GitHub

To install R packages from GitHub, you need a working R development environment. So if you have not done so already, and you use Windows, install the Rtools version for your version of R. If you use a Mac, install Xcode from the Mac App Store. Then 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 added static vignettes to 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. For your information, you can include 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 the packages below with the commands:


library(devtools)
devtools::install_github("jfq3/RDPutils")
devtools::install_github("jfq3/ggordiplots")
devtools::install_github("jfq3/QsRutils")

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 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.