Welcome

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 genetic distances
• 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

Citation

Please cite poppr as:

Kamvar ZN, Tabima JF, Grünwald NJ. (2014) Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction. PeerJ 2:e281 http://dx.doi.org/10.7717/peerj.281

You can obtain citation information in R by typing:

citation(package = "poppr")

Help

Users who have any questions/comments/suggestions regarding any version of poppr (stable or development) should direct their comments to the Poppr google group

Installation

If the image above says "Passing", then that means it should be safe to install with the latest version of R. If it does not say "Passing", I am probably trying to fix whatever problem is causing it as fast as I can.

From CRAN

Binary versions for mac and windows are available for R ≥ 2.15.1 here.

To install, make sure R is at least version 2.15.1 (the authors recommend ≥ 3.0), and in your console, type:

install.packages("poppr")

If you want the absolute latest version of poppr, see about installing from github below.

Stable and Development versions

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

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

For Linux users, make sure that the function getOption("unzip") returns "unzip" or "internal". If it doesn't, then run options(unzip = "internal").

Now you can use the install_github() function:

For the latest stable release:

library(devtools)
install_github(repo = "grunwaldlab/poppr")
library(poppr)

For the bleeding edge (development) version:

library(devtools)
install_github(repo = "grunwaldlab/poppr", ref = "devel")
library(poppr)

You can view the manual by typing: vignette("poppr_manual") after installation or by clicking here

Be sure to visit our Webpage with FAQs and tutorials coming soon.

Enjoy!