I have written several R packages (described further down this page) that are available on GitHub:
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ggordiplotsRDPutilsQsRutilsspeedytax
Two of these, ggordiplots and speedytax, are now available on CRAN, but to install the others from GitHub, you need a working R development environment – i.e. tools to compile from source. These have changed with R version 4, and also depend on your operating system. For instructions on how to install the necessary tools:
If you use Windows and an R version 4+, go here.
If you use Windows and an R version earlier than version 4, go here.
If you use Mac OS, you will need Apple Xcode and a Fortran compiler. Go here for instructions.
After installing suitable build tools, install the R package devtools from the CRAN repository. After that, from the R console you can install R packages from GitHub with a command of the form:
devtools:install_github("author_user_name/package_name")
By default, vignettes are not built when packages are installed this way, but I have tried (maybe not always successfully) to include static vignettes in the packages so that you should not have to build them . There are also links below that you may download vignettes and manuals from this site. You can include building vignettes when installing from GitHub by adding build_vignettes = TRUE to the command, but it may fail if you do not have all necessary programs and packages installed. My GitHub user name is jfq3, so you can install my packages below with the commands:
library(devtools)
devtools::install_github("jfq3/RDPutils", dependencies = TRUE)
devtools::install_github("jfq3/ggordiplots", dependencies = TRUE)
devtools::install_github("jfq3/QsRutils", dependencies = TRUE)
devtools::install_github("jfq3/speedytax", dependencies = TRUE)
If installation fails with a warning beginning with:
Error: (converted from warning) package ….
try entering the following in the R console:
Sys.setenv(R_REMOTES_NO_ERRORS_FROM_WARNINGS=TRUE)and then try installing again.
If you use any of my packages in a published work, please cite. In addition to including a citation for R, you should always include citations for the individual packages that you use. You can get citations from within R with the command citation("package_name").
RDPutils – R Utilities for Processing RDPTools Output
RDPutils is an R package originally written to provide means to construct phyloseq objects from the output of RDP’s web-based tools for clustering and classifying DNA sequences from high-throughput amplicon sequencing projects. It has since been expanded to handle output from RDP’s command line tools as well as USEARCH (utax and sintax) and iTagger (JGI) output. That you may see what the package is about without installing it, the manual is here, a vignette on using it with RDP output is here, and another on importing USEARCH results is here.
ggordiplots
The vegan package includes several functions for adding features to ordination plots: ordiarrows, ordibubbles, ordiellipse, ordihull, ordispider, ordisurf. The R package ggordiplots adds these same features to ordination plots made with ggplot2. That you may see what the package is about without installing it, the manual is here, a vignette on making plots is here, and instructions for modifying the plots are here.
QsRutils – Functions Useful for Community Ecology
Mostly. I have included some other stuff, too. I use some QsRutils functions in the exercises on this web site, so installing this package will make it easier for you to work through the exercises. The manual is here.
speedytax – Refactored Functions for Importing Classifier Results
RDPutils includes several functions for importing classifier results into phyloseq, but they are generally slow. I have rewritten several to import RDP Classifier, sintax and QIIME2 classification results into phyloseq much more quickly.