an R package for genetic analysis of populations with mixed reproduction


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Documentation for package ‘poppr’ version 1.0.6

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Aeut Oomycete root rot pathogen _Aphanomyces euteiches_ AFLP data
bruvo.boot Create a tree using Bruvo's Distance with non-parametric bootstrapping.
bruvo.dist Calculate the average Bruvo's Distance over all loci in a population.
bruvo.msn Create minimum spanning network of selected populations using Brvuo's distance.
bruvomat-class bruvomat object
clonecorrect Remove potential bias caused by cloned genotypes in genind object.
dim-method Methods used for the bruvomat object.
diss.dist Calculate a distance matrix based on relative dissimilarity
genind2genalex Exporting data from genind objects to genalex formatted *.csv files.
getfile Get a file name and path and store them in a list.
greycurve Display a greyscale gradient adjusted to specific parameters
ia Index of Association
informloci Remove all non-phylogentically informative loci
initialize-method Methods used for the bruvomat object.
missingno How to deal with missing data in a genind object.
mlg Create counts, vectors, and matrices of multilocus genotypes.
mlg.crosspop Create counts, vectors, and matrices of multilocus genotypes.
mlg.table Create counts, vectors, and matrices of multilocus genotypes.
mlg.vector Create counts, vectors, and matrices of multilocus genotypes.
partial_clone Simulated data illustrating a Minimum Spanning Network based on Bruvo's Distance
poppr Produce a basic summary table for population genetic analyses.
poppr.all Process a list of files with poppr
poppr.msn Create a minimum spanning network of selected populations using a distance matrix.
popsub Subset a 'genind' object by population
read.genalex Importing data from genalex formatted *.csv files.
shufflepop Shuffle individuals in a 'genind' object independently over each locus.
splitcombine Split a or combine items within a data frame in 'genind' objects.
[-method Methods used for the bruvomat object.