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poppr (version 1.1.1)

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

6,110

Version

1.1.1

License

GPL-2 | GPL-3

Maintainer

Zhian N. Kamvar

Last Published

July 27th, 2014

Functions in poppr (1.1.1)

bruvo.dist

Bruvo's distance for microsatellites
bruvo.boot

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

Create minimum spanning network of selected populations using Bruvo's distance.
bootgen-class

Bootgen object
nei.dist

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

Process a list of files with poppr
popsub

Subset a genclone or genind object by population
poppr-package

The poppr R package.
as.genclone

Create a genclone object from a genind object.
greycurve

Display a greyscale gradient adjusted to specific parameters
plot_poppr_msn

Plot minimum spanning networks produced in poppr.
clonecorrect

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

Access and manipulate the population hierarchy for genclone objects.
initialize,bruvomat-method

Methods used for the bruvomat object.
genind2genalex

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

Recode polyploid microsatellite data for use in frequency based statistics.
genclone-class

Genclone class
splitcombine

Split a or combine items within a data frame in genind objects (DEPRECATED).
[,bootgen,ANY,ANY,ANY-method

Methods used for the bootgen object.
genotype_curve

Produce a genotype accumulation curve
monpop

Peach brown rot pathogen Monilinia fructicola
is.genclone

Check for validity of a genclone object
aboot

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

Index of Association
private_alleles

Tabulate alleles the occur in only one population.
shufflepop

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

Manipulate the population factor of genclone objects.
Pinf

Phytophthora infestans data from Mexico and South America.
poppr.amova

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

Oomycete root rot pathogen Aphanomyces euteiches AFLP data
informloci

Remove all non-phylogentically informative loci
mlg

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

How to deal with missing data in a genind object.
bruvomat-class

bruvomat object
info_table

Create a table summarizing missing data or ploidy information of a genind or genclone object
getfile

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

Produce a basic summary table for population genetic analyses.
locus_table

Create a table of summary statistics per locus.
read.genalex

Importing data from genalex formatted *.csv files.
partial_clone

Simulated data illustrating a Minimum Spanning Network based on Bruvo's Distance
poppr.msn

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

Calculate a distance matrix based on relative dissimilarity
[,genclone,ANY,ANY,ANY-method

Methods used for the genclone object