Poppr version 2.0

In development:
Build Status Coverage Status

On CRAN:
Downloads from Rstudio mirror per month Downloads from Rstudio mirror CRAN version

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:

New in version 2.0:

For full details, see the NEWS file or type in your R console:

news(Version == "2.0.1", package = "poppr")

Citation

If you use poppr at all, please cite:

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

Additionally, if you use any following functionalities:

Please also cite:

Kamvar ZN, Brooks JC and Grünwald NJ (2015) Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality. Front. Genet. 6:208. doi: 10.3389/fgene.2015.00208

You can obtain citation information in R by typing:

citation(package = "poppr")

Installation

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:

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:

devtools::install_github(repo = "grunwaldlab/poppr", build_vignettes = TRUE)
library("poppr")

For the bleeding edge (development) version:

devtools::install_github(repo = "grunwaldlab/poppr@devel", build_vignettes = TRUE)
library("poppr")

Help / Documentation

User Group

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

Vignettes

A few vignettes have been written for poppr:

Title Command
Algorightms and Equations vignette("algo", "poppr")
Data import and manipulation vignette("poppr_manual", "poppr")
Migration from poppr version 1 vignette("how_to_migrate", "poppr")
Multilocus Genotype Analysis vignette("mlg", "poppr")

Book/Primer

In Spring of 2014, Dr. Niklaus J. Grünwald, Dr. Sydney E. Everhart and Zhian N. Kamvar wrote a primer for population genetic analysis in R located at http://grunwaldlab.github.io/Population_Genetics_in_R.