Poppr version 2

In development:

On CRAN:

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 genetic distances
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

New in version 2.0:

handling of genomic SNP data
custom multilocus genotype definitions
collapse multilocus lineages by genetic distance
calculate reticulate minimum spanning networks
calculate index of association in a sliding window across snps
bootstrapping of MLG diversity statistics
interactive exploration of minimum spanning networks
and more!

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

news(Version >= "2.0.0", package = "poppr")

Citation

If you use poppr at all, please specify the version and 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

If you use poppr in a presentation please mention it as the poppr R package, specify the version, and use our logo.

Additionally, if you use any following functionalities:

minimum spanning networks with reticulation
collapsing multilocus genotypes into multilocus lineages with mlg.filter()
custom multilocus genotype definitions with mlg.custom()
index of association for genomic data with win.ia() or samp.ia()
bootstrapping any genetic distance with genind, genlight, or genpop objects with aboot()

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")

Known issues on CRAN

This R package is not a small package, and because of that, it is not unfathomable that there occasionally might be bugs. For bugs that exist within R code, they can be fixed by visiting https://gist.github.com/zkamvar/b64078a0d04d2452c905 and sourcing the code from there. Below is a list of known issues in version 2.0.2 that are fixed on GitHub, but not yet on CRAN:

The function read.genalex() cannot read in single-locus data. See issue #58 for details.

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:

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:

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.

Contributing

Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms. If you wish to contribute code to poppr, please fork the repository and create a pull request with your added feature.

craigcitro / poppr