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
- 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 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()
orsamp.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")
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.
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.
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:
devtools::install_github(repo = "grunwaldlab/poppr", build_vignettes = TRUE)
library("poppr")
devtools::install_github(repo = "grunwaldlab/poppr@devel", build_vignettes = TRUE)
library("poppr")
Users who have any questions/comments/suggestions regarding any version of poppr (stable or development) should direct their comments to the Poppr google group
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") |
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.
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.