Function reference • poppr

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.between(): 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 snpclone-class snpclone: 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.

upgma(): UPGMA

win.ia(): Calculate windows of the index of association for genlight objects.