poppr2.9.6 package

Calculate a dendrogram with bootstrap support using any distance appli...

Calculate dissimilarity or Euclidean distance for genlight objects

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

Bootstrap the index of association

Bootgen object

Methods used for the bootgen object.

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

Bruvo's distance for microsatellites

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

bruvomat object

Methods used for the bruvomat object.

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

Switch between genind and genclone objects.

Predict cutoff thresholds for use with mlg.filter

Calculate a distance matrix based on relative dissimilarity

Perform a bootstrap analysis on diversity statistics

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

Produce a table of diversity statistics

Utilize all algorithms of mlg.filter

Find and fix inconsistent repeat lengths

GENclone and SNPclone classes

Methods used for the genclone object

Calculate Genetic Distance for a genind or genclone object.

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

Produce a genotype accumulation curve

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

magrittr forward-pipe operator

Display a greyscale gradient adjusted to specific parameters

Index of Association

Create minimum spanning networks interactively

Check for samples that are incomparable due to missing data

Create a table summarizing missing data or ploidy information of a gen...

Define custom multilocus lineages

Remove all non-phylogentically informative loci

Check for validity of a genclone or snpclone object

Unique and Duplicated implementations for MLG objects

Create a table of summary statistics per locus.

Split samples from a genind object into pseudo-haplotypes

Treat missing data

Produce a basic summary table for population genetic analyses.

Accessors for the MLG object

MLG class

Methods used for MLG objects

MLG definitions based on genetic distance

Create counts, vectors, and matrices of multilocus genotypes.

Access and manipulate multilocus lineages.

Determines whether openMP is support on this system.

Reset multilocus lineages

Convert an old genclone object to a new genclone object

Genotype Probability

Plot the results of filter_stats

Plot minimum spanning networks produced in poppr.

The poppr R package

Process a list of files with poppr

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

Create a minimum spanning network of selected populations using a dist...

Internal function to plot the results from ia() and poppr()

Subset data by population

Tabulate alleles the occur in only one population.

Probability of encountering a genotype more than once by chance

Correcting rare allele frequencies

Importing data from genalex formatted *.csv files.

Recode polyploid microsatellite data for use in frequency based statis...

Round Robin Allele Frequencies

Round Robin Multilocus Genotypes

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

Shuffle individuals in a genclone or genind object independently o...

Create a snpclone object from a genlight object.

Methods used for the snpclone object

Test repeat length consistency.

Unique and Duplicated implementations for MLG objects

UPGMA

Calculate windows of the index of association for genlight objects.