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Frequently Asked Questions

Here lives a short list of frequently asked questions and answers to them. Many questions and answers can be found over at the poppr google group. If you can't find answers on this page, search there.

What is poppr?

Poppr is an R package implementing functions to analyze population genetic data with particular emphasis on populations that have mixed modes of reproduction including clonal and sexual reproduction.

How do I cite poppr?

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

If you use poppr in a presentation please mention it as the poppr R package 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")

What R packages does poppr depend on?

Currently poppr depends on the following packages:

  • adegenet
  • ape
  • ggplot2
  • pegas
  • phangorn
  • vegan
  • igraph

Why should I use poppr?

You should use poppr if you have a need for using any of the following functions:

  • 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 Bruvo's distance
  • drawing of minimum spanning networks for genetic distances
  • calculation of the index of association (equation) or equation
  • batch processing on any server that has R (>2.15.0) installed
  • calculation of Bruvo's distance for microsatellite (SSR) markers (implemented in C for speed)
  • import of data from and export to GenAlEx

I can't install the package.

​Do you have the correct version of R? (≥ 2.15.1). If you are on mac or windows and you are attempting to install poppr via CRAN, you must make sure that your version is at least 3.0, since the binaries for mac and windows are built under R 3.0. For an alternative, see our intsallation page.

For any other issues, please send an email of any errors you are recieving to kamvarz *at* science *dot* oregonstate *dot* edu.