All functions

Aeut

Oomycete root rot pathogen *Aphanomyces euteiches* AFLP data

Pinf

Phytophthora infestans data from Mexico and South America.

Pram

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

aboot()

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

bitwise.dist()

Calculate dissimilarity or Euclidean distance for genlight objects

boot.ia()

Bootstrap the index of association

bruvo.boot()

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

bruvo.dist()

Bruvo's distance for microsatellites

bruvo.msn()

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

clonecorrect()

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

bootgen2genind() as.genclone() genclone2genind() as.genambig()

Switch between genind and genclone objects.

cutoff_predictor()

Predict cutoff thresholds for use with mlg.filter

diss.dist()

Calculate a distance matrix based on relative dissimilarity

diversity_boot()

Perform a bootstrap analysis on diversity statistics

diversity_ci()

Perform bootstrap statistics, calculate, and plot confidence intervals.

diversity_stats()

Produce a table of diversity statistics

filter_stats()

Utilize all algorithms of mlg.filter

fix_replen()

Find and fix inconsistent repeat lengths

genclone-class

GENclone and SNPclone classes

nei.dist() edwards.dist() rogers.dist() reynolds.dist() provesti.dist() prevosti.dist

Calculate Genetic Distance for a genind or genclone object.

genind2genalex()

Export data from genind objects to genalex formatted \*.csv files.

genotype_curve()

Produce a genotype accumulation curve

getfile()

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

greycurve()

Display a greyscale gradient adjusted to specific parameters

ia() pair.ia() resample.ia() jack.ia()

Index of Association

imsn()

Create minimum spanning networks interactively

incomp()

Check for samples that are incomparable due to missing data

info_table()

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

informloci()

Remove all non-phylogentically informative loci

is.snpclone() is.clone() is.genclone()

Check for validity of a genclone or snpclone object

locus_table()

Create a table of summary statistics per locus.

make_haplotypes()

Split samples from a genind object into pseudo-haplotypes

missingno()

Treat missing data

mlg() mlg.table() mlg.vector() mlg.crosspop() mlg.id()

Create counts, vectors, and matrices of multilocus genotypes.

mlg.filter() `mlg.filter<-`()

MLG definitions based on genetic distance

mll() nmll() `mll<-`()

Access and manipulate multilocus lineages.

mll.custom() `mll.custom<-`() mll.levels() `mll.levels<-`()

Define custom multilocus lineages

mll.reset()

Reset multilocus lineages

monpop

Peach brown rot pathogen *Monilinia fructicola*

old2new_genclone()

Convert an old genclone object to a new genclone object

partial_clone

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

pgen()

Genotype Probability

plot_poppr_msn()

Plot minimum spanning networks produced in poppr.

poppr-package

The poppr R package

poppr()

Produce a basic summary table for population genetic analyses.

poppr.all()

Process a list of files with poppr

poppr.amova()

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

poppr.msn()

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

poppr_has_parallel()

Determines whether openMP is support on this system.

popsub()

Subset data by population

private_alleles()

Tabulate alleles the occur in only one population.

psex()

Probability of encountering a genotype more than once by chance

rare_allele_correction

Correcting rare allele frequencies

read.genalex()

Importing data from genalex formatted \*.csv files.

recode_polyploids()

Recode polyploid microsatellite data for use in frequency based statistics.

rraf()

Round Robin Allele Frequencies

rrmlg()

Round Robin Multilocus Genotypes

samp.ia()

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

shufflepop()

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

as.snpclone()

Create a snpclone object from a genlight object.

test_replen()

Test repeat length consistency.

win.ia()

Calculate windows of the index of association for genlight objects.