Man pages for grunwaldlab/poppr
Genetic Analysis of Populations with Mixed Reproduction

abootCalculate a dendrogram with bootstrap support using any...
AeutOomycete root rot pathogen *Aphanomyces euteiches* AFLP data
bitwise.distCalculate dissimilarity or Euclidean distance for genlight...
bitwise.iaCalculate the index of association between samples in a...
bootgen-classBootgen object
bootgen-methodsMethods used for the bootgen object.
boot.iaBootstrap the index of association
bruvo.bootCreate a tree using Bruvo's Distance with non-parametric...
bruvo.distBruvo's distance for microsatellites
bruvomat-classbruvomat object
bruvomat-methodsMethods used for the bruvomat object.
bruvo.msnCreate minimum spanning network of selected populations using...
clonecorrectRemove potential bias caused by cloned genotypes in genind or...
coercion-methodsSwitch between genind and genclone objects.
cutoff_predictorPredict cutoff thresholds for use with mlg.filter
diss.distCalculate a distance matrix based on relative dissimilarity
diversity_bootPerform a bootstrap analysis on diversity statistics
diversity_ciPerform bootstrap statistics, calculate, and plot confidence...
diversity_statsProduce a table of diversity statistics
filter_statsUtilize all algorithms of mlg.filter
fix_replenFind and fix inconsistent repeat lengths
genclone-classGENclone and SNPclone classes
genclone-methodMethods used for the genclone object
genetic_distanceCalculate Genetic Distance for a genind or genclone object.
genind2genalexExport data from genind objects to genalex formatted *.csv...
genotype_curveProduce a genotype accumulation curve
getfileGet a file name and path and store them in a list.
grapes-greater-than-grapesmagrittr forward-pipe operator
greycurveDisplay a greyscale gradient adjusted to specific parameters
iaIndex of Association
imsnCreate minimum spanning networks interactively
incompCheck for samples that are incomparable due to missing data
informlociRemove all non-phylogentically informative loci
info_tableCreate a table summarizing missing data or ploidy information...
is.cloneCheck for validity of a genclone or snpclone object
levels-methodsUnique and Duplicated implementations for MLG objects
locus_tableCreate a table of summary statistics per locus.
make_haplotypes-methodSplit samples from a genind object into pseudo-haplotypes
missingnoTreat missing data
mlgCreate counts, vectors, and matrices of multilocus genotypes.
MLG-accessorsAccessors for the MLG object
MLG-classMLG class
mlg.filterMLG definitions based on genetic distance
MLG-methodMethods used for MLG objects
mll.customDefine custom multilocus lineages
mll-methodAccess and manipulate multilocus lineages.
mll.reset-methodReset multilocus lineages
monpopPeach brown rot pathogen *Monilinia fructicola*
old2new_gencloneConvert an old genclone object to a new genclone object
partial_cloneSimulated data illustrating a Minimum Spanning Network based...
pgenGenotype Probability
PinfPhytophthora infestans data from Mexico and South America.
plot_filter_statsPlot the results of filter_stats
plot_poppr_msnPlot minimum spanning networks produced in poppr.
popprProduce a basic summary table for population genetic...
poppr.allProcess a list of files with poppr
poppr.amovaPerform Analysis of Molecular Variance (AMOVA) on genind or...
poppr_has_parallelDetermines whether openMP is support on this system.
poppr.msnCreate a minimum spanning network of selected populations...
poppr-packageThe 'poppr' R package
poppr.plotInternal function to plot the results from ia() and poppr()
popsubSubset data by population
PramPhytophthora ramorum data from OR Forests and Nurseries (OR...
private_allelesTabulate alleles the occur in only one population.
psexProbability of encountering a genotype more than once by...
rare_allele_correctionCorrecting rare allele frequencies
read.genalexImporting data from genalex formatted *.csv files.
recode_polyploidsRecode polyploid microsatellite data for use in frequency...
rrafRound Robin Allele Frequencies
rrmlgRound Robin Multilocus Genotypes
samp.iaCalculate random samples of the index of association for...
shufflepopShuffle individuals in a 'genclone' or 'genind' object...
snpclone-coercion-methodsCreate a snpclone object from a genlight object.
snpclone-methodMethods used for the snpclone object
test_replenTest repeat length consistency.
unique-methodsUnique and Duplicated implementations for MLG objects
win.iaCalculate windows of the index of association for genlight...
grunwaldlab/poppr documentation built on Sept. 1, 2018, 5:26 a.m.