Genetic Analysis of Populations with Mixed Reproduction

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Documentation for package ‘poppr’ version 2.9.7

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A B C D E F G I J L M N O P R S T U W

poppr-package The 'poppr' R package

-- A --

aboot Calculate a dendrogram with bootstrap support using any distance applicable to genind or genclone objects.
Aeut Oomycete root rot pathogen *Aphanomyces euteiches* AFLP data
amova Perform Analysis of Molecular Variance (AMOVA) on genind or genclone objects.
as.genambig Switch between genind and genclone objects.
as.genambig-method Switch between genind and genclone objects.
as.genclone Switch between genind and genclone objects.
as.genclone-method Switch between genind and genclone objects.
as.snpclone Create a snpclone object from a genlight object.
as.snpclone-method Create a snpclone object from a genlight object.

-- B --

bitwise.dist Calculate dissimilarity or Euclidean distance for genlight objects
boot.ia Bootstrap the index of association
bootgen2genind Switch between genind and genclone objects.
bootgen2genind-method Switch between genind and genclone objects.
bootstrap Calculate a dendrogram with bootstrap support using any distance applicable to genind or genclone objects.
bruvo.between Bruvo's distance for microsatellites
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.

-- C --

clonecorrect Remove potential bias caused by cloned genotypes in genind or genclone object.
cutoff_predictor Predict cutoff thresholds for use with mlg.filter

-- D --

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

-- E --

edwards.dist Calculate Genetic Distance for a genind or genclone object.

-- F --

filter_stats Utilize all algorithms of mlg.filter
fix_replen Find and fix inconsistent repeat lengths

-- G --

genclone GENclone and SNPclone classes
genclone-class GENclone and SNPclone classes
genclone2genind Switch between genind and genclone objects.
genclone2genind-method Switch between genind and genclone objects.
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

-- I --

ia Index of Association
imsn Create minimum spanning networks interactively
incomp Check for samples that are incomparable due to missing data
informloci Remove all non-phylogentically informative loci
info_table Create a table summarizing missing data or ploidy information of a genind or genclone object
is.clone Check for validity of a genclone or snpclone object
is.genclone Check for validity of a genclone or snpclone object
is.snpclone Check for validity of a genclone or snpclone object

-- J --

jack.ia Index of Association

-- L --

locus_table Create a table of summary statistics per locus.

-- M --

make_haplotypes Split samples from a genind object into pseudo-haplotypes
make_haplotypes-method Split samples from a genind object into pseudo-haplotypes
missingno Treat missing data
mlg Create counts, vectors, and matrices of multilocus genotypes.
mlg.crosspop Create counts, vectors, and matrices of multilocus genotypes.
mlg.filter MLG definitions based on genetic distance
mlg.filter-method MLG definitions based on genetic distance
mlg.filter<- MLG definitions based on genetic distance
mlg.filter<--method MLG definitions based on genetic distance
mlg.id 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.
mll Access and manipulate multilocus lineages.
mll-method Access and manipulate multilocus lineages.
mll.custom Define custom multilocus lineages
mll.custom-method Define custom multilocus lineages
mll.custom<- Define custom multilocus lineages
mll.custom<--method Define custom multilocus lineages
mll.levels Define custom multilocus lineages
mll.levels-method Define custom multilocus lineages
mll.levels<- Define custom multilocus lineages
mll.levels<--method Define custom multilocus lineages
mll.reset Reset multilocus lineages
mll.reset-method Reset multilocus lineages
mll<- Access and manipulate multilocus lineages.
mll<--method Access and manipulate multilocus lineages.
monpop Peach brown rot pathogen *Monilinia fructicola*
msn.bruvo Create minimum spanning network of selected populations using Bruvo's distance.
msn.poppr Create a minimum spanning network of selected populations using a distance matrix.

-- N --

nei.dist Calculate Genetic Distance for a genind or genclone object.
nmll Access and manipulate multilocus lineages.
nmll-method Access and manipulate multilocus lineages.

-- O --

old2new_genclone Convert an old genclone object to a new genclone object
old_partial_clone Simulated data illustrating a Minimum Spanning Network based on Bruvo's Distance
old_Pinf Phytophthora infestans data from Mexico and South America.

-- P --

pair.ia Index of Association
partial_clone Simulated data illustrating a Minimum Spanning Network based on Bruvo's Distance
pgen Genotype Probability
Pinf Phytophthora infestans data from Mexico and South America.
plot_poppr_msn Plot minimum spanning networks produced in poppr.
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
Pram Phytophthora ramorum data from OR Forests and Nurseries (OR and CA)
prevosti.dist Calculate Genetic Distance for a genind or genclone object.
private_alleles Tabulate alleles the occur in only one population.
provesti.dist Calculate Genetic Distance for a genind or genclone object.
psex Probability of encountering a genotype more than once by chance

-- R --

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.
resample.ia Index of Association
reynolds.dist Calculate Genetic Distance for a genind or genclone object.
rogers.dist Calculate Genetic Distance for a genind or genclone object.
rraf Round Robin Allele Frequencies
rrmlg Round Robin Multilocus Genotypes

-- S --

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.
snpclone GENclone and SNPclone classes
snpclone-class GENclone and SNPclone classes

-- T --

test_replen Test repeat length consistency.

-- U --

upgma UPGMA

-- W --

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