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Poppr is an R package designed for analysis of populations with mixed modes ofsexual and clonal reproduction. It is built around the framework ofadegenet'sgenind 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()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 toGenAlEx

• 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")

If you usepoppr at all, please specify the version and cite:

Kamvar ZN, Tabima JF, Grünwald NJ. (2014) Poppr: an R package for geneticanalysis of populations with clonal, partially clonal, and/or sexualreproduction. PeerJ 2:e281https://doi.org/10.7717/peerj.281

If you usepoppr in a presentation please mention it as thepoppr 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 withmlg.filter()
• custom multilocus genotype definitions withmlg.custom()
• index of association for genomic data withwin.ia() orsamp.ia()
• bootstrapping any genetic distance with genind, genlight, or genpop objects withaboot()

Please also cite:

Kamvar ZN, Brooks JC and Grünwald NJ (2015) Novel R tools for analysis ofgenome-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")

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

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 ofpoppr, see about installingunreleased versions below.

New features are occasionally added to {poppr}, but it can take time for it toget to CRAN. If you know that you want the latest version of {poppr}, (whichwill contain bug fixes and new features to be included in future releases), thenyou can use the custom R-Universe repository, which is updated hourly:https://zkamvar.r-universe.dev/builds

To install poppr from the R-Universe, you can use the following code:

universe<- c("https://zkamvar.r-universe.dev","https://cloud.r-project.org")install.packages("poppr",repos=universe)

The universe repository also contain up-to-date versions of {adegenet} and{hierfstat}, which are commonly used in conjunction with {poppr} and arenotoriously out of date on CRAN.

All Development versions of {poppr} will be on GitHub, but need to be compiled.

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

• Xcode (OSX)ORRtools (Windows)
• {remotes} (to install, use:install.packages("remotes"))

For Linux users, make sure that the functiongetOption("unzip") returns"unzip" or"internal". If it does not, then runoptions(unzip = "internal").

Once you have {remotes} and a C compiler installed, you can use theinstall_github() function to install the current version from github.

All new features in testing will be released on different branches. Thesefeatures will be in various stages of development and may or may not bedocumented. Install with caution. The below command would install features onthe branch called "devel". Note that these branches might be out of datefrom the main branch. Note: if you don't have LaTeX installed, you should setbuild_vignettes = FALSE.

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

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

package?poppr

A few vignettes have been written for poppr:

Users who have any questions/comments/suggestions regarding any version of poppr(stable or development) should direct their comments to thePoppr googlegroup

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 athttps://grunwaldlab.github.io/Population_Genetics_in_R.

Please note that this project is released with aContributor Code ofConduct. Byparticipating in this project you agree to abide by itsterms. If you wish to contribute code topoppr, please fork the repository andcreate a pull request with your added feature.