Poppr is an R package designed for analysis of populations with mixed modes of sexual and clonal reproduction. It is built around the framework of adegenet's genind object and offers the following implementations:

• clone censoring of populations at any of multiple levels of a hierarchy
• convenient counting of multilocus genotypes and sub-setting of populations with multiple levels of hierarchy
• define multilocus genotypes
• calculation of indices of genotypic diversity, evenness, richness, and rarefaction
• drawing of dendrograms with bootstrap support for Bruvo's distance
• drawing of minimum spanning networks for Bruvo's distance
• calculation of the index of association () or
• batch processing on any server that has R (>2.15.1) installed
• calculation of Bruvo's distance for microsatellite (SSR) markers (implemented in C for speed)
• import of data from and export to GenAlEx

To install this package from github, make sure you have the following:

• devtools (to install, use: install.packages("devtools"))
• Xcode (OSX)
• Rtools (Windows)

Now you can use the install_github() function:

library(devtools)
install_github("poppr", "poppr")
library(poppr)

You can view the manual by typing: vignette("poppr_manual")

Enjoy!

This software was authored by Zhian N. Kamvar and Javier F. Tabima, graduate students at Oregon State University; and Dr. Nik Grünwald, an employee of USDA-ARS.

Permission to use, copy, modify, and distribute this software and its documentation for educational, research and non-profit purposes, without fee, and without a written agreement is hereby granted, provided that the statement above is incorporated into the material, giving appropriate attribution to the authors.

Permission to incorporate this software into commercial products may be obtained by contacting USDA ARS and OREGON STATE UNIVERSITY Office for Commercialization and Corporate Development. The software program and documentation are supplied "as is", without any accompanying services from the USDA or the University. USDA ARS or the University do not warrant that the operation of the program will be uninterrupted or error-free. The end-user understands that the program was developed for research purposes and is advised not to rely exclusively on the program for any reason.

IN NO EVENT SHALL USDA ARS OR OREGON STATE UNIVERSITY BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF THE OREGON STATE UNIVERSITY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. USDA ARS OR OREGON STATE UNIVERSITY SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE AND ANY STATUTORY WARRANTY OF NON-INFRINGEMENT. THE SOFTWARE PROVIDED HEREUNDER IS ON AN "AS IS" BASIS, AND USDA ARS AND OREGON STATE UNIVERSITY HAVE NO OBLIGATIONS TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS.