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poppr (version 2.1.1)

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

2.1.1

License

GPL-2 | GPL-3

Issues

17

Pull Requests

0

Stars

70

Forks

27

Maintainer

Zhian N. Kamvar

Last Published

March 15th, 2016

Functions in poppr (2.1.1)

getfile

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

Peach brown rot pathogen Monilinia fructicola
bruvo.msn

Create minimum spanning network of selected populations using Bruvo's distance.
[,snpclone,ANY,ANY,ANY-method

Methods used for the snpclone object
info_table

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

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

Index of Association
genind2genalex

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

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

Create a table of summary statistics per locus.
as.genclone

Switch between genind and genclone objects.
poppr-package

The poppr R package.
cutoff_predictor

Predict cutoff thresholds for use with mlg.filter
mll.custom

Define custom multilocus lineages
Pram

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

Accessors for the MLG object
bruvo.dist

Bruvo's distance for microsatellites
fix_replen

Find and fix inconsistent repeat lengths
mlg.filter

Statistics on Clonal Filtering of Genotype Data
diversity_stats

Produce a table of diversity statistics
imsn

Create minimum spanning networks interactively
[,bootgen,ANY,ANY,ANY-method

Methods used for the bootgen object.
bitwise.ia

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

DEPRECATED FUNCTIONS
rrmlg

Round Robin Multilocus Genotypes
genclone-class

GENclone and SNPclone classes
poppr_has_parallel

Determines whether openMP is support on this system.
missingno

Treat missing data
bitwise.dist

Calculate a dissimilarity distance matrix for SNP data.
unique,MLG-method

Unique and Duplicated implementations for MLG objects
aboot

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

Methods used for the genclone object
recode_polyploids

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

Round Robin Allele Frequencies
test_replen

Test repeat length consistency.
filter_stats

Utilize all algorithms of mlg.filter
poppr.msn

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

Perform a bootstrap analysis on diversity statistics
bruvo.boot

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

Create a snpclone object from a genlight object.
nei.dist

Calculate Genetic Distance for a genind or genclone object.
win.ia

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

Produce a basic summary table for population genetic analyses.
popsub

Subset data by population
diss.dist

Calculate a distance matrix based on relative dissimilarity
private_alleles

Tabulate alleles the occur in only one population.
mll

Access and manipulate multilocus lineages.
clonecorrect

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

Plot minimum spanning networks produced in poppr.
samp.ia

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

Check for validity of a genclone or snpclone object
mlg

Create counts, vectors, and matrices of multilocus genotypes.
poppr.all

Process a list of files with poppr
mll.reset

Reset multilocus lineages
bootgen-class

Bootgen object
greycurve

Display a greyscale gradient adjusted to specific parameters
psex

Probability of encountering a genotype more than once by chance
initialize,MLG-method

Methods used for MLG objects
genotype_curve

Produce a genotype accumulation curve
MLG-class

MLG class
Pinf

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

Perform Analysis of Molecular Variance (AMOVA) on genind or genclone objects.
old2new_genclone

Convert an old genclone object to a new genclone object
rare_allele_correction

Correct minor allele frequencies derived from rraf (INTERNAL)
bruvomat-class

bruvomat object
levels,MLG-method

Unique and Duplicated implementations for MLG objects
pgen

Genotype Probability
informloci

Remove all non-phylogentically informative loci
plot_filter_stats

Plot the results of filter_stats
Aeut

Oomycete root rot pathogen Aphanomyces euteiches AFLP data
partial_clone

Simulated data illustrating a Minimum Spanning Network based on Bruvo's Distance
initialize,bruvomat-method

Methods used for the bruvomat object.
read.genalex

Importing data from genalex formatted *.csv files.