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poppr (version 1.0.1)

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

1.0.1

License

GPL-2

Maintainer

Zhian N. Kamvar

Last Published

July 2nd, 2013

Functions in poppr (1.0.1)

bruvo.msn

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

Remove potential bias caused by cloned genotypes in genind object.
poppr.msn

Create a minimum spanning network of selected populations using a distance matrix.
diss.dist

Calculate a distance matrix based on relative dissimilarity
popsub

Subset a genind object by population
bruvo.boot

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

Index of Association
Aeut

Oomycete root rot pathogen Aphanomyces euteiches AFLP data
poppr.all

Process a list of files with poppr
mlg

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

Display a greyscale gradient adjusted to specific parameters
poppr

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

Calculate the average Bruvo's Distance over all loci in a population.
partial_clone

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

Shuffle individuals in a genind object independently over each locus.
genind2genalex

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

Importing data from genalex formatted *.csv files.
splitcombine

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

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

How to deal with missing data in a genind object.