This page contains instructions on how to install the dependencies for this workshop without internet access. If you are doing this, you are probably reading this page from a file provided by the instructor rather than over the internet. Along with the website files (what you are reading now), there should be a directory called “software” that contains the software to install. If you have internet access, use the standard way of installing software described here

Installing R

For Mac and Windows, use the installer included in the “software/r/mac” or “software/r/windows”. This tutorial does currently not provide a way to install R on Linux offline.

Installing Rstudio

Use the installers in “software/rstudio/mac,”software/rstudio/windows" or “software/rstudio/linux”, depending on your operating system.

Installing R packages

The following packages are used in this workshop:

[1] "vegan"     "metacoder" "ggplot2"   "dplyr"     "readr"     "stringr"   "agricolae" "ape"      
[9] "phyloseq" 

However, these depend on many other packages that must also be installed, so the complete list is:

  [1] "vegan"                 "metacoder"             "ggplot2"              
  [4] "dplyr"                 "readr"                 "stringr"              
  [7] "agricolae"             "ape"                   "phyloseq"             
 [10] "permute"               "lattice"               "MASS"                 
 [13] "cluster"               "mgcv"                  "graphics"             
 [16] "grDevices"             "stats"                 "utils"                
 [19] "grid"                  "methods"               "nlme"                 
 [22] "Matrix"                "splines"               "igraph"               
 [25] "taxize"                "seqinr"                "RCurl"                
 [28] "lazyeval"              "magrittr"              "rlang"                
 [31] "ggfittext"             "cowplot"               "GA"                   
 [34] "Rcpp"                  "crayon"                "tibble"               
 [37] "R6"                    "tools"                 "parallel"             
 [40] "gtable"                "scales"                "ellipsis"             
 [43] "generics"              "glue"                  "lifecycle"            
 [46] "tidyselect"            "vctrs"                 "pillar"               
 [49] "foreach"               "iterators"             "cli"                  
 [52] "stringi"               "shades"                "digest"               
 [55] "isoband"               "withr"                 "pkgconfig"            
 [58] "bitops"                "clipr"                 "hms"                  
 [61] "vroom"                 "ade4"                  "segmented"            
 [64] "crul"                  "xml2"                  "jsonlite"             
 [67] "zoo"                   "data.table"            "bold"                 
 [70] "rredlist"              "rotl"                  "ritis"                
 [73] "worrms"                "natserv"               "wikitaxa"             
 [76] "phangorn"              "conditionz"            "fansi"                
 [79] "pixmap"                "sp"                    "reshape"              
 [82] "plyr"                  "uuid"                  "curl"                 
 [85] "urltools"              "httpcode"              "mime"                 
 [88] "codetools"             "fastmatch"             "quadprog"             
 [91] "utf8"                  "solrium"               "assertthat"           
 [94] "httr"                  "rentrez"               "rncl"                 
 [97] "farver"                "labeling"              "munsell"              
[100] "RColorBrewer"          "viridisLite"           "purrr"                
[103] "bit64"                 "tzdb"                  "WikidataR"            
[106] "bit"                   "openssl"               "colorspace"           
[109] "XML"                   "progress"              "triebeard"            
[112] "WikipediR"             "WikidataQueryServiceR" "Hmisc"                
[115] "pbapply"               "survival"              "Formula"              
[118] "latticeExtra"          "rpart"                 "nnet"                 
[121] "foreign"               "gridExtra"             "htmlTable"            
[124] "viridis"               "htmltools"             "base64enc"            
[127] "askpass"               "prettyunits"           "ratelimitr"           
[130] "rex"                   "sys"                   "knitr"                
[133] "checkmate"             "htmlwidgets"           "rstudioapi"           
[136] "png"                   "jpeg"                  "backports"            
[139] "yaml"                  "evaluate"              "highr"                
[142] "markdown"              "xfun"                  "klaR"                 
[145] "AlgDesign"             "combinat"              "questionr"            
[148] "shiny"                 "miniUI"                "styler"               
[151] "classInt"              "labelled"              "e1071"                
[154] "class"                 "KernSmooth"            "haven"                
[157] "tidyr"                 "httpuv"                "xtable"               
[160] "sourcetools"           "later"                 "promises"             
[163] "fastmap"               "commonmark"            "bslib"                
[166] "cachem"                "R.cache"               "rematch2"             
[169] "rprojroot"             "sass"                  "jquerylib"            
[172] "proxy"                 "forcats"               "R.methodsS3"          
[175] "R.oo"                  "R.utils"               "fs"                   
[178] "rappdirs"              "Biobase"               "BiocGenerics"         
[181] "biomformat"            "Biostrings"            "multtest"             
[184] "reshape2"              "rhdf5"                 "S4Vectors"            
[187] "IRanges"               "XVector"               "stats4"               
[190] "Rhdf5lib"              "zlibbioc"             

Windows

> setwd('path/to/workshop/folder') # If the workshop folder is an rstudio project, this is not needed
> pkg_info <- read.csv(file = 'software/packages/package_info.csv', stringsAsFactors = FALSE)
> install.packages(pkg_info$win_path, repos = NULL, type = "win.binary")

macOS and Linux

> setwd('path/to/workshop/folder') # If the workshop folder is an rstudio project, this is not needed
> pkg_info <- read.csv(file = 'software/packages/package_info.csv', stringsAsFactors = FALSE)
> install.packages(pkg_info$source_path, repos = NULL, type = "source")

Mac OSX (El Capitan)

> setwd('path/to/workshop/folder') # If the workshop folder is an rstudio project, this is not needed
> pkg_info <- read.csv(file = 'software/packages/package_info.csv', stringsAsFactors = FALSE)
> install.packages(pkg_info$osx_path, repos = NULL, type = "mac.binary.el-capitan")

Metacoder's documentation by The Grunwald lab and the USDA Horticultural Crops Research Unit is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.
Based on a work at https://github.com/grunwaldlab/metacoder_documentation.