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poppr (version 1.1.2)

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

5,302

Version

1.1.2

License

GPL-2 | GPL-3

Maintainer

Zhian N. Kamvar

Last Published

July 29th, 2014

Functions in poppr (1.1.2)

as.genclone

Create a genclone object from a genind object.
locus_table

Create a table of summary statistics per locus.
genind2genalex

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

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

Phytophthora infestans data from Mexico and South America.
ia

Index of Association
nei.dist

Calculate Genetic Distance for a genind or genclone object.
bootgen-class

Bootgen object
info_table

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

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

Access and manipulate the population hierarchy for genclone objects.
poppr.all

Process a list of files with poppr
bruvomat-class

bruvomat object
getfile

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

Split a or combine items within a data frame in genind objects (DEPRECATED).
poppr.msn

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

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

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

Peach brown rot pathogen Monilinia fructicola
private_alleles

Tabulate alleles the occur in only one population.
genclone-class

Genclone class
aboot

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

Recode polyploid microsatellite data for use in frequency based statistics.
poppr-package

The poppr R package.
[,bootgen,ANY,ANY,ANY-method

Methods used for the bootgen object.
genotype_curve

Produce a genotype accumulation curve
setpop

Manipulate the population factor of genclone objects.
diss.dist

Calculate a distance matrix based on relative dissimilarity
initialize,bruvomat-method

Methods used for the bruvomat object.
shufflepop

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

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

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

Plot minimum spanning networks produced in poppr.
greycurve

Display a greyscale gradient adjusted to specific parameters
read.genalex

Importing data from genalex formatted *.csv files.
Aeut

Oomycete root rot pathogen Aphanomyces euteiches AFLP data
popsub

Subset a genclone or genind object by population
poppr

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

Bruvo's distance for microsatellites
[,genclone,ANY,ANY,ANY-method

Methods used for the genclone object
informloci

Remove all non-phylogentically informative loci
partial_clone

Simulated data illustrating a Minimum Spanning Network based on Bruvo's Distance
is.genclone

Check for validity of a genclone object