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poppr (version 1.0.5)

an R package for genetic analysis of populations with mixed reproduction

Description

Population genetic analyses for hierarchical analysis of partially clonal populations built upon the architecture of the adegenet package.

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Version

Install

install.packages('poppr')

Monthly Downloads

5,837

Version

1.0.5

License

GPL-2

Maintainer

Zhian N. Kamvar

Last Published

December 12th, 2013

Functions in poppr (1.0.5)

Aeut

Oomycete root rot pathogen Aphanomyces euteiches AFLP data
greycurve

Display a greyscale gradient adjusted to specific parameters
ia

Index of Association
poppr.msn

Create a minimum spanning network of selected populations using a distance matrix.
bruvo.msn

Create minimum spanning network of selected populations using Brvuo's distance.
read.genalex

Importing data from genalex formatted *.csv files.
bruvo.dist

Calculate the average Bruvo's Distance over all loci in a population.
bruvomat-class

bruvomat object
genind2genalex

Exporting data from genind objects to genalex formatted *.csv files.
splitcombine

Split a or combine items within a data frame in genind objects.
clonecorrect

Remove potential bias caused by cloned genotypes in genind object.
mlg

Create counts, vectors, and matrices of multilocus genotypes.
popsub

Subset a genind object by population
shufflepop

Shuffle individuals in a genind object independently over each locus.
informloci

Remove all non-phylogentically informative loci
bruvo.boot

Create a tree using Bruvo's Distance with non-parametric bootstrapping.
missingno

How to deal with missing data in a genind object.
poppr

Produce a basic summary table for population genetic analyses.
diss.dist

Calculate a distance matrix based on relative dissimilarity
poppr.all

Process a list of files with poppr
initialize,bruvomat-method

Methods used for the bruvomat object.
partial_clone

Simulated data illustrating a Minimum Spanning Network based on Bruvo's Distance
getfile

Get a file name and path and store them in a list.