The Carpentries Workbench

The Carpentries Workbench is a trio of R packages that deploy, validate, and style Carpentries-style lessons in a modular way. This design allows lesson developers, maintainers, and contributors to focus on the content, not the tooling. Installation To install the workbench, you need to have R, git, and pandoc installed. It is recommended to use RStudio, but it is possible to do so without RStudio. Once you have these installed, you can install the Workbench packages like so:

poppr

Poppr provides open-source, cross-platform tools for quick analysis of population genetic data enabling focus on data analysis and interpretation. While there are a plethora of packages for population genetic analysis, few are able to offer quick and easy analysis of populations with mixed reproductive modes. Poppr’s main advantage is the ease of use and integration with other packages such as adegenet and vegan, including support for novel methods such as clone correction, multilocus genotype analysis, calculation of Bruvo’s distance, and the index of association.

adegenet

Adegenet was created by Thibaut Jombart and has been on CRAN since April, 2007. I was involved in the migration to version 2.0 in the summer of 2015, which included consolitading S4 methods and including the strata() methods. I have been maintaining the package by fixing bugs and responding to CRAN requests since 2020. Abstract Toolset for the exploration of genetic and genomic data. Adegenet provides formal (S4) classes for storing and handling various genetic data, including genetic markers with varying ploidy and hierarchical population structure (‘genind’ class), alleles counts by populations (‘genpop’), and genome-wide SNP data (‘genlight’).