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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

Issues

17

Pull Requests

0

Stars

71

Forks

27

Maintainer

Zhian N. Kamvar

Last Published

December 1st, 2015

Functions in poppr (2.1.0)

mlg.filter

Statistics on Clonal Filtering of Genotype Data
info_table

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

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

Oomycete root rot pathogen Aphanomyces euteiches AFLP data
informloci

Remove all non-phylogentically informative loci
bitwise.dist

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

Phytophthora infestans data from Mexico and South America.
poppr-package

The poppr R package.
bootgen-class

Bootgen object
as.snpclone

Create a snpclone object from a genlight object.
MLG-class

MLG class
fix_replen

Find and fix inconsistent repeat lengths
win.ia

Calculate windows of the index of association for genlight objects.
locus_table

Create a table of summary statistics per locus.
greycurve

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
shufflepop

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

Reset multilocus lineages
recode_polyploids

Recode polyploid microsatellite data for use in frequency based statistics.
read.genalex

Importing data from genalex formatted *.csv files.
bitwise.ia

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

Bruvo's distance for microsatellites
cutoff_predictor

Predict cutoff thresholds for use with mlg.filter
plot_poppr_msn

Plot minimum spanning networks produced in poppr.
missingno

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

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

Create counts, vectors, and matrices of multilocus genotypes.
bruvo.boot

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

Genotype Probability
filter_stats

Utilize all algorithms of mlg.filter
visible

Accessors for the MLG object
diversity_ci

Perform bootstrap statistics, calculate, and plot confidence intervals.
monpop

Peach brown rot pathogen Monilinia fructicola
as.genclone

Switch between genind and genclone objects.
clonecorrect

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

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
mll.custom

Define custom multilocus lineages
ia

Index of Association
[,snpclone,ANY,ANY,ANY-method

Methods used for the snpclone object
poppr.amova

Perform Analysis of Molecular Variance (AMOVA) on genind or genclone objects.
genind2genalex

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

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

Create minimum spanning networks interactively
is.snpclone

Check for validity of a genclone or snpclone object
psex

Probability of encountering a genotype more than once by chance
genotype_curve

Produce a genotype accumulation curve
poppr.msn

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-class

bruvomat object
nei.dist

Calculate Genetic Distance for a genind or genclone object.
unique,MLG-method

Unique and Duplicated implementations for MLG objects
rrmlg

Round Robin Multilocus Genotypes
samp.ia

Calculate random samples of the index of association for genlight objects.
genclone-class

GENclone and SNPclone classes
aboot

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

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.
getfile

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

DEPRECATED FUNCTIONS
mll

Access and manipulate multilocus lineages.
rraf

Round Robin Allele Frequencies
test_replen

Test repeat length consistency.
diversity_boot

Perform a bootstrap analysis on diversity statistics
plot_filter_stats

Plot the results of filter_stats
poppr.all

Process a list of files with poppr
popsub

Subset a genclone or genind object by population