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poppr (version 2.1.0)

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

2.1.0

License

GPL-2 | GPL-3

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Repository

http://github.com/grunwaldlab/poppr

Homepage

http://grunwaldlab.github.io/Population_Genetics_in_R/

Maintainer

Zhian N. Kamvar

Last Published

December 1st, 2015

Functions in poppr (2.1.0)

Statistics on Clonal Filtering of Genotype Data

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

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

Oomycete root rot pathogen Aphanomyces euteiches AFLP data

Remove all non-phylogentically informative loci

Calculate a distance matrix comparing samples based on the number of alleles that differ in zygosity.

Phytophthora infestans data from Mexico and South America.

The poppr R package.

Create a snpclone object from a genlight object.

Find and fix inconsistent repeat lengths

Calculate windows of the index of association for genlight objects.

Create a table of summary statistics per locus.

Display a greyscale gradient adjusted to specific parameters

levels,MLG-method

Unique and Duplicated implementations for MLG objects

diversity_stats

Produce a table of diversity statistics

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

Reset multilocus lineages

recode_polyploids

Recode polyploid microsatellite data for use in frequency based statistics.

Importing data from genalex formatted *.csv files.

Calculate the index of association between samples in a genlight object.

Bruvo's distance for microsatellites

cutoff_predictor

Predict cutoff thresholds for use with mlg.filter

Plot minimum spanning networks produced in poppr.

How to deal with missing data in a genind object.

Phytophthora ramorum data from OR Forests and Nurseries (OR and CA)

Create counts, vectors, and matrices of multilocus genotypes.

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

Genotype Probability

Utilize all algorithms of mlg.filter

Accessors for the MLG object

Perform bootstrap statistics, calculate, and plot confidence intervals.

Peach brown rot pathogen Monilinia fructicola

Switch between genind and genclone objects.

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

Produce a basic summary table for population genetic analyses.

private_alleles

Tabulate alleles the occur in only one population.

initialize,MLG-method

Methods used for MLG objects

Define custom multilocus lineages

Index of Association

[,snpclone,ANY,ANY,ANY-method

Methods used for the snpclone object

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

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

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

Create minimum spanning networks interactively

Check for validity of a genclone or snpclone object

Probability of encountering a genotype more than once by chance

Produce a genotype accumulation curve

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

old2new_genclone

Convert an old genclone object to a new genclone object

initialize,genclone-method

Methods used for the genclone object

[,bootgen,ANY,ANY,ANY-method

Methods used for the bootgen object.

bruvomat object

Calculate Genetic Distance for a genind or genclone object.

unique,MLG-method

Unique and Duplicated implementations for MLG objects

Round Robin Multilocus Genotypes

Calculate random samples of the index of association for genlight objects.

GENclone and SNPclone classes

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

Calculate a distance matrix based on relative dissimilarity

poppr_has_parallel

Determines whether openMP is support on this system.

initialize,bruvomat-method

Methods used for the bruvomat object.

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

DEPRECATED FUNCTIONS

Access and manipulate multilocus lineages.

Round Robin Allele Frequencies

Test repeat length consistency.

Perform a bootstrap analysis on diversity statistics

plot_filter_stats

Plot the results of filter_stats

Process a list of files with poppr

Subset a genclone or genind object by population