │ structure(" function.", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("An ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("otu_table", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" object.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("import_mothur", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/import_mothur_otu_table.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/import_mothur_otu_table.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ import_mothur_otulist (list) = structure(list(structure(list(structure("Import mothur list file and return as list object in R.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("import_mothur_otulist", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("import_mothur_otulist", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("internal", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This is a user-available module of a more comprehensive function for importing\n", Rd_tag = "TEXT"), │ │ │ │ @@ -3268,15 +3268,15 @@ │ │ │ │ structure(" dependent on the choice for ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("cutoff", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(".\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("show_mothur_cutoffs", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(", ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("import_mothur", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/import_mothur_otulist.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/import_mothur_otulist.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ import_mothur_shared (list) = structure(list(structure(list(structure("Import mothur shared file and return an otu_table", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("import_mothur_shared", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("import_mothur_shared", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("internal", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Import mothur shared file and return an otu_table\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -3291,15 +3291,15 @@ │ │ │ │ structure(".", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("An ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("otu_table", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" object.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("import_mothur", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/import_mothur_shared.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/import_mothur_shared.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ import_pyrotagger_tab (list) = structure(list(structure(list(structure("Imports a tab-delimited version of the pyrotagger output file.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("import_pyrotagger_tab", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("import_pyrotagger_tab", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("PyroTagger is a web-server that takes raw, barcoded 16S rRNA amplicon sequences\n", Rd_tag = "TEXT"), │ │ │ │ structure("and returns an excel spreadsheet (", Rd_tag = "TEXT"), │ │ │ │ @@ -3365,15 +3365,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("An ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("otuTax", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" object containing both the otu_table and TaxonomyTable data\n", Rd_tag = "TEXT"), │ │ │ │ structure(" components, parsed from the pyrotagger output.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure("http://pyrotagger.jgi-psf.org/", Rd_tag = "VERB")), Rd_tag = "\\url"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\references"), │ │ │ │ - structure(list(structure("\n", Rd_tag = "RCODE"), structure("## New_otuTaxObject <- import_pyrotagger_tab(pyrotagger_tab_file)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/import_pyrotagger_tab.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("\n", Rd_tag = "RCODE"), structure("## New_otuTaxObject <- import_pyrotagger_tab(pyrotagger_tab_file)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/import_pyrotagger_tab.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ import_qiime (list) = structure(list(structure(list(structure("Import function to read the now legacy-format QIIME OTU table.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("import_qiime", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("import_qiime", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("QIIME produces several files that can be directly imported by\n", Rd_tag = "TEXT"), │ │ │ │ structure("the ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ @@ -3571,15 +3571,15 @@ │ │ │ │ structure(list(structure(list(structure("read_tree_greengenes", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("XStringSet-io", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("Biostrings", Rd_tag = "TEXT"))), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure(" otufile <- system.file(\"extdata\", \"GP_otu_table_rand_short.txt.gz\", package=\"phyloseq\")\n", Rd_tag = "RCODE"), │ │ │ │ structure(" mapfile <- system.file(\"extdata\", \"master_map.txt\", package=\"phyloseq\")\n", Rd_tag = "RCODE"), │ │ │ │ structure(" trefile <- system.file(\"extdata\", \"GP_tree_rand_short.newick.gz\", package=\"phyloseq\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" import_qiime(otufile, mapfile, trefile)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/import_qiime.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" import_qiime(otufile, mapfile, trefile)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/import_qiime.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ import_qiime_otu_tax (list) = structure(list(structure(list(structure("Import now legacy-format QIIME OTU table as a list of two matrices.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("import_qiime_otu_tax", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("import_qiime_otu_tax", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Now a legacy-format, older versions of QIIME\n", Rd_tag = "TEXT"), │ │ │ │ structure("produced an OTU file that typically contains both OTU-abundance\n", Rd_tag = "TEXT"), │ │ │ │ @@ -3669,15 +3669,15 @@ │ │ │ │ structure(list(structure(list(structure("read_tree", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("read_tree_greengenes", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("import_env_file", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure(" otufile <- system.file(\"extdata\", \"GP_otu_table_rand_short.txt.gz\", package=\"phyloseq\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" import_qiime_otu_tax(otufile)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/import_qiime_otu_tax.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" import_qiime_otu_tax(otufile)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/import_qiime_otu_tax.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ import_qiime_sample_data (list) = structure(list(structure(list(structure("Import just ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("sample_data", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" file from QIIME pipeline.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("import_qiime_sample_data", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("import_qiime_sample_data", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -3718,15 +3718,15 @@ │ │ │ │ structure(list(structure(list(structure("import_qiime", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("import_qiime_otu_tax", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("import_env_file", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure(" mapfile <- system.file(\"extdata\", \"master_map.txt\", package = \"phyloseq\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" import_qiime_sample_data(mapfile)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/import_qiime_sample_data.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" import_qiime_sample_data(mapfile)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/import_qiime_sample_data.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ import_uparse (list) = structure(list(structure(list(structure("Import ", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("http://www.drive5.com/usearch/manual/opt_uparseout.html", Rd_tag = "VERB")), │ │ │ │ list(structure("UPARSE file format", Rd_tag = "TEXT"))), Rd_tag = "\\href")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("import_uparse", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("import_uparse", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -3817,15 +3817,15 @@ │ │ │ │ structure("and post it as an issue on the \n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("https://github.com/joey711/phyloseq/issues", Rd_tag = "VERB")), │ │ │ │ list(structure("phyloseq issues tracker", Rd_tag = "TEXT"))), Rd_tag = "\\href"), │ │ │ │ structure(".\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("import_usearch_uc", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ - structure(list(structure("\n", Rd_tag = "RCODE"), structure("###\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/import_uparse.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("\n", Rd_tag = "RCODE"), structure("###\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/import_uparse.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ import_usearch_uc (list) = structure(list(structure(list(structure("Import usearch table format (", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(".uc", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(") to OTU table", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("import_usearch_uc", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("import_usearch_uc", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -3930,15 +3930,15 @@ │ │ │ │ structure(list(structure("import", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("import_biom", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("import_qiime", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("usearchfile <- system.file(\"extdata\", \"usearch.uc\", package=\"phyloseq\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("import_usearch_uc(usearchfile)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/import_usearch_uc.Rd", class = "Rd", meta = list( │ │ │ │ + structure("import_usearch_uc(usearchfile)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/import_usearch_uc.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ index_reorder (list) = structure(list(structure(list(structure("Force index order of phyloseq objects", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("index_reorder", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("index_reorder", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("index_reorder,phyloseq-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("internal", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ @@ -3960,15 +3960,15 @@ │ │ │ │ structure(list(structure("c(\"both\", \"taxa\", \"samples\")", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(".\n", Rd_tag = "TEXT"), structure("Default is ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("\"both\"", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(", meaning samples and taxa indices\n", Rd_tag = "TEXT"), │ │ │ │ structure("will be checked/re-ordered.", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("## data(\"GlobalPatterns\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("## GP = index_reorder(GlobalPatterns)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/index_reorder.Rd", class = "Rd", meta = list( │ │ │ │ + structure("## GP = index_reorder(GlobalPatterns)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/index_reorder.Rd", class = "Rd", meta = list( │ │ │ │ docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ intersect_taxa (list) = structure(list(structure(list(structure("Returns the intersection of species and samples for the components of x", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("intersect_taxa", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("intersect_taxa", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("internal", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function is used internally as part of the infrastructure to ensure that\n", Rd_tag = "TEXT"), │ │ │ │ @@ -3991,15 +3991,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("Reduce", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(", ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("intersect", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("#\n", Rd_tag = "RCODE"), │ │ │ │ structure("## data(GlobalPatterns)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("## head(intersect_taxa(GlobalPatterns), 10)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/intersect_taxa.Rd", class = "Rd", meta = list( │ │ │ │ + structure("## head(intersect_taxa(GlobalPatterns), 10)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/intersect_taxa.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ make_network (list) = structure(list(structure(list(structure("Make microbiome network (igraph)", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("make_network", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("make_network", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("A specialized function for creating a network representation of microbiomes,\n", Rd_tag = "TEXT"), │ │ │ │ structure("sample-wise or taxa-wise,\n", Rd_tag = "TEXT"), │ │ │ │ @@ -4109,15 +4109,15 @@ │ │ │ │ structure("ih <- make_network(enterotype, max.dist=0.3, distance=jaccdist)\n", Rd_tag = "RCODE"), │ │ │ │ structure("# Provide \"custom\" function.\n", Rd_tag = "RCODE"), │ │ │ │ structure("ii <- make_network(enterotype, max.dist=0.3, distance=function(x){vegan::vegdist(x, \"jaccard\")})\n", Rd_tag = "RCODE"), │ │ │ │ structure("# The have equal results:\t\t\n", Rd_tag = "RCODE"), │ │ │ │ structure("all.equal(ig, ih)\n", Rd_tag = "RCODE"), structure("all.equal(ig, ii)\n", Rd_tag = "RCODE"), │ │ │ │ structure("# \n", Rd_tag = "RCODE"), structure("# Try out making a trivial \"network\" of the 3-sample esophagus data,\n", Rd_tag = "RCODE"), │ │ │ │ structure("# with weighted-UniFrac as distance\n", Rd_tag = "RCODE"), │ │ │ │ - structure("data(esophagus)\n", Rd_tag = "RCODE"), structure("ij <- make_network(esophagus, \"samples\", \"unifrac\", weighted=TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/make_network.Rd", class = "Rd", meta = list( │ │ │ │ + structure("data(esophagus)\n", Rd_tag = "RCODE"), structure("ij <- make_network(esophagus, \"samples\", \"unifrac\", weighted=TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/make_network.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ merge_phyloseq (list) = structure(list(structure(list(structure("Merge arguments into one phyloseq object.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("merge_phyloseq", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("merge_phyloseq", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Takes a comma-separated list of phyloseq objects as arguments,\n", Rd_tag = "TEXT"), │ │ │ │ structure("and returns the most-comprehensive single phyloseq object possible.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -4169,15 +4169,15 @@ │ │ │ │ structure("## map1 <- data.frame( matrix(sample(0:3,250,TRUE),25,10), \n", Rd_tag = "RCODE"), │ │ │ │ structure("## matrix(sample(c(\"a\",\"b\",\"c\"),150,TRUE), 25, 6) ) \n", Rd_tag = "RCODE"), │ │ │ │ structure("## map1 <- sample_data(map1)\n", Rd_tag = "RCODE"), │ │ │ │ structure("## exam1 <- phyloseq(OTU1, map1, tax1)\n", Rd_tag = "RCODE"), │ │ │ │ structure("## x <- exam1\n", Rd_tag = "RCODE"), structure("## x <- phyloseq(exam1)\n", Rd_tag = "RCODE"), │ │ │ │ structure("## y <- tax_table(exam1)\n", Rd_tag = "RCODE"), │ │ │ │ structure("## merge_phyloseq(x, y)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("## merge_phyloseq(y, y, y, y)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/merge_phyloseq.Rd", class = "Rd", meta = list( │ │ │ │ + structure("## merge_phyloseq(y, y, y, y)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/merge_phyloseq.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ merge_phyloseq_pair-methods (list) = structure(list(structure(list(structure("Merge pair of phyloseq component data objects of the same class.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("merge_phyloseq_pair", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("merge_phyloseq_pair", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("merge_phyloseq_pair,otu_table,otu_table-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("merge_phyloseq_pair,taxonomyTable,taxonomyTable-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -4264,15 +4264,15 @@ │ │ │ │ structure("## matrix(sample(c(\"a\",\"b\",\"c\"),150,TRUE),25,6) )\n", Rd_tag = "RCODE"), │ │ │ │ structure("## x <- sample_data(x)\n", Rd_tag = "RCODE"), │ │ │ │ structure("## y <- data.frame( matrix(sample(4:6,200,TRUE),20,10), \n", Rd_tag = "RCODE"), │ │ │ │ structure("## matrix(sample(c(\"d\",\"e\",\"f\"),120,TRUE),20,8) )\n", Rd_tag = "RCODE"), │ │ │ │ structure("## y <- sample_data(y)\n", Rd_tag = "RCODE"), │ │ │ │ structure("## merge_phyloseq_pair(x, y)\n", Rd_tag = "RCODE"), │ │ │ │ structure("## data.frame(merge_phyloseq_pair(x, y))\n", Rd_tag = "RCODE"), │ │ │ │ - structure("## data.frame(merge_phyloseq_pair(y, x))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/merge_phyloseq_pair-methods.Rd", class = "Rd", meta = list( │ │ │ │ + structure("## data.frame(merge_phyloseq_pair(y, x))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/merge_phyloseq_pair-methods.Rd", class = "Rd", meta = list( │ │ │ │ docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ merge_samples-methods (list) = structure(list(structure(list(structure("Merge samples based on a sample variable or factor.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("merge_samples", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("merge_samples", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("merge_samples,sample_data-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("merge_samples,otu_table-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -4353,15 +4353,15 @@ │ │ │ │ structure("OTUnames10 = names(sort(taxa_sums(GP), TRUE)[1:10])\n", Rd_tag = "RCODE"), │ │ │ │ structure("GP10 = prune_taxa(OTUnames10, GP)\n", Rd_tag = "RCODE"), │ │ │ │ structure("mGP10 = prune_taxa(OTUnames10, mergedGP)\n", Rd_tag = "RCODE"), │ │ │ │ structure("ocean_samples = sample_names(subset(sample_data(GP), SampleType==\"Ocean\"))\n", Rd_tag = "RCODE"), │ │ │ │ structure("print(ocean_samples)\n", Rd_tag = "RCODE"), │ │ │ │ structure("otu_table(GP10)[, ocean_samples]\n", Rd_tag = "RCODE"), │ │ │ │ structure("rowSums(otu_table(GP10)[, ocean_samples])\n", Rd_tag = "RCODE"), │ │ │ │ - structure("otu_table(mGP10)[\"Ocean\", ]\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/merge_samples-methods.Rd", class = "Rd", meta = list( │ │ │ │ + structure("otu_table(mGP10)[\"Ocean\", ]\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/merge_samples-methods.Rd", class = "Rd", meta = list( │ │ │ │ docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ merge_taxa-methods (list) = structure(list(structure(list(structure("Merge a subset of the species in ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("x", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" into one species/taxa/OTU.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("merge_taxa", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("merge_taxa", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -4464,15 +4464,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("#\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(esophagus)\n", Rd_tag = "RCODE"), structure("tree <- phy_tree(esophagus)\n", Rd_tag = "RCODE"), │ │ │ │ structure("otu <- otu_table(esophagus)\n", Rd_tag = "RCODE"), │ │ │ │ structure("otutree0 <- phyloseq(otu, tree)\n", Rd_tag = "RCODE"), │ │ │ │ structure("# plot_tree(otutree0)\n", Rd_tag = "RCODE"), │ │ │ │ structure("otutree1 <- merge_taxa(otutree0, 1:8, 2)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("# plot_tree(esophagus, ladderize=\"left\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/merge_taxa-methods.Rd", class = "Rd", meta = list( │ │ │ │ + structure("# plot_tree(esophagus, ladderize=\"left\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/merge_taxa-methods.Rd", class = "Rd", meta = list( │ │ │ │ docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ metaMDS (list) = structure(list(structure(list(structure("S3 class placeholder definition (list) for metaMDS", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("metaMDS", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("metaMDS", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("internal", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("The ape package does export a version of its ", Rd_tag = "TEXT"), │ │ │ │ @@ -4489,15 +4489,15 @@ │ │ │ │ structure("judiciously and within phyloseq.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("metaMDS\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("An object of class ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("metaMDS", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" of length 0.\n", Rd_tag = "TEXT")), Rd_tag = "\\format"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("metaMDS", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("vegan", Rd_tag = "TEXT"))), Rd_tag = "\\code"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/metaMDS.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/metaMDS.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ microbio_me_qiime (list) = structure(list(structure(list(structure("Import microbio.me/qiime (QIIME-DB) data package", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("microbio_me_qiime", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("microbio_me_qiime", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Originally, this function was for accessing microbiome datasets from the\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("http://www.microbio.me/qiime/index.psp", Rd_tag = "VERB")), │ │ │ │ @@ -4621,15 +4621,15 @@ │ │ │ │ structure("tarps; zipps\n", Rd_tag = "RCODE"), structure("plot_heatmap(tarps)\n", Rd_tag = "RCODE"), │ │ │ │ structure("# An example that used to work, before the QIIME-DB server was turned off by its host.\n", Rd_tag = "RCODE"), │ │ │ │ structure("# # Smokers dataset\n", Rd_tag = "RCODE"), │ │ │ │ structure("# smokezip = \"ftp://thebeast.colorado.edu/pub/QIIME_DB_Public_Studies/study_524_split_library_seqs_and_mapping.zip\"\n", Rd_tag = "RCODE"), │ │ │ │ structure("# smokers1 = microbio_me_qiime(smokezip)\n", Rd_tag = "RCODE"), │ │ │ │ structure("# # Alternatively, just use the study number\n", Rd_tag = "RCODE"), │ │ │ │ structure("# smokers2 = microbio_me_qiime(524)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("# identical(smokers1, smokers2)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/microbio_me_qiime.Rd", class = "Rd", meta = list( │ │ │ │ + structure("# identical(smokers1, smokers2)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/microbio_me_qiime.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ mt-methods (list) = structure(list(structure(list(structure("Multiple testing of taxa abundance according to sample categories/classes", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("mt", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("mt", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("mt,phyloseq,ANY-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("mt,otu_table,integer-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -4740,15 +4740,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("## # Simple example, testing genera that sig correlate with Enterotypes\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(enterotype)\n", Rd_tag = "RCODE"), structure("# Filter samples that don't have Enterotype\n", Rd_tag = "RCODE"), │ │ │ │ structure("x <- subset_samples(enterotype, !is.na(Enterotype))\n", Rd_tag = "RCODE"), │ │ │ │ structure("# (the taxa are at the genera level in this dataset)\n", Rd_tag = "RCODE"), │ │ │ │ structure("res = mt(x, \"Enterotype\", method=\"fdr\", test=\"f\", B=300)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(res, 10)\n", Rd_tag = "RCODE"), structure("## # Not surprisingly, Prevotella and Bacteroides top the list.\n", Rd_tag = "RCODE"), │ │ │ │ structure("## # Different test, multiple-adjusted t-test, whether samples are ent-2 or not.\n", Rd_tag = "RCODE"), │ │ │ │ - structure("## mt(x, get_variable(x, \"Enterotype\")==2)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/mt-methods.Rd", class = "Rd", meta = list( │ │ │ │ + structure("## mt(x, get_variable(x, \"Enterotype\")==2)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/mt-methods.Rd", class = "Rd", meta = list( │ │ │ │ docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ nodeplotblank (list) = structure(list(structure(list(structure("Function to avoid plotting node labels", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("nodeplotblank", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("nodeplotblank", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Unlike, ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("nodeplotdefault", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ @@ -4786,15 +4786,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("nodeplotboot", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("plot_tree", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(\"esophagus\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("plot_tree(esophagus)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("plot_tree(esophagus, nodelabf=nodeplotblank)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/nodeplotblank.Rd", class = "Rd", meta = list( │ │ │ │ + structure("plot_tree(esophagus, nodelabf=nodeplotblank)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/nodeplotblank.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ nodeplotboot (list) = structure(list(structure(list(structure("Generates a function for labeling bootstrap values on a phylogenetic tree.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("nodeplotboot", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("nodeplotboot", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Is not a labeling function itself, but returns one.\n", Rd_tag = "TEXT"), │ │ │ │ structure("The returned function is specialized for labeling bootstrap values.\n", Rd_tag = "TEXT"), │ │ │ │ @@ -4855,15 +4855,15 @@ │ │ │ │ structure(list(structure("nodeplotdefault", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("nodeplotblank", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("plot_tree", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("nodeplotboot()\n", Rd_tag = "RCODE"), │ │ │ │ - structure("nodeplotboot(3, -0.4)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/nodeplotboot.Rd", class = "Rd", meta = list( │ │ │ │ + structure("nodeplotboot(3, -0.4)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/nodeplotboot.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ nodeplotdefault (list) = structure(list(structure(list(structure("Generates a default node-label function", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("nodeplotdefault", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("nodeplotdefault", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Is not a labeling function itself, but returns one.\n", Rd_tag = "TEXT"), │ │ │ │ structure("The returned function is capable of adding\n", Rd_tag = "TEXT"), │ │ │ │ @@ -4906,15 +4906,15 @@ │ │ │ │ structure(list(structure("nodeplotboot", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("nodeplotblank", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("plot_tree", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("nodeplotdefault()\n", Rd_tag = "RCODE"), │ │ │ │ - structure("nodeplotdefault(3, -0.4)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/nodeplotdefault.Rd", class = "Rd", meta = list( │ │ │ │ + structure("nodeplotdefault(3, -0.4)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/nodeplotdefault.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ nsamples-methods (list) = structure(list(structure(list(structure("Get the number of samples.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("nsamples", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("nsamples", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("nsamples,ANY-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("nsamples,phyloseq-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -4952,15 +4952,15 @@ │ │ │ │ structure(list(structure(list(structure("ntaxa", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("#\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(\"esophagus\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("tree <- phy_tree(esophagus)\n", Rd_tag = "RCODE"), │ │ │ │ structure("OTU1 <- otu_table(esophagus)\n", Rd_tag = "RCODE"), │ │ │ │ structure("nsamples(OTU1)\n", Rd_tag = "RCODE"), structure("physeq1 <- phyloseq(OTU1, tree)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("nsamples(physeq1)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/nsamples-methods.Rd", class = "Rd", meta = list( │ │ │ │ + structure("nsamples(physeq1)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/nsamples-methods.Rd", class = "Rd", meta = list( │ │ │ │ docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ ntaxa-methods (list) = structure(list(structure(list(structure("Get the number of taxa/species.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("ntaxa", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("ntaxa", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("ntaxa,ANY-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("ntaxa,phyloseq-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -4998,15 +4998,15 @@ │ │ │ │ structure(", or\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("phylo", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("ape", Rd_tag = "TEXT"))), Rd_tag = "\\code"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("An integer indicating the number of taxa / species.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("taxa_names\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(\"esophagus\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("ntaxa(esophagus)\n", Rd_tag = "RCODE"), structure("phy_tree(esophagus)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("ntaxa(phy_tree(esophagus))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/ntaxa-methods.Rd", class = "Rd", meta = list( │ │ │ │ + structure("ntaxa(phy_tree(esophagus))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/ntaxa-methods.Rd", class = "Rd", meta = list( │ │ │ │ docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ ordinate (list) = structure(list(structure(list(structure("Perform an ordination on phyloseq data", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("ordinate", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("ordinate", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function wraps several commonly-used ordination methods. The type of \n", Rd_tag = "TEXT"), │ │ │ │ structure("ordination depends upon the argument to ", Rd_tag = "TEXT"), │ │ │ │ @@ -5268,15 +5268,15 @@ │ │ │ │ list(structure("Analysis of Ecological and Environmental Data", Rd_tag = "TEXT"))), Rd_tag = "\\href"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("http://cran.r-project.org/web/views/Multivariate.html", Rd_tag = "VERB")), │ │ │ │ list(structure("Multivariate Statistics", Rd_tag = "TEXT"))), Rd_tag = "\\href"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("# See http://joey711.github.io/phyloseq/plot_ordination-examples\n", Rd_tag = "RCODE"), │ │ │ │ structure("# for many more examples.\n", Rd_tag = "RCODE"), │ │ │ │ - structure("# plot_ordination(GP, ordinate(GP, \"DCA\"), \"samples\", color=\"SampleType\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/ordinate.Rd", class = "Rd", meta = list( │ │ │ │ + structure("# plot_ordination(GP, ordinate(GP, \"DCA\"), \"samples\", color=\"SampleType\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/ordinate.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ otu_table-class (list) = structure(list(structure(list(structure("The S4 class for storing taxa-abundance information.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("otu_table-class", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("otu_table-class", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Because orientation of these tables can vary by method, the orientation is\n", Rd_tag = "TEXT"), │ │ │ │ structure("defined explicitly in the ", Rd_tag = "TEXT"), │ │ │ │ @@ -5299,15 +5299,15 @@ │ │ │ │ structure(" ", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(list( │ │ │ │ structure(".Data", Rd_tag = "TEXT")), list(structure("This slot is inherited from the ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("matrix", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" class.", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT")), Rd_tag = "\\describe"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\details")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/otu_table-class.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\details")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/otu_table-class.Rd", class = "Rd", meta = list( │ │ │ │ docType = "class", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ otu_table-methods (list) = structure(list(structure(list(structure("Build or access the otu_table.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("otu_table", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("otu_table", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("otu_table,phyloseq-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("otu_table,otu_table-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -5379,15 +5379,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("phyloseq", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(", ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("merge_phyloseq", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("#\n", Rd_tag = "RCODE"), │ │ │ │ structure("# data(GlobalPatterns)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("# otu_table(GlobalPatterns)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/otu_table-methods.Rd", class = "Rd", meta = list( │ │ │ │ + structure("# otu_table(GlobalPatterns)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/otu_table-methods.Rd", class = "Rd", meta = list( │ │ │ │ docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ parseTaxonomy-functions (list) = structure(list(structure(list(structure("Parse elements of a taxonomy vector", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("parse_taxonomy_default", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("parse_taxonomy_default", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("parse_taxonomy_greengenes", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("parse_taxonomy_qiime", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -5456,15 +5456,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("import_qiime", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure(" taxvec1 = c(\"Root\", \"k__Bacteria\", \"p__Firmicutes\", \"c__Bacilli\", \"o__Bacillales\", \"f__Staphylococcaceae\")\n", Rd_tag = "RCODE"), │ │ │ │ structure(" parse_taxonomy_default(taxvec1)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" parse_taxonomy_greengenes(taxvec1)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" taxvec2 = c(\"Root;k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Staphylococcaceae\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" parse_taxonomy_qiime(taxvec2)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/parseTaxonomy-functions.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" parse_taxonomy_qiime(taxvec2)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/parseTaxonomy-functions.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ pcoa (list) = structure(list(structure(list(structure("S3 class for ape-calculated MDS results", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("pcoa", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("pcoa", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("internal", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Nothing to import, because ape doesn't (yet) export this S3 class.\n", Rd_tag = "TEXT"), │ │ │ │ @@ -5472,15 +5472,15 @@ │ │ │ │ structure("For the moment, its only use is for proper dispatch in our extensions\n", Rd_tag = "TEXT"), │ │ │ │ structure("to the scores S3 generic from vegan,\n", Rd_tag = "TEXT"), │ │ │ │ structure("for generic extraction of coordinates and possibly other features from\n", Rd_tag = "TEXT"), │ │ │ │ structure("any ordination results.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("pcoa\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("An object of class ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("pcoa", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ - structure(" of length 0.\n", Rd_tag = "TEXT")), Rd_tag = "\\format")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/pcoa.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" of length 0.\n", Rd_tag = "TEXT")), Rd_tag = "\\format")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/pcoa.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ phy_tree-methods (list) = structure(list(structure(list(structure("Retrieve phylogenetic tree (", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("phylo", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("ape", Rd_tag = "TEXT"))), Rd_tag = "\\code"), │ │ │ │ structure("-class) from object.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("phy_tree", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("phy_tree", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -5551,15 +5551,15 @@ │ │ │ │ structure(list(structure(list(structure("refseq", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(",\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("phyloseq", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(", ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("merge_phyloseq", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure(" data(GlobalPatterns)\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" phy_tree(GlobalPatterns)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/phy_tree-methods.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" phy_tree(GlobalPatterns)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/phy_tree-methods.Rd", class = "Rd", meta = list( │ │ │ │ docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ phylo (list) = structure(list(structure(list(structure("S3 class placeholder definition (list) for phylogenetic trees.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("phylo", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("phylo", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("internal", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("The ape package does not export a version of its ", Rd_tag = "TEXT"), │ │ │ │ @@ -5585,30 +5585,30 @@ │ │ │ │ structure("the ape package if possible and available.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("phylo\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("An object of class ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("phylo", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" of length 0.\n", Rd_tag = "TEXT")), Rd_tag = "\\format"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("phylo", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("ape", Rd_tag = "TEXT"))), Rd_tag = "\\code"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/phylo.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/phylo.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ phylo-class (list) = structure(list(structure(list(structure("An S4 placeholder of the main phylogenetic tree class from the ape package.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("phylo-class", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("phylo-class", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("See the ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("ape", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("ape", Rd_tag = "TEXT"))), Rd_tag = "\\code"), │ │ │ │ structure(" package for details about this type of\n", Rd_tag = "TEXT"), │ │ │ │ structure("representation of a phylogenetic tree.\n", Rd_tag = "TEXT"), │ │ │ │ structure("It is used throughout the ape package.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("phylo", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("ape", Rd_tag = "TEXT"))), Rd_tag = "\\code"), │ │ │ │ structure(", ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("setOldClass", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/phylo-class.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/phylo-class.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ phyloseq (list) = structure(list(structure(list(structure("Build phyloseq-class objects from their components.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("phyloseq", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("phyloseq", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure("phyloseq()", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ @@ -5654,15 +5654,15 @@ │ │ │ │ structure("# # data(GlobalPatterns)\n", Rd_tag = "RCODE"), │ │ │ │ structure("# # GP <- GlobalPatterns\n", Rd_tag = "RCODE"), │ │ │ │ structure("# # phyloseq(sample_data(GP), otu_table(GP))\n", Rd_tag = "RCODE"), │ │ │ │ structure("# # phyloseq(otu_table(GP), phy_tree(GP))\n", Rd_tag = "RCODE"), │ │ │ │ structure("# # phyloseq(tax_table(GP), otu_table(GP))\n", Rd_tag = "RCODE"), │ │ │ │ structure("# # phyloseq(phy_tree(GP), otu_table(GP), sample_data(GP))\n", Rd_tag = "RCODE"), │ │ │ │ structure("# # phyloseq(otu_table(GP), tax_table(GP), sample_data(GP))\n", Rd_tag = "RCODE"), │ │ │ │ - structure("# # phyloseq(otu_table(GP), phy_tree(GP), tax_table(GP), sample_data(GP))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/phyloseq.Rd", class = "Rd", meta = list( │ │ │ │ + structure("# # phyloseq(otu_table(GP), phy_tree(GP), tax_table(GP), sample_data(GP))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/phyloseq.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ phyloseq-class (list) = structure(list(structure(list(structure("The main experiment-level class for phyloseq data", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("phyloseq-class", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("phyloseq-class", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Contains all currently-supported component data classes: \n", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("otu_table-class", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ @@ -5738,15 +5738,15 @@ │ │ │ │ structure("sample_data", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(",\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("tax_table", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(", ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("phy_tree", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(", and ", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("refseq", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ - structure(".\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/phyloseq-class.Rd", class = "Rd", meta = list( │ │ │ │ + structure(".\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/phyloseq-class.Rd", class = "Rd", meta = list( │ │ │ │ docType = "class", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ phyloseq-deprecated (list) = structure(list(structure(list(structure("Depcrecated functions in the phyloseq package.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("phyloseq-deprecated", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("phyloseq-deprecated", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("deprecated_phyloseq_function", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("plot_taxa_bar", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -6040,15 +6040,15 @@ │ │ │ │ structure(list(), Rd_tag = "\\cr"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure("taxTab<-", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(), Rd_tag = "\\tab"), │ │ │ │ structure(" now a synonym for ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("tax_table<-", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(list(), Rd_tag = "\\cr"), structure("\n", Rd_tag = "TEXT"))), Rd_tag = "\\tabular"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\details")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/phyloseq-deprecated.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\details")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/phyloseq-deprecated.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ phyloseq-package (list) = structure(list(structure(list(structure("Handling and analysis of high-throughput phylogenetic sequence data.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("phyloseq-package", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("phyloseq-package", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("package", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("There are already several ecology and phylogenetic packages available in R,\n", Rd_tag = "TEXT"), │ │ │ │ @@ -6077,15 +6077,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(), Rd_tag = "\\item"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("http://dx.plos.org/10.1371/journal.pone.0061217", Rd_tag = "VERB")), Rd_tag = "\\url"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(), Rd_tag = "\\item"), structure(" Report bugs at ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("https://github.com/joey711/phyloseq/issues", Rd_tag = "VERB")), Rd_tag = "\\url"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\itemize"), │ │ │ │ - structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/phyloseq-package.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/phyloseq-package.Rd", class = "Rd", meta = list( │ │ │ │ docType = "package", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ phyloseq_to_deseq2 (list) = structure(list(structure(list(structure("Convert phyloseq data to DESeq2 dds object", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("phyloseq_to_deseq2", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("phyloseq_to_deseq2", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("No testing is performed by this function. The phyloseq data is converted\n", Rd_tag = "TEXT"), │ │ │ │ structure("to the relevant ", Rd_tag = "TEXT"), structure(list( │ │ │ │ @@ -6155,15 +6155,15 @@ │ │ │ │ structure("results", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("DESeq2", Rd_tag = "TEXT"))), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(" \n", Rd_tag = "TEXT"), │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("DESeqDataSetFromMatrix", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("DESeq2", Rd_tag = "TEXT"))), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure(" # Check out the vignette phyloseq-mixture-models for more details.\n", Rd_tag = "RCODE"), │ │ │ │ structure(" # vignette(\"phyloseq-mixture-models\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" data(soilrep)\n", Rd_tag = "RCODE"), structure(" phyloseq_to_deseq2(soilrep, ~warmed)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/phyloseq_to_deseq2.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" data(soilrep)\n", Rd_tag = "RCODE"), structure(" phyloseq_to_deseq2(soilrep, ~warmed)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/phyloseq_to_deseq2.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ phyloseq_to_metagenomeSeq (list) = structure(list(structure(list(structure("Convert phyloseq data to MetagenomeSeq MRexperiment object", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("phyloseq_to_metagenomeSeq", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("phyloseq_to_metagenomeSeq", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("No testing is performed by this function. The phyloseq data is converted\n", Rd_tag = "TEXT"), │ │ │ │ structure("to the relevant ", Rd_tag = "TEXT"), structure(list( │ │ │ │ @@ -6201,15 +6201,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("MRtable", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("metagenomeSeq", Rd_tag = "TEXT"))), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("MRfulltable", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("metagenomeSeq", Rd_tag = "TEXT"))), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure(" # Check out the vignette metagenomeSeq for more details.\n", Rd_tag = "RCODE"), │ │ │ │ structure(" # vignette(\"metagenomeSeq\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" data(soilrep)\n", Rd_tag = "RCODE"), structure(" phyloseq_to_metagenomeSeq(soilrep)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/phyloseq_to_metagenomeSeq.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" data(soilrep)\n", Rd_tag = "RCODE"), structure(" phyloseq_to_metagenomeSeq(soilrep)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/phyloseq_to_metagenomeSeq.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ plot_bar (list) = structure(list(structure(list(structure("A flexible, informative barplot phyloseq data", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plot_bar", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plot_bar", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("There are many useful examples of phyloseq barplot graphics in the\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("http://joey711.github.io/phyloseq/plot_bar-examples", Rd_tag = "VERB")), │ │ │ │ @@ -6307,15 +6307,15 @@ │ │ │ │ structure("qplot", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(\"GlobalPatterns\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("gp.ch = subset_taxa(GlobalPatterns, Phylum == \"Chlamydiae\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("plot_bar(gp.ch)\n", Rd_tag = "RCODE"), structure("plot_bar(gp.ch, fill=\"Genus\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("plot_bar(gp.ch, x=\"SampleType\", fill=\"Genus\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("plot_bar(gp.ch, \"SampleType\", fill=\"Genus\", facet_grid=~Family)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("# See additional examples in the plot_bar online tutorial. Link above.\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/plot_bar.Rd", class = "Rd", meta = list( │ │ │ │ + structure("# See additional examples in the plot_bar online tutorial. Link above.\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/plot_bar.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ plot_clusgap (list) = structure(list(structure(list(structure("Create a ggplot summary of gap statistic results", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plot_clusgap", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plot_clusgap", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Create a ggplot summary of gap statistic results\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("plot_clusgap(clusgap, title = \"Gap Statistic results\")\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -6363,15 +6363,15 @@ │ │ │ │ structure("plot_clusgap(gs)\n", Rd_tag = "RCODE"), structure("print(gs, method=\"Tibs2001SEmax\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("# Non-ordination example, use cluster::clusGap function directly\n", Rd_tag = "RCODE"), │ │ │ │ structure("library(\"cluster\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("pam1 = function(x, k){list(cluster = pam(x, k, cluster.only=TRUE))}\n", Rd_tag = "RCODE"), │ │ │ │ structure("gs.pam.RU = clusGap(ruspini, FUN = pam1, K.max = 8, B = 60)\n", Rd_tag = "RCODE"), │ │ │ │ structure("gs.pam.RU\n", Rd_tag = "RCODE"), structure("plot(gs.pam.RU, main = \"Gap statistic for the 'ruspini' data\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("mtext(\"k = 4 is best .. and k = 5 pretty close\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("plot_clusgap(gs.pam.RU)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/plot_clusgap.Rd", class = "Rd", meta = list( │ │ │ │ + structure("plot_clusgap(gs.pam.RU)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/plot_clusgap.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ plot_heatmap (list) = structure(list(structure(list(structure("Create an ecologically-organized heatmap using ggplot2 graphics", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plot_heatmap", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plot_heatmap", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("There are many useful examples of phyloseq heatmap graphics in the\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("http://joey711.github.io/phyloseq/plot_heatmap-examples", Rd_tag = "VERB")), │ │ │ │ @@ -6664,15 +6664,15 @@ │ │ │ │ structure("# First, arbitrary edge, ordering\n", Rd_tag = "RCODE"), │ │ │ │ structure("plot_heatmap(gpac, method=NULL)\n", Rd_tag = "RCODE"), │ │ │ │ structure("# Second, biological-ordering (instead of default ordination-ordering), but arbitrary edge\n", Rd_tag = "RCODE"), │ │ │ │ structure("plot_heatmap(gpac, taxa.order=\"Family\", sample.order=\"SampleType\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("# Third, biological ordering, selected edges\n", Rd_tag = "RCODE"), │ │ │ │ structure("plot_heatmap(gpac, taxa.order=\"Family\", sample.order=\"SampleType\", first.taxa=\"546313\", first.sample=\"NP2\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("# Fourth, add meaningful labels\n", Rd_tag = "RCODE"), │ │ │ │ - structure("plot_heatmap(gpac, sample.label=\"SampleType\", taxa.label=\"Family\", taxa.order=\"Family\", sample.order=\"SampleType\", first.taxa=\"546313\", first.sample=\"NP2\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/plot_heatmap.Rd", class = "Rd", meta = list( │ │ │ │ + structure("plot_heatmap(gpac, sample.label=\"SampleType\", taxa.label=\"Family\", taxa.order=\"Family\", sample.order=\"SampleType\", first.taxa=\"546313\", first.sample=\"NP2\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/plot_heatmap.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ plot_net (list) = structure(list(structure(list(structure("Microbiome Network Plot using ggplot2", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plot_net", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plot_net", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("There are many useful examples of phyloseq network graphics in the\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("http://joey711.github.io/phyloseq/plot_net-examples", Rd_tag = "VERB")), │ │ │ │ @@ -6849,15 +6849,15 @@ │ │ │ │ structure("plot_network", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(enterotype)\n", Rd_tag = "RCODE"), │ │ │ │ structure("plot_net(enterotype, color=\"SeqTech\", maxdist = 0.3)\n", Rd_tag = "RCODE"), │ │ │ │ structure("plot_net(enterotype, color=\"SeqTech\", maxdist = 0.3, laymeth = \"auto\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("plot_net(enterotype, color=\"SeqTech\", maxdist = 0.3, laymeth = \"svd\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("plot_net(enterotype, color=\"SeqTech\", maxdist = 0.3, laymeth = \"circle\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("plot_net(enterotype, color=\"SeqTech\", shape=\"Enterotype\", maxdist = 0.3, laymeth = \"circle\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/plot_net.Rd", class = "Rd", meta = list( │ │ │ │ + structure("plot_net(enterotype, color=\"SeqTech\", shape=\"Enterotype\", maxdist = 0.3, laymeth = \"circle\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/plot_net.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ plot_network (list) = structure(list(structure(list(structure("Microbiome Network Plot using ggplot2", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plot_network", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plot_network", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("There are many useful examples of phyloseq network graphics in the\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("http://joey711.github.io/phyloseq/plot_network-examples", Rd_tag = "VERB")), │ │ │ │ @@ -7010,15 +7010,15 @@ │ │ │ │ structure(list(structure("make_network", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(enterotype)\n", Rd_tag = "RCODE"), structure("ig <- make_network(enterotype, max.dist=0.3)\n", Rd_tag = "RCODE"), │ │ │ │ structure("plot_network(ig, enterotype, color=\"SeqTech\", shape=\"Enterotype\", line_weight=0.3, label=NULL)\n", Rd_tag = "RCODE"), │ │ │ │ structure("# Change distance parameter\n", Rd_tag = "RCODE"), │ │ │ │ structure("ig <- make_network(enterotype, max.dist=0.2)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("plot_network(ig, enterotype, color=\"SeqTech\", shape=\"Enterotype\", line_weight=0.3, label=NULL)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/plot_network.Rd", class = "Rd", meta = list( │ │ │ │ + structure("plot_network(ig, enterotype, color=\"SeqTech\", shape=\"Enterotype\", line_weight=0.3, label=NULL)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/plot_network.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ plot_ordination (list) = structure(list(structure(list(structure("General ordination plotter based on ggplot2.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plot_ordination", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plot_ordination", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("There are many useful examples of phyloseq ordination graphics in the\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("http://joey711.github.io/phyloseq/plot_ordination-examples", Rd_tag = "VERB")), │ │ │ │ @@ -7176,15 +7176,15 @@ │ │ │ │ structure("plot_phyloseq", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("# See other examples at\n", Rd_tag = "RCODE"), │ │ │ │ structure("# http://joey711.github.io/phyloseq/plot_ordination-examples\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(GlobalPatterns)\n", Rd_tag = "RCODE"), │ │ │ │ structure("GP = prune_taxa(names(sort(taxa_sums(GlobalPatterns), TRUE)[1:50]), GlobalPatterns)\n", Rd_tag = "RCODE"), │ │ │ │ structure("gp_bray_pcoa = ordinate(GP, \"CCA\", \"bray\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("plot_ordination(GP, gp_bray_pcoa, \"samples\", color=\"SampleType\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/plot_ordination.Rd", class = "Rd", meta = list( │ │ │ │ + structure("plot_ordination(GP, gp_bray_pcoa, \"samples\", color=\"SampleType\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/plot_ordination.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ plot_phyloseq-methods (list) = structure(list(structure(list(structure("Generic plot defaults for phyloseq.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plot_phyloseq", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plot_phyloseq", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("plot_phyloseq,phyloseq-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("There are many useful examples of phyloseq graphics functions in the\n", Rd_tag = "TEXT"), │ │ │ │ @@ -7229,15 +7229,15 @@ │ │ │ │ structure(list(structure(list(structure("plot_network", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("plot_bar", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("plot_richness", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(esophagus)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("plot_phyloseq(esophagus)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/plot_phyloseq-methods.Rd", class = "Rd", meta = list( │ │ │ │ + structure("plot_phyloseq(esophagus)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/plot_phyloseq-methods.Rd", class = "Rd", meta = list( │ │ │ │ docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ plot_richness (list) = structure(list(structure(list(structure("Plot alpha diversity, flexibly with ggplot2", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plot_richness", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plot_richness", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("There are many useful examples of alpha-diversity graphics in the\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("http://joey711.github.io/phyloseq/plot_richness-examples", Rd_tag = "VERB")), │ │ │ │ @@ -7423,15 +7423,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("## There are many more interesting examples at the phyloseq online tutorials.\n", Rd_tag = "RCODE"), │ │ │ │ structure("## http://joey711.github.io/phyloseq/plot_richness-examples\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(\"soilrep\")\n", Rd_tag = "RCODE"), structure("plot_richness(soilrep, measures=c(\"InvSimpson\", \"Fisher\"))\n", Rd_tag = "RCODE"), │ │ │ │ structure("plot_richness(soilrep, \"Treatment\", \"warmed\", measures=c(\"Chao1\", \"ACE\", \"InvSimpson\"), nrow=3)\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(\"GlobalPatterns\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("plot_richness(GlobalPatterns, x=\"SampleType\", measures=c(\"InvSimpson\"))\n", Rd_tag = "RCODE"), │ │ │ │ structure("plot_richness(GlobalPatterns, x=\"SampleType\", measures=c(\"Chao1\", \"ACE\", \"InvSimpson\"), nrow=3)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("plot_richness(GlobalPatterns, x=\"SampleType\", measures=c(\"Chao1\", \"ACE\", \"InvSimpson\"), nrow=3, sortby = \"Chao1\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/plot_richness.Rd", class = "Rd", meta = list( │ │ │ │ + structure("plot_richness(GlobalPatterns, x=\"SampleType\", measures=c(\"Chao1\", \"ACE\", \"InvSimpson\"), nrow=3, sortby = \"Chao1\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/plot_richness.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ plot_scree (list) = structure(list(structure(list(structure("General ordination eigenvalue plotter using ggplot2.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plot_scree", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plot_scree", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Convenience wrapper for plotting ordination eigenvalues (if available) \n", Rd_tag = "TEXT"), │ │ │ │ structure("using a ", Rd_tag = "TEXT"), structure(list( │ │ │ │ @@ -7484,15 +7484,15 @@ │ │ │ │ structure("# Constrained ordinations\n", Rd_tag = "RCODE"), │ │ │ │ structure("plot_scree(ordinate(GP, \"CCA\", formula=~SampleType))\n", Rd_tag = "RCODE"), │ │ │ │ structure("plot_scree(ordinate(GP, \"RDA\", formula=~SampleType)) \n", Rd_tag = "RCODE"), │ │ │ │ structure("plot_scree(ordinate(GP, \"CAP\", formula=~SampleType)) \n", Rd_tag = "RCODE"), │ │ │ │ structure("# Deprecated example of constrained ordination (emits a warning)\n", Rd_tag = "RCODE"), │ │ │ │ structure("#plot_scree(ordinate(GP ~ SampleType, \"RDA\")) \n", Rd_tag = "RCODE"), │ │ │ │ structure("plot_scree(ordinate(GP, \"DCA\"))\n", Rd_tag = "RCODE"), │ │ │ │ - structure("plot_ordination(GP, ordinate(GP, \"DCA\"), type=\"scree\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/plot_scree.Rd", class = "Rd", meta = list( │ │ │ │ + structure("plot_ordination(GP, ordinate(GP, \"DCA\"), type=\"scree\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/plot_scree.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ plot_tree (list) = structure(list(structure(list(structure("Plot a phylogenetic tree with optional annotations", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plot_tree", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plot_tree", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("There are many useful examples of phyloseq tree graphics in the\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("http://joey711.github.io/phyloseq/plot_tree-examples", Rd_tag = "VERB")), │ │ │ │ @@ -7773,15 +7773,15 @@ │ │ │ │ structure("# # in the online tutorials\"\n", Rd_tag = "RCODE"), │ │ │ │ structure("# # http://joey711.github.io/phyloseq/plot_tree-examples\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(esophagus)\n", Rd_tag = "RCODE"), structure("# plot_tree(esophagus)\n", Rd_tag = "RCODE"), │ │ │ │ structure("# plot_tree(esophagus, color=\"Sample\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("# plot_tree(esophagus, size=\"Abundance\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("# plot_tree(esophagus, size=\"Abundance\", color=\"samples\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("plot_tree(esophagus, size=\"Abundance\", color=\"Sample\", base.spacing=0.03)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("plot_tree(esophagus, size=\"abundance\", color=\"samples\", base.spacing=0.03)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/plot_tree.Rd", class = "Rd", meta = list( │ │ │ │ + structure("plot_tree(esophagus, size=\"abundance\", color=\"samples\", base.spacing=0.03)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/plot_tree.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ prune_samples-methods (list) = structure(list(structure(list(structure("Define a subset of samples to keep in a phyloseq object.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("prune_samples", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("prune_samples", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("prune_samples,character,otu_table-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("prune_samples,character,sample_data-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -7827,15 +7827,15 @@ │ │ │ │ structure(list(structure("subset_samples", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure(" data(GlobalPatterns)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" # Subset to just the Chlamydiae phylum.\n", Rd_tag = "RCODE"), │ │ │ │ structure(" GP.chl <- subset_taxa(GlobalPatterns, Phylum==\"Chlamydiae\")\n", Rd_tag = "RCODE"), │ │ │ │ structure(" # Remove the samples that have less than 20 total reads from Chlamydiae\n", Rd_tag = "RCODE"), │ │ │ │ structure(" GP.chl <- prune_samples(sample_sums(GP.chl)>=20, GP.chl)\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" # (p <- plot_tree(GP.chl, color=\"SampleType\", shape=\"Family\", label.tips=\"Genus\", size=\"abundance\"))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/prune_samples-methods.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" # (p <- plot_tree(GP.chl, color=\"SampleType\", shape=\"Family\", label.tips=\"Genus\", size=\"abundance\"))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/prune_samples-methods.Rd", class = "Rd", meta = list( │ │ │ │ docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ prune_taxa-methods (list) = structure(list(structure(list(structure("Prune unwanted OTUs / taxa from a phylogenetic object.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("prune_taxa", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("prune_taxa", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("prune_taxa,NULL,ANY-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("prune_taxa,logical,ANY-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -7914,15 +7914,15 @@ │ │ │ │ structure("http://cran.at.r-project.org/web/packages/picante/index.html", Rd_tag = "VERB")), │ │ │ │ list(structure("prune.sample", Rd_tag = "TEXT"))), Rd_tag = "\\href"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(\"esophagus\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("esophagus\n", Rd_tag = "RCODE"), structure("plot(sort(taxa_sums(esophagus), TRUE), type=\"h\", ylim=c(0, 50))\n", Rd_tag = "RCODE"), │ │ │ │ structure("x1 = prune_taxa(taxa_sums(esophagus) > 10, esophagus) \n", Rd_tag = "RCODE"), │ │ │ │ structure("x2 = prune_taxa(names(sort(taxa_sums(esophagus), TRUE))[1:9], esophagus) \n", Rd_tag = "RCODE"), │ │ │ │ - structure("identical(x1, x2)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/prune_taxa-methods.Rd", class = "Rd", meta = list( │ │ │ │ + structure("identical(x1, x2)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/prune_taxa-methods.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ psmelt (list) = structure(list(structure(list(structure("Melt phyloseq data object into large data.frame", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("psmelt", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("psmelt", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("The psmelt function is a specialized melt function for melting phyloseq objects\n", Rd_tag = "TEXT"), │ │ │ │ structure("(instances of the phyloseq class), usually for producing graphics\n", Rd_tag = "TEXT"), │ │ │ │ @@ -7994,15 +7994,15 @@ │ │ │ │ structure("mdf = psmelt(gp.ch)\n", Rd_tag = "RCODE"), │ │ │ │ structure("nrow(mdf)\n", Rd_tag = "RCODE"), structure("ncol(mdf)\n", Rd_tag = "RCODE"), │ │ │ │ structure("colnames(mdf)\n", Rd_tag = "RCODE"), structure("head(rownames(mdf))\n", Rd_tag = "RCODE"), │ │ │ │ structure("# Create a ggplot similar to\n", Rd_tag = "RCODE"), │ │ │ │ structure("library(\"ggplot2\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("p = ggplot(mdf, aes(x=SampleType, y=Abundance, fill=Genus))\n", Rd_tag = "RCODE"), │ │ │ │ structure("p = p + geom_bar(color=\"black\", stat=\"identity\", position=\"stack\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("print(p)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/psmelt.Rd", class = "Rd", meta = list( │ │ │ │ + structure("print(p)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/psmelt.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ rank_names (list) = structure(list(structure(list(structure("Retrieve the names of the taxonomic ranks", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("rank_names", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("rank_names", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This is a simple accessor function to make it more convenient to determine\n", Rd_tag = "TEXT"), │ │ │ │ structure("the taxonomic ranks that are available in a given ", Rd_tag = "TEXT"), │ │ │ │ @@ -8029,15 +8029,15 @@ │ │ │ │ structure(list(structure("get_taxa", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("taxa_names", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("sample_names", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(enterotype)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("rank_names(enterotype)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/rank_names.Rd", class = "Rd", meta = list( │ │ │ │ + structure("rank_names(enterotype)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/rank_names.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ rarefy_even_depth (list) = structure(list(structure(list(structure("Resample an OTU table such that all samples have the same library size.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("rarefy_even_depth", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("rarefy_even_depth", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Please note that the authors of phyloseq do not advocate using this\n", Rd_tag = "TEXT"), │ │ │ │ structure("as a normalization procedure, despite its recent popularity.\n", Rd_tag = "TEXT"), │ │ │ │ @@ -8195,15 +8195,15 @@ │ │ │ │ structure("sample_sums(esophagus)\n", Rd_tag = "RCODE"), │ │ │ │ structure("sample_sums(esorepT)\n", Rd_tag = "RCODE"), │ │ │ │ structure("sample_sums(esorepF)\n", Rd_tag = "RCODE"), │ │ │ │ structure("## NRun Manually: Too slow!\n", Rd_tag = "RCODE"), │ │ │ │ structure("# data(\"GlobalPatterns\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("# GPrepT = rarefy_even_depth(GlobalPatterns, 1E5, replace=TRUE)\n", Rd_tag = "RCODE"), │ │ │ │ structure("## Actually just this one is slow\n", Rd_tag = "RCODE"), │ │ │ │ - structure("# system.time(GPrepF <- rarefy_even_depth(GlobalPatterns, 1E5, replace=FALSE))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/rarefy_even_depth.Rd", class = "Rd", meta = list( │ │ │ │ + structure("# system.time(GPrepF <- rarefy_even_depth(GlobalPatterns, 1E5, replace=FALSE))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/rarefy_even_depth.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ read_tree (list) = structure(list(structure(list(structure("Somewhat flexible tree-import function", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("read_tree", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("read_tree", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function is a convenience wrapper around the\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("read.tree", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("ape", Rd_tag = "TEXT"))), Rd_tag = "\\code"), │ │ │ │ @@ -8256,15 +8256,15 @@ │ │ │ │ structure(list(structure(list(structure("phylo", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("read.tree", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("ape", Rd_tag = "TEXT"))), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(" \n", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("read.nexus", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("ape", Rd_tag = "TEXT"))), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("read_tree(system.file(\"extdata\", \"esophagus.tree.gz\", package=\"phyloseq\"))\n", Rd_tag = "RCODE"), │ │ │ │ - structure("read_tree(system.file(\"extdata\", \"GP_tree_rand_short.newick.gz\", package=\"phyloseq\"))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/read_tree.Rd", class = "Rd", meta = list( │ │ │ │ + structure("read_tree(system.file(\"extdata\", \"GP_tree_rand_short.newick.gz\", package=\"phyloseq\"))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/read_tree.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ read_tree_greengenes (list) = structure(list(structure(list(structure("Read GreenGenes tree released in annotated newick format", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("read_tree_greengenes", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("read_tree_greengenes", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("In principal, this is a standard newick format, that can be imported\n", Rd_tag = "TEXT"), │ │ │ │ structure("into R using ", Rd_tag = "TEXT"), structure(list( │ │ │ │ @@ -8312,15 +8312,15 @@ │ │ │ │ structure("treefile = system.file(\"extdata\", \"gg13-5-73.tree.gz\", package=\"phyloseq\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("x = read_tree_greengenes(treefile)\n", Rd_tag = "RCODE"), │ │ │ │ structure("x\n", Rd_tag = "RCODE"), structure("class(x)\n", Rd_tag = "RCODE"), │ │ │ │ structure("y = read_tree(treefile)\n", Rd_tag = "RCODE"), │ │ │ │ structure("y\n", Rd_tag = "RCODE"), structure("class(y)\n", Rd_tag = "RCODE"), │ │ │ │ structure("## Not run, causes an error:\n", Rd_tag = "RCODE"), │ │ │ │ structure("# library(\"ape\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("# read.tree(treefile)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/read_tree_greengenes.Rd", class = "Rd", meta = list( │ │ │ │ + structure("# read.tree(treefile)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/read_tree_greengenes.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ reconcile_categories (list) = structure(list(structure(list(structure("Cleans absent levels in sample_data/data.frame.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("reconcile_categories", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("reconcile_categories", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("internal", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This is used internally by the builder method, ", Rd_tag = "TEXT"), │ │ │ │ @@ -8350,15 +8350,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("# # # data(GlobalPatterns)\n", Rd_tag = "RCODE"), │ │ │ │ structure("# # # SM <- sample_data(GlobalPatterns)\n", Rd_tag = "RCODE"), │ │ │ │ structure("# # # DF <- data.frame(SM)\n", Rd_tag = "RCODE"), │ │ │ │ structure("# # # DF <- data.frame(DF, col1=1:nrow(DF), col2=paste(1:nrow(DF), \"t\", sep=\"\"))\n", Rd_tag = "RCODE"), │ │ │ │ structure("# # # DF <- reconcile_categories(DF)\n", Rd_tag = "RCODE"), │ │ │ │ structure("# # # SM <- sample_data(reconcile_categories(SM))\n", Rd_tag = "RCODE"), │ │ │ │ structure("# # # sapply(DF, class)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("# # # sapply(SM, class)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/reconcile_categories.Rd", class = "Rd", meta = list( │ │ │ │ + structure("# # # sapply(SM, class)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/reconcile_categories.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ refseq-methods (list) = structure(list(structure(list(structure("Retrieve reference sequences (", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("XStringSet", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("Biostrings", Rd_tag = "TEXT"))), Rd_tag = "\\code"), │ │ │ │ structure("-class) from object.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("refseq", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("refseq", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -8417,15 +8417,15 @@ │ │ │ │ structure(list(structure(list(structure("phy_tree", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(",\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("phyloseq", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(", ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("merge_phyloseq", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure(" data(GlobalPatterns)\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" refseq(GlobalPatterns, FALSE)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/refseq-methods.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" refseq(GlobalPatterns, FALSE)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/refseq-methods.Rd", class = "Rd", meta = list( │ │ │ │ docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ rm_outlierf (list) = structure(list(structure(list(structure("Set to FALSE any outlier species greater than f fractional abundance.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("rm_outlierf", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("rm_outlierf", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This is for removing overly-abundant outlier taxa, not for trimming low-abundance\n", Rd_tag = "TEXT"), │ │ │ │ structure("taxa.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -8457,15 +8457,15 @@ │ │ │ │ structure("## Use simulated abundance matrix\n", Rd_tag = "RCODE"), │ │ │ │ structure("set.seed(711)\n", Rd_tag = "RCODE"), structure("testOTU <- otu_table(matrix(sample(1:50, 25, replace=TRUE), 5, 5), taxa_are_rows=FALSE)\n", Rd_tag = "RCODE"), │ │ │ │ structure("taxa_sums(testOTU)\n", Rd_tag = "RCODE"), │ │ │ │ structure("f1 <- filterfun_sample(rm_outlierf(0.1))\n", Rd_tag = "RCODE"), │ │ │ │ structure("(wh1 <- genefilter_sample(testOTU, f1, A=1))\n", Rd_tag = "RCODE"), │ │ │ │ structure("wh2 <- c(TRUE, TRUE, TRUE, FALSE, FALSE)\n", Rd_tag = "RCODE"), │ │ │ │ structure("prune_taxa(wh1, testOTU)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("prune_taxa(wh2, testOTU) \n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/rm_outlierf.Rd", class = "Rd", meta = list( │ │ │ │ + structure("prune_taxa(wh2, testOTU) \n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/rm_outlierf.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ safeDeparse (closure) = function (obj) │ │ │ │ { │ │ │ │ tryCatch({ │ │ │ │ deparse(obj) │ │ │ │ }, error = function(e) { │ │ │ │ @@ -8489,15 +8489,15 @@ │ │ │ │ structure(" it should contain the sample names.\n", Rd_tag = "TEXT"), │ │ │ │ structure(" ", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(list( │ │ │ │ structure("names", Rd_tag = "TEXT")), list(structure("Inherited from the data.frame class.", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(" ", Rd_tag = "TEXT")), Rd_tag = "\\describe"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\details")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/sample_data-class.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\details")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/sample_data-class.Rd", class = "Rd", meta = list( │ │ │ │ docType = "class", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ sample_data-methods (list) = structure(list(structure(list(structure("Build or access sample_data.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("sample_data", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("sample_data", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("sample_data,ANY-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("sample_data,data.frame-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -8564,15 +8564,15 @@ │ │ │ │ structure("otu_table", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("phyloseq", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(", ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("merge_phyloseq", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("#\n", Rd_tag = "RCODE"), │ │ │ │ - structure("data(soilrep)\n", Rd_tag = "RCODE"), structure("head(sample_data(soilrep))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/sample_data-methods.Rd", class = "Rd", meta = list( │ │ │ │ + structure("data(soilrep)\n", Rd_tag = "RCODE"), structure("head(sample_data(soilrep))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/sample_data-methods.Rd", class = "Rd", meta = list( │ │ │ │ docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ sample_names-methods (list) = structure(list(structure(list(structure("Get sample names.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("sample_names", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("sample_names", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("sample_names,ANY-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("sample_names,phyloseq-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -8607,15 +8607,15 @@ │ │ │ │ structure(".\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("taxa_names", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(", ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("nsamples", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(esophagus)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("sample_names(esophagus)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/sample_names-methods.Rd", class = "Rd", meta = list( │ │ │ │ + structure("sample_names(esophagus)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/sample_names-methods.Rd", class = "Rd", meta = list( │ │ │ │ docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ sample_sums (list) = structure(list(structure(list(structure("Returns the total number of individuals observed from each sample.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("sample_sums", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("sample_sums", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("A convenience function equivalent to rowSums or colSums, but where\n", Rd_tag = "TEXT"), │ │ │ │ structure("the orientation of the otu_table is automatically handled.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -8641,15 +8641,15 @@ │ │ │ │ structure(", ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("rowSums", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(", ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("colSums", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(enterotype)\n", Rd_tag = "RCODE"), │ │ │ │ structure("sample_sums(enterotype)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("data(esophagus)\n", Rd_tag = "RCODE"), structure("sample_sums(esophagus)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/sample_sums.Rd", class = "Rd", meta = list( │ │ │ │ + structure("data(esophagus)\n", Rd_tag = "RCODE"), structure("sample_sums(esophagus)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/sample_sums.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ sample_variables (list) = structure(list(structure(list(structure("Get the sample variables present in sample_data", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("sample_variables", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("sample_variables", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This is a simple accessor function to make it more convenient to determine\n", Rd_tag = "TEXT"), │ │ │ │ structure("the sample variable names of a particular ", Rd_tag = "TEXT"), │ │ │ │ @@ -8678,15 +8678,15 @@ │ │ │ │ structure(list(structure("get_taxa", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("taxa_names", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("sample_names", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(enterotype)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("sample_variables(enterotype)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/sample_variables.Rd", class = "Rd", meta = list( │ │ │ │ + structure("sample_variables(enterotype)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/sample_variables.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ show-methods (list) = structure(list(structure(list(structure("method extensions to show for phyloseq objects.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("show,otu_table-method", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("show,otu_table-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("show,sample_data-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("show,taxonomyTable-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -8710,15 +8710,15 @@ │ │ │ │ list(structure("object", Rd_tag = "TEXT")), list(structure("Any R object", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("show", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("methods", Rd_tag = "TEXT"))), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("# data(GlobalPatterns)\n", Rd_tag = "RCODE"), │ │ │ │ structure("# show(GlobalPatterns)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("# GlobalPatterns\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/show-methods.Rd", class = "Rd", meta = list( │ │ │ │ + structure("# GlobalPatterns\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/show-methods.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ show_mothur_cutoffs (list) = structure(list(structure(list(structure("Show cutoff values available in a mothur file.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("show_mothur_cutoffs", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("show_mothur_cutoffs", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This is a helper function to report back to the user the different cutoff\n", Rd_tag = "TEXT"), │ │ │ │ structure("values available in a given mothur file -- \n", Rd_tag = "TEXT"), │ │ │ │ @@ -8744,15 +8744,15 @@ │ │ │ │ structure("mothur", Rd_tag = "TEXT")), Rd_tag = "\\emph"), │ │ │ │ structure(" output. This an important extra step prior to\n", Rd_tag = "TEXT"), │ │ │ │ structure(" importing data with the ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("import_mothur", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" function.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("import_mothur", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/show_mothur_cutoffs.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/show_mothur_cutoffs.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ splat.phyloseq.objects (list) = structure(list(structure(list(structure("Convert ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("phyloseq-class", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" into a named list of its non-empty components.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("splat.phyloseq.objects", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("splat.phyloseq.objects", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -8777,15 +8777,15 @@ │ │ │ │ structure("x", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(". Each element is named according to its slot-name in\n", Rd_tag = "TEXT"), │ │ │ │ structure("the phyloseq-object from which it is derived. \n", Rd_tag = "TEXT"), │ │ │ │ structure("If ", Rd_tag = "TEXT"), structure(list(structure("x", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" is already a component data object,\n", Rd_tag = "TEXT"), │ │ │ │ structure("then a list of length (1) is returned, also named.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("merge_phyloseq\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ - structure(list(structure("\n", Rd_tag = "RCODE"), structure("#\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/splat.phyloseq.objects.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("\n", Rd_tag = "RCODE"), structure("#\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/splat.phyloseq.objects.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ subset_ord_plot (list) = structure(list(structure(list(structure("Subset points from an ordination-derived ggplot", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("subset_ord_plot", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("subset_ord_plot", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Easily retrieve a plot-derived ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("data.frame", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ @@ -8879,15 +8879,15 @@ │ │ │ │ list(structure("http://joey711.github.io/phyloseq/subset_ord_plot-examples", Rd_tag = "VERB")), │ │ │ │ list(structure("phyloseq online tutorial", Rd_tag = "TEXT"))), Rd_tag = "\\href"), │ │ │ │ structure(" for this function.\n", Rd_tag = "TEXT"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("plot_ordination", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("## See the online tutorials.\n", Rd_tag = "RCODE"), │ │ │ │ - structure("## http://joey711.github.io/phyloseq/subset_ord_plot-examples\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/subset_ord_plot.Rd", class = "Rd", meta = list( │ │ │ │ + structure("## http://joey711.github.io/phyloseq/subset_ord_plot-examples\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/subset_ord_plot.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ subset_samples-methods (list) = structure(list(structure(list(structure("Subset samples by sample_data expression", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("subset_samples", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("subset_samples", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This is a convenience wrapper around the ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("subset", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ @@ -8934,15 +8934,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("A subsetted object with the same class as ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("physeq", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(".\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("subset_taxa", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure(" # data(GlobalPatterns)\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" # subset_samples(GlobalPatterns, SampleType==\"Ocean\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/subset_samples-methods.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" # subset_samples(GlobalPatterns, SampleType==\"Ocean\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/subset_samples-methods.Rd", class = "Rd", meta = list( │ │ │ │ docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ subset_taxa-methods (list) = structure(list(structure(list(structure("Subset species by taxonomic expression", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("subset_taxa", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("subset_taxa", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This is a convenience wrapper around the ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("subset", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ @@ -8992,15 +8992,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("A subsetted object with the same class as ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("physeq", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(".\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("subset_samples", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ - structure(list(structure("\n", Rd_tag = "RCODE"), structure("## ex3 <- subset_taxa(GlobalPatterns, Phylum==\"Bacteroidetes\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/subset_taxa-methods.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("\n", Rd_tag = "RCODE"), structure("## ex3 <- subset_taxa(GlobalPatterns, Phylum==\"Bacteroidetes\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/subset_taxa-methods.Rd", class = "Rd", meta = list( │ │ │ │ docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ tax_glom (list) = structure(list(structure(list(structure("Agglomerate taxa of the same type.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("tax_glom", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("tax_glom", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This method merges species that have the same taxonomy at a certain \n", Rd_tag = "TEXT"), │ │ │ │ structure("taxonomic rank. \n", Rd_tag = "TEXT"), structure("Its approach is analogous to ", Rd_tag = "TEXT"), │ │ │ │ @@ -9080,15 +9080,15 @@ │ │ │ │ structure("# ## agglomerate at the Family taxonomic rank\n", Rd_tag = "RCODE"), │ │ │ │ structure("# (x1 <- tax_glom(GlobalPatterns, taxrank=\"Family\") )\n", Rd_tag = "RCODE"), │ │ │ │ structure("# ## How many taxa before/after agglomeration?\n", Rd_tag = "RCODE"), │ │ │ │ structure("# ntaxa(GlobalPatterns); ntaxa(x1)\n", Rd_tag = "RCODE"), │ │ │ │ structure("# ## Look at enterotype dataset...\n", Rd_tag = "RCODE"), │ │ │ │ structure("# data(enterotype)\n", Rd_tag = "RCODE"), │ │ │ │ structure("# ## print the available taxonomic ranks. Shows only 1 rank available, not useful for tax_glom\n", Rd_tag = "RCODE"), │ │ │ │ - structure("# colnames(tax_table(enterotype))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/tax_glom.Rd", class = "Rd", meta = list( │ │ │ │ + structure("# colnames(tax_table(enterotype))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/tax_glom.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ tax_table-methods (list) = structure(list(structure(list(structure("Build or access the taxonomyTable.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("tax_table", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("tax_table", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("tax_table,ANY-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("tax_table,matrix-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -9153,15 +9153,15 @@ │ │ │ │ structure(list(structure(list(structure("phyloseq", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(", ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("merge_phyloseq", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("#\n", Rd_tag = "RCODE"), │ │ │ │ structure("# tax1 <- tax_table(matrix(\"abc\", 30, 8))\n", Rd_tag = "RCODE"), │ │ │ │ structure("# data(GlobalPatterns)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("# tax_table(GlobalPatterns)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/tax_table-methods.Rd", class = "Rd", meta = list( │ │ │ │ + structure("# tax_table(GlobalPatterns)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/tax_table-methods.Rd", class = "Rd", meta = list( │ │ │ │ docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ taxa_are_rows-methods (list) = structure(list(structure(list(structure("Access taxa_are_rows slot from otu_table objects.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("taxa_are_rows", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("taxa_are_rows", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("taxa_are_rows,ANY-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("taxa_are_rows,otu_table-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -9184,15 +9184,15 @@ │ │ │ │ structure(", or ", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("otu_table-class", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(".", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("A logical indicating the orientation of the otu_table.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("otu_table", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/taxa_are_rows-methods.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/taxa_are_rows-methods.Rd", class = "Rd", meta = list( │ │ │ │ docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ taxa_names-methods (list) = structure(list(structure(list(structure("Get species / taxa names.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("taxa_names", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("taxa_names", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("taxa_names,ANY-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("taxa_names,phyloseq-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -9240,15 +9240,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("ntaxa\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("#\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(\"esophagus\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("tree <- phy_tree(esophagus)\n", Rd_tag = "RCODE"), │ │ │ │ structure("OTU1 <- otu_table(esophagus)\n", Rd_tag = "RCODE"), │ │ │ │ structure("taxa_names(tree)\n", Rd_tag = "RCODE"), structure("taxa_names(OTU1)\n", Rd_tag = "RCODE"), │ │ │ │ structure("physeq1 <- phyloseq(OTU1, tree)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("taxa_names(physeq1)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/taxa_names-methods.Rd", class = "Rd", meta = list( │ │ │ │ + structure("taxa_names(physeq1)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/taxa_names-methods.Rd", class = "Rd", meta = list( │ │ │ │ docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ taxa_sums (list) = structure(list(structure(list(structure("Returns the total number of individuals observed from each species/taxa/OTU.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("taxa_sums", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("taxa_sums", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("A convenience function equivalent to rowSums or colSums, but where\n", Rd_tag = "TEXT"), │ │ │ │ structure("the orientation of the otu_table is automatically handled.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -9272,30 +9272,30 @@ │ │ │ │ structure(", ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("rowSums", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(", ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("colSums", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(enterotype)\n", Rd_tag = "RCODE"), │ │ │ │ structure("taxa_sums(enterotype)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("data(esophagus)\n", Rd_tag = "RCODE"), structure("taxa_sums(esophagus)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/taxa_sums.Rd", class = "Rd", meta = list( │ │ │ │ + structure("data(esophagus)\n", Rd_tag = "RCODE"), structure("taxa_sums(esophagus)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/taxa_sums.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ taxonomyTable-class (list) = structure(list(structure(list(structure("An S4 class that holds taxonomic classification data as a character\n", Rd_tag = "TEXT"), │ │ │ │ structure("matrix.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("taxonomyTable-class", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("taxonomyTable-class", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Row indices represent taxa, columns represent taxonomic classifiers.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure(".Data", Rd_tag = "TEXT")), │ │ │ │ list(structure("This slot is inherited from the ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("matrix", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" class.", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\describe"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\details")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/taxonomyTable-class.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\details")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/taxonomyTable-class.Rd", class = "Rd", meta = list( │ │ │ │ docType = "class", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ threshrank (list) = structure(list(structure(list(structure("Thresholded rank transformation.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("threshrank", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("threshrank", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("The lowest ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("thresh", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ @@ -9338,15 +9338,15 @@ │ │ │ │ structure("threshrank(a_vector, 5, keep0s=TRUE)\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(GlobalPatterns)\n", Rd_tag = "RCODE"), │ │ │ │ structure("GP <- GlobalPatterns\n", Rd_tag = "RCODE"), │ │ │ │ structure("## These three approaches result in identical otu_table\n", Rd_tag = "RCODE"), │ │ │ │ structure("(x1 <- transform_sample_counts( otu_table(GP), threshrankfun(500)) )\n", Rd_tag = "RCODE"), │ │ │ │ structure("(x2 <- otu_table(apply(otu_table(GP), 2, threshrankfun(500)), taxa_are_rows(GP)) )\n", Rd_tag = "RCODE"), │ │ │ │ structure("identical(x1, x2)\n", Rd_tag = "RCODE"), structure("(x3 <- otu_table(apply(otu_table(GP), 2, threshrank, thresh=500), taxa_are_rows(GP)) )\n", Rd_tag = "RCODE"), │ │ │ │ - structure("identical(x1, x3)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/threshrank.Rd", class = "Rd", meta = list( │ │ │ │ + structure("identical(x1, x3)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/threshrank.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ threshrankfun (list) = structure(list(structure(list(structure("A closure version of the ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("threshrank", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" function.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("threshrankfun", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("threshrankfun", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -9383,15 +9383,15 @@ │ │ │ │ structure("threshrankfun", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(",\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("threshrank", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(esophagus)\n", Rd_tag = "RCODE"), │ │ │ │ structure("x1 = transform_sample_counts(esophagus, threshrankfun(50))\n", Rd_tag = "RCODE"), │ │ │ │ structure("otu_table(x1)\n", Rd_tag = "RCODE"), structure("x2 = transform_sample_counts(esophagus, rank)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("otu_table(x2)\n", Rd_tag = "RCODE"), structure("identical(x1, x2)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/threshrankfun.Rd", class = "Rd", meta = list( │ │ │ │ + structure("otu_table(x2)\n", Rd_tag = "RCODE"), structure("identical(x1, x2)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/threshrankfun.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ tip_glom (list) = structure(list(structure(list(structure("Agglomerate closely-related taxa using single-linkage clustering.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("tip_glom", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("tip_glom", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("All tips of the tree separated by a cophenetic distance smaller than \n", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("h", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ @@ -9466,15 +9466,15 @@ │ │ │ │ structure(list(structure(list(structure("cophenetic.phylo", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("ape", Rd_tag = "TEXT"))), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("phylo", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("ape", Rd_tag = "TEXT"))), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(\"esophagus\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("# for speed\n", Rd_tag = "RCODE"), structure("esophagus = prune_taxa(taxa_names(esophagus)[1:25], esophagus)\n", Rd_tag = "RCODE"), │ │ │ │ structure("plot_tree(esophagus, label.tips=\"taxa_names\", size=\"abundance\", title=\"Before tip_glom()\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("plot_tree(tip_glom(esophagus, h=0.2), label.tips=\"taxa_names\", size=\"abundance\", title=\"After tip_glom()\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/tip_glom.Rd", class = "Rd", meta = list( │ │ │ │ + structure("plot_tree(tip_glom(esophagus, h=0.2), label.tips=\"taxa_names\", size=\"abundance\", title=\"After tip_glom()\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/tip_glom.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ topf (list) = structure(list(structure(list(structure("Make filter fun. that returns the top f fraction of taxa in a sample.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("topf", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("topf", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("As opposed to ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("topp", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ @@ -9508,15 +9508,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("t1 <- 1:10; names(t1)<-paste(\"t\", 1:10, sep=\"\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("topf(0.6)(t1)\n", Rd_tag = "RCODE"), structure("## Use simulated abundance matrix\n", Rd_tag = "RCODE"), │ │ │ │ structure("set.seed(711)\n", Rd_tag = "RCODE"), structure("testOTU <- otu_table(matrix(sample(1:50, 25, replace=TRUE), 5, 5), taxa_are_rows=FALSE)\n", Rd_tag = "RCODE"), │ │ │ │ structure("f1 <- filterfun_sample(topf(0.4))\n", Rd_tag = "RCODE"), │ │ │ │ structure("(wh1 <- genefilter_sample(testOTU, f1, A=1))\n", Rd_tag = "RCODE"), │ │ │ │ structure("wh2 <- c(TRUE, TRUE, TRUE, FALSE, FALSE)\n", Rd_tag = "RCODE"), │ │ │ │ structure("prune_taxa(wh1, testOTU)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("prune_taxa(wh2, testOTU)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/topf.Rd", class = "Rd", meta = list( │ │ │ │ + structure("prune_taxa(wh2, testOTU)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/topf.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ topk (list) = structure(list(structure(list(structure("Make filter fun. the most abundant ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("k", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" taxa", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("topk", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("topk", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -9548,15 +9548,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("## Use simulated abundance matrix\n", Rd_tag = "RCODE"), │ │ │ │ structure("set.seed(711)\n", Rd_tag = "RCODE"), structure("testOTU <- otu_table(matrix(sample(1:50, 25, replace=TRUE), 5, 5), taxa_are_rows=FALSE)\n", Rd_tag = "RCODE"), │ │ │ │ structure("f1 <- filterfun_sample(topk(2))\n", Rd_tag = "RCODE"), │ │ │ │ structure("wh1 <- genefilter_sample(testOTU, f1, A=2)\n", Rd_tag = "RCODE"), │ │ │ │ structure("wh2 <- c(TRUE, TRUE, TRUE, FALSE, FALSE)\n", Rd_tag = "RCODE"), │ │ │ │ structure("prune_taxa(wh1, testOTU)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("prune_taxa(wh2, testOTU)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/topk.Rd", class = "Rd", meta = list( │ │ │ │ + structure("prune_taxa(wh2, testOTU)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/topk.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ topp (list) = structure(list(structure(list(structure("Make filter fun. that returns the most abundant ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("p", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" fraction of taxa", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("topp", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("topp", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -9592,15 +9592,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("## Use simulated abundance matrix\n", Rd_tag = "RCODE"), │ │ │ │ structure("set.seed(711)\n", Rd_tag = "RCODE"), structure("testOTU <- otu_table(matrix(sample(1:50, 25, replace=TRUE), 5, 5), taxa_are_rows=FALSE)\n", Rd_tag = "RCODE"), │ │ │ │ structure("sample_sums(testOTU)\n", Rd_tag = "RCODE"), │ │ │ │ structure("f1 <- filterfun_sample(topp(0.2))\n", Rd_tag = "RCODE"), │ │ │ │ structure("(wh1 <- genefilter_sample(testOTU, f1, A=1))\n", Rd_tag = "RCODE"), │ │ │ │ structure("wh2 <- c(TRUE, TRUE, TRUE, FALSE, FALSE)\n", Rd_tag = "RCODE"), │ │ │ │ structure("prune_taxa(wh1, testOTU)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("prune_taxa(wh2, testOTU)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/topp.Rd", class = "Rd", meta = list( │ │ │ │ + structure("prune_taxa(wh2, testOTU)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/topp.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ transformcounts (list) = structure(list(structure(list(structure("Transform abundance data in an ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("otu_table", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(", sample-by-sample.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("transform_sample_counts", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("transform_sample_counts", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -9656,15 +9656,15 @@ │ │ │ │ structure("head(otu_table(x1), 10)\n", Rd_tag = "RCODE"), │ │ │ │ structure("x2 = transform_sample_counts(esophagus, rank)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(otu_table(x2), 10)\n", Rd_tag = "RCODE"), │ │ │ │ structure("identical(x1, x2)\n", Rd_tag = "RCODE"), structure("x3 = otu_table(esophagus) + 5\n", Rd_tag = "RCODE"), │ │ │ │ structure("x3 = transform_sample_counts(x3, log)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(otu_table(x3), 10)\n", Rd_tag = "RCODE"), │ │ │ │ structure("x4 = transform_sample_counts(esophagus, function(x) round(x^2.2, 0))\n", Rd_tag = "RCODE"), │ │ │ │ - structure("head(otu_table(x4), 10)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/transformcounts.Rd", class = "Rd", meta = list( │ │ │ │ + structure("head(otu_table(x4), 10)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/transformcounts.Rd", class = "Rd", meta = list( │ │ │ │ docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ transpose-methods (list) = structure(list(structure(list(structure("Transpose ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("otu_table-class", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" or ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("phyloseq-class", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("t", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ @@ -9695,15 +9695,15 @@ │ │ │ │ structure(". The ", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure("otu_table", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" is\n", Rd_tag = "TEXT"), structure("transposed, and ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("taxa_are_rows", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" value is toggled.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(GlobalPatterns)\n", Rd_tag = "RCODE"), │ │ │ │ structure("otu_table(GlobalPatterns)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("t( otu_table(GlobalPatterns) )\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/transpose-methods.Rd", class = "Rd", meta = list( │ │ │ │ + structure("t( otu_table(GlobalPatterns) )\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/transpose-methods.Rd", class = "Rd", meta = list( │ │ │ │ docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ tree_layout (list) = structure(list(structure(list(structure("Returns a data table defining the line segments of a phylogenetic tree.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("tree_layout", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("tree_layout", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function takes a ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("phylo", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ @@ -9794,10 +9794,10 @@ │ │ │ │ structure("treeSegs1 = tree_layout(esophagus)\n", Rd_tag = "RCODE"), │ │ │ │ structure("edgeMap = aes(x=xleft, xend=xright, y=y, yend=y)\n", Rd_tag = "RCODE"), │ │ │ │ structure("vertMap = aes(x=x, xend=x, y=vmin, yend=vmax)\n", Rd_tag = "RCODE"), │ │ │ │ structure("p0 = ggplot(treeSegs0$edgeDT, edgeMap) + geom_segment() + geom_segment(vertMap, data=treeSegs0$vertDT)\n", Rd_tag = "RCODE"), │ │ │ │ structure("p1 = ggplot(treeSegs1$edgeDT, edgeMap) + geom_segment() + geom_segment(vertMap, data=treeSegs1$vertDT)\n", Rd_tag = "RCODE"), │ │ │ │ structure("print(p0)\n", Rd_tag = "RCODE"), structure("print(p1)\n", Rd_tag = "RCODE"), │ │ │ │ structure("plot_tree(esophagus, \"treeonly\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("plot_tree(esophagus, \"treeonly\", ladderize=\"left\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-phyloseq/man/tree_layout.Rd", class = "Rd", meta = list( │ │ │ │ + structure("plot_tree(esophagus, \"treeonly\", ladderize=\"left\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-phyloseq-1.56.0+dfsg/man/tree_layout.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ ├── ./usr/lib/R/site-library/phyloseq/help/phyloseq.rdx │ │ │ ├── phyloseq.rdx-content │ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {} │ │ │ │ │ @@ -1,799 +1,799 @@ │ │ │ │ │ $variables │ │ │ │ │ $variables$DPCoA │ │ │ │ │ -[1] 281 4626 │ │ │ │ │ +[1] 292 4639 │ │ │ │ │ │ │ │ │ │ $variables$JSD │ │ │ │ │ -[1] 5184 2913 │ │ │ │ │ +[1] 5222 2928 │ │ │ │ │ │ │ │ │ │ $variables$`UniFrac-methods` │ │ │ │ │ -[1] 8385 8038 │ │ │ │ │ +[1] 8449 8052 │ │ │ │ │ │ │ │ │ │ $variables$access │ │ │ │ │ -[1] 16702 2414 │ │ │ │ │ +[1] 16792 2428 │ │ │ │ │ │ │ │ │ │ $variables$`assign-otu_table` │ │ │ │ │ -[1] 19404 1739 │ │ │ │ │ +[1] 19520 1754 │ │ │ │ │ │ │ │ │ │ $variables$`assign-phy_tree` │ │ │ │ │ -[1] 21428 1488 │ │ │ │ │ +[1] 21573 1503 │ │ │ │ │ │ │ │ │ │ $variables$`assign-sample_data` │ │ │ │ │ -[1] 23205 2876 │ │ │ │ │ +[1] 23377 2888 │ │ │ │ │ │ │ │ │ │ $variables$`assign-sample_names` │ │ │ │ │ -[1] 26369 1873 │ │ │ │ │ +[1] 26566 1886 │ │ │ │ │ │ │ │ │ │ $variables$`assign-tax_table` │ │ │ │ │ -[1] 28532 2316 │ │ │ │ │ +[1] 28752 2327 │ │ │ │ │ │ │ │ │ │ $variables$`assign-taxa_are_rows` │ │ │ │ │ -[1] 31139 1473 │ │ │ │ │ +[1] 31382 1487 │ │ │ │ │ │ │ │ │ │ $variables$`assign-taxa_names` │ │ │ │ │ -[1] 32900 2041 │ │ │ │ │ +[1] 33170 2056 │ │ │ │ │ │ │ │ │ │ $variables$build_tax_table │ │ │ │ │ -[1] 35229 2093 │ │ │ │ │ +[1] 35525 2109 │ │ │ │ │ │ │ │ │ │ $variables$`capscale-phyloseq-methods` │ │ │ │ │ -[1] 37612 3660 │ │ │ │ │ +[1] 37934 3676 │ │ │ │ │ │ │ │ │ │ $variables$`cca-rda-phyloseq-methods` │ │ │ │ │ -[1] 41561 2948 │ │ │ │ │ +[1] 41910 2963 │ │ │ │ │ │ │ │ │ │ $variables$chunkReOrder │ │ │ │ │ -[1] 44793 1243 │ │ │ │ │ +[1] 45170 1259 │ │ │ │ │ │ │ │ │ │ $variables$`data-GlobalPatterns` │ │ │ │ │ -[1] 46327 2691 │ │ │ │ │ +[1] 46729 2705 │ │ │ │ │ │ │ │ │ │ $variables$`data-enterotype` │ │ │ │ │ -[1] 49306 2661 │ │ │ │ │ +[1] 49733 2675 │ │ │ │ │ │ │ │ │ │ $variables$`data-esophagus` │ │ │ │ │ -[1] 52255 2917 │ │ │ │ │ +[1] 52705 2930 │ │ │ │ │ │ │ │ │ │ $variables$`data-soilrep` │ │ │ │ │ -[1] 55457 4147 │ │ │ │ │ +[1] 55930 4157 │ │ │ │ │ │ │ │ │ │ $variables$decorana │ │ │ │ │ -[1] 59886 1448 │ │ │ │ │ +[1] 60379 1466 │ │ │ │ │ │ │ │ │ │ $variables$`dist-class` │ │ │ │ │ -[1] 61615 861 │ │ │ │ │ +[1] 62139 878 │ │ │ │ │ │ │ │ │ │ $variables$distance │ │ │ │ │ -[1] 62758 5495 │ │ │ │ │ +[1] 63309 5510 │ │ │ │ │ │ │ │ │ │ $variables$distanceMethodList │ │ │ │ │ -[1] 68544 5168 │ │ │ │ │ +[1] 69120 5183 │ │ │ │ │ │ │ │ │ │ $variables$envHash2otu_table │ │ │ │ │ -[1] 74002 1980 │ │ │ │ │ +[1] 74605 1996 │ │ │ │ │ │ │ │ │ │ $variables$estimate_richness │ │ │ │ │ -[1] 76270 2889 │ │ │ │ │ +[1] 76902 2905 │ │ │ │ │ │ │ │ │ │ $variables$export_env_file │ │ │ │ │ -[1] 79445 1901 │ │ │ │ │ +[1] 80108 1916 │ │ │ │ │ │ │ │ │ │ $variables$export_mothur_dist │ │ │ │ │ -[1] 81636 2469 │ │ │ │ │ +[1] 82326 2485 │ │ │ │ │ │ │ │ │ │ $variables$`extract-methods` │ │ │ │ │ -[1] 84392 2904 │ │ │ │ │ +[1] 85110 2918 │ │ │ │ │ │ │ │ │ │ $variables$filter_taxa │ │ │ │ │ -[1] 87582 2802 │ │ │ │ │ +[1] 88324 2817 │ │ │ │ │ │ │ │ │ │ $variables$filterfun_sample │ │ │ │ │ -[1] 90672 1623 │ │ │ │ │ +[1] 91442 1636 │ │ │ │ │ │ │ │ │ │ $variables$fix_phylo │ │ │ │ │ -[1] 92578 845 │ │ │ │ │ +[1] 93371 861 │ │ │ │ │ │ │ │ │ │ $variables$gapstat_ord │ │ │ │ │ -[1] 93709 3896 │ │ │ │ │ +[1] 94527 3912 │ │ │ │ │ │ │ │ │ │ $variables$`genefilter_sample-methods` │ │ │ │ │ -[1] 97899 3515 │ │ │ │ │ +[1] 98746 3531 │ │ │ │ │ │ │ │ │ │ $variables$get.component.classes │ │ │ │ │ -[1] 101703 893 │ │ │ │ │ +[1] 102579 908 │ │ │ │ │ │ │ │ │ │ $variables$`get_sample-methods` │ │ │ │ │ -[1] 102885 1730 │ │ │ │ │ +[1] 103789 1746 │ │ │ │ │ │ │ │ │ │ $variables$`get_taxa-methods` │ │ │ │ │ -[1] 104903 1729 │ │ │ │ │ +[1] 105836 1746 │ │ │ │ │ │ │ │ │ │ $variables$get_taxa_unique │ │ │ │ │ -[1] 106920 1945 │ │ │ │ │ +[1] 107883 1960 │ │ │ │ │ │ │ │ │ │ $variables$get_variable │ │ │ │ │ -[1] 109150 1666 │ │ │ │ │ +[1] 110140 1682 │ │ │ │ │ │ │ │ │ │ $variables$getslots.phyloseq │ │ │ │ │ -[1] 111100 1466 │ │ │ │ │ +[1] 112118 1481 │ │ │ │ │ │ │ │ │ │ $variables$import │ │ │ │ │ -[1] 112845 3044 │ │ │ │ │ +[1] 113891 3058 │ │ │ │ │ │ │ │ │ │ $variables$import_RDP_cluster │ │ │ │ │ -[1] 116183 2322 │ │ │ │ │ +[1] 117252 2335 │ │ │ │ │ │ │ │ │ │ $variables$import_RDP_otu │ │ │ │ │ -[1] 118793 1897 │ │ │ │ │ +[1] 119887 1910 │ │ │ │ │ │ │ │ │ │ $variables$import_biom │ │ │ │ │ -[1] 120975 8447 │ │ │ │ │ +[1] 122093 8460 │ │ │ │ │ │ │ │ │ │ $variables$import_env_file │ │ │ │ │ -[1] 129708 2099 │ │ │ │ │ +[1] 130853 2112 │ │ │ │ │ │ │ │ │ │ $variables$import_mothur │ │ │ │ │ -[1] 132094 5992 │ │ │ │ │ +[1] 133263 6004 │ │ │ │ │ │ │ │ │ │ $variables$import_mothur_constaxonomy │ │ │ │ │ -[1] 138383 1766 │ │ │ │ │ +[1] 139575 1780 │ │ │ │ │ │ │ │ │ │ $variables$import_mothur_dist │ │ │ │ │ -[1] 140439 1388 │ │ │ │ │ +[1] 141657 1401 │ │ │ │ │ │ │ │ │ │ $variables$import_mothur_groups │ │ │ │ │ -[1] 142118 1701 │ │ │ │ │ +[1] 143361 1716 │ │ │ │ │ │ │ │ │ │ $variables$import_mothur_otu_table │ │ │ │ │ -[1] 144112 2250 │ │ │ │ │ +[1] 145383 2266 │ │ │ │ │ │ │ │ │ │ $variables$import_mothur_otulist │ │ │ │ │ -[1] 146653 2659 │ │ │ │ │ +[1] 147953 2673 │ │ │ │ │ │ │ │ │ │ $variables$import_mothur_shared │ │ │ │ │ -[1] 149603 1075 │ │ │ │ │ +[1] 150929 1090 │ │ │ │ │ │ │ │ │ │ $variables$import_pyrotagger_tab │ │ │ │ │ -[1] 150972 3296 │ │ │ │ │ +[1] 152324 3311 │ │ │ │ │ │ │ │ │ │ $variables$import_qiime │ │ │ │ │ -[1] 154555 7855 │ │ │ │ │ +[1] 155932 7871 │ │ │ │ │ │ │ │ │ │ $variables$import_qiime_otu_tax │ │ │ │ │ -[1] 162703 4061 │ │ │ │ │ +[1] 164107 4076 │ │ │ │ │ │ │ │ │ │ $variables$import_qiime_sample_data │ │ │ │ │ -[1] 167058 2208 │ │ │ │ │ +[1] 168490 2223 │ │ │ │ │ │ │ │ │ │ $variables$import_uparse │ │ │ │ │ -[1] 169553 3737 │ │ │ │ │ +[1] 171010 3746 │ │ │ │ │ │ │ │ │ │ $variables$import_usearch_uc │ │ │ │ │ -[1] 173581 4359 │ │ │ │ │ +[1] 175056 4366 │ │ │ │ │ │ │ │ │ │ $variables$index_reorder │ │ │ │ │ -[1] 178224 1347 │ │ │ │ │ +[1] 179720 1363 │ │ │ │ │ │ │ │ │ │ $variables$intersect_taxa │ │ │ │ │ -[1] 179856 1471 │ │ │ │ │ +[1] 181382 1486 │ │ │ │ │ │ │ │ │ │ $variables$make_network │ │ │ │ │ -[1] 181611 4449 │ │ │ │ │ +[1] 183166 4462 │ │ │ │ │ │ │ │ │ │ $variables$merge_phyloseq │ │ │ │ │ -[1] 186342 2723 │ │ │ │ │ +[1] 187924 2736 │ │ │ │ │ │ │ │ │ │ $variables$`merge_phyloseq_pair-methods` │ │ │ │ │ -[1] 189356 3391 │ │ │ │ │ +[1] 190965 3406 │ │ │ │ │ │ │ │ │ │ $variables$`merge_samples-methods` │ │ │ │ │ -[1] 193040 3330 │ │ │ │ │ +[1] 194675 3344 │ │ │ │ │ │ │ │ │ │ $variables$`merge_taxa-methods` │ │ │ │ │ -[1] 196661 3775 │ │ │ │ │ +[1] 198321 3789 │ │ │ │ │ │ │ │ │ │ $variables$metaMDS │ │ │ │ │ -[1] 200719 1448 │ │ │ │ │ +[1] 202404 1465 │ │ │ │ │ │ │ │ │ │ $variables$microbio_me_qiime │ │ │ │ │ -[1] 202458 4902 │ │ │ │ │ +[1] 204171 4916 │ │ │ │ │ │ │ │ │ │ $variables$`mt-methods` │ │ │ │ │ -[1] 207644 4418 │ │ │ │ │ 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│ │ │ │ │ +[1] 273679 3794 │ │ │ │ │ │ │ │ │ │ $variables$plot_clusgap │ │ │ │ │ -[1] 275449 2535 │ │ │ │ │ +[1] 277770 2551 │ │ │ │ │ │ │ │ │ │ $variables$plot_heatmap │ │ │ │ │ -[1] 278270 10373 │ │ │ │ │ +[1] 280618 10389 │ │ │ │ │ │ │ │ │ │ $variables$plot_net │ │ │ │ │ -[1] 288926 6372 │ │ │ │ │ +[1] 291301 6389 │ │ │ │ │ │ │ │ │ │ $variables$plot_network │ │ │ │ │ -[1] 295580 5598 │ │ │ │ │ +[1] 297987 5612 │ │ │ │ │ │ │ │ │ │ $variables$plot_ordination │ │ │ │ │ -[1] 301466 5639 │ │ │ │ │ +[1] 303897 5652 │ │ │ │ │ │ │ │ │ │ $variables$`plot_phyloseq-methods` │ │ │ │ │ -[1] 307389 2281 │ │ │ │ │ +[1] 309849 2300 │ │ │ │ │ │ │ │ │ │ $variables$plot_richness │ │ │ │ │ -[1] 309956 6739 │ │ │ │ │ +[1] 312446 6756 │ │ │ │ │ │ │ │ │ │ $variables$plot_scree │ │ │ │ │ -[1] 316975 2326 │ │ │ │ │ +[1] 319498 2339 │ │ │ │ │ │ │ │ │ │ $variables$plot_tree │ │ │ │ │ -[1] 319585 9587 │ │ │ │ │ +[1] 322132 9603 │ │ │ │ │ │ │ │ │ │ $variables$`prune_samples-methods` │ │ │ │ │ -[1] 329460 2167 │ │ │ │ │ +[1] 332040 2182 │ │ │ │ │ │ │ │ │ │ $variables$`prune_taxa-methods` │ │ │ │ │ -[1] 331919 3131 │ │ │ │ │ +[1] 334524 3145 │ │ │ │ │ │ │ │ │ │ $variables$psmelt │ │ │ │ │ -[1] 335327 3433 │ │ │ │ │ +[1] 337960 3445 │ │ │ │ │ │ │ │ │ │ $variables$rank_names │ │ │ │ │ -[1] 339039 1575 │ │ │ │ │ +[1] 341701 1589 │ │ │ │ │ │ │ │ │ │ $variables$rarefy_even_depth │ │ │ │ │ -[1] 340906 6410 │ │ │ │ │ +[1] 343592 6417 │ │ │ │ │ │ │ │ │ │ $variables$read_tree │ │ │ │ │ -[1] 347595 2733 │ │ │ │ │ +[1] 350304 2747 │ │ │ │ │ │ │ │ │ │ $variables$read_tree_greengenes │ │ │ │ │ -[1] 350615 2628 │ │ │ │ │ +[1] 353353 2640 │ │ │ │ │ │ │ │ │ │ $variables$reconcile_categories │ │ │ │ │ -[1] 353530 1646 │ │ │ │ │ +[1] 356295 1659 │ │ │ │ │ │ │ │ │ │ $variables$`refseq-methods` │ │ │ │ │ -[1] 355463 2664 │ │ │ │ │ +[1] 358251 2679 │ │ │ │ │ │ │ │ │ │ $variables$rm_outlierf │ │ │ │ │ -[1] 358408 1794 │ │ │ │ │ +[1] 361226 1809 │ │ │ │ │ │ │ │ │ │ $variables$`sample_data-class` │ │ │ │ │ -[1] 360491 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