# Genetic Analysis of Populations with Mixed Reproduction

## Documentation for package ‘poppr’ version 2.9.3

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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.