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poppr (version 1.1.5)

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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Install

install.packages('poppr')

Monthly Downloads

6,110

Version

1.1.5

License

GPL-2 | GPL-3

Issues

17

Pull Requests

0

Stars

70

Forks

27

Maintainer

Zhian N. Kamvar

Last Published

May 12th, 2015

Functions in poppr (1.1.5)

genind2genalex

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

Create a table of summary statistics per locus.
Aeut

Oomycete root rot pathogen Aphanomyces euteiches AFLP data
aboot

Calculate a dendrogram with bootstrap support using any distance applicable to genind or genclone objects.
is.genclone

Check for validity of a genclone object
poppr.amova

Perform Analysis of Molecular Variance (AMOVA) on genind or genclone objects.
diss.dist

Calculate a distance matrix based on relative dissimilarity
info_table

Create a table summarizing missing data or ploidy information of a genind or genclone object
read.genalex

Importing data from genalex formatted *.csv files.
Pinf

Phytophthora infestans data from Mexico and South America.
as.genclone

Create a genclone object from a genind object.
popsub

Subset a genclone or genind object by population
genclone-class

Genclone class
bootgen-class

Bootgen object
shufflepop

Shuffle individuals in a genclone or genind object independently over each locus.
recode_polyploids

Recode polyploid microsatellite data for use in frequency based statistics.
ia

Index of Association
monpop

Peach brown rot pathogen Monilinia fructicola
getfile

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

Display a greyscale gradient adjusted to specific parameters
gethierarchy

Access and manipulate the population hierarchy for genclone objects.
setpop

Manipulate the population factor of genclone objects.
genotype_curve

Produce a genotype accumulation curve
initialize,bruvomat-method

Methods used for the bruvomat object.
[,bootgen,ANY,ANY,ANY-method

Methods used for the bootgen object.
bruvo.boot

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

Produce a basic summary table for population genetic analyses.
informloci

Remove all non-phylogentically informative loci
partial_clone

Simulated data illustrating a Minimum Spanning Network based on Bruvo's Distance
[,genclone,ANY,ANY,ANY-method

Methods used for the genclone object
plot_poppr_msn

Plot minimum spanning networks produced in poppr.
bruvo.msn

Create minimum spanning network of selected populations using Bruvo's distance.
missingno

How to deal with missing data in a genind object.
nei.dist

Calculate Genetic Distance for a genind or genclone object.
poppr.msn

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

Split a or combine items within a data frame in genind objects (DEPRECATED).
bruvo.dist

Bruvo's distance for microsatellites
poppr.all

Process a list of files with poppr
private_alleles

Tabulate alleles the occur in only one population.
clonecorrect

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

Create counts, vectors, and matrices of multilocus genotypes.
bruvomat-class

bruvomat object
poppr-package

The poppr R package.