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README.md

Poppr version 2

In Development: Build Status Coverage Status

CRAN Status: CRAN version CRAN check status

Usage: Downloads from Rstudio mirror Research software impact

What is poppr?

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 and genlight objects 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 (Index of association) or (Standardized index of association)
  • 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 https://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: (png) | (svg).

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")

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").

Once you have devtools and a C compiler installed, you can use the install_github() function to install the current version from github.

Stable version

This release will contain bug fixes and new, documented, and stable features that will be included in future releases. Note: if you don't have LaTeX installed, you should set build_vignettes = FALSE.

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

Unstable/Development versions

All new features in testing will be released on different branches. These features will be in various stages of development and may or may not be documented. Install with caution. The below command would install features on the the branch called "devel". Note that these branches might be out of date from the master branch.

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

Help / Documentation

R documentation

To access a descriptive index of help files in poppr, type in your console:

package?poppr

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")
Multilocus Genotype Analysis vignette("mlg", "poppr")

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

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.