Genetic Analysis of Populations with Mixed Reproduction


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Documentation for package ‘poppr’ version 1.1.5

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poppr-package The 'poppr' R package.
aboot Calculate a dendrogram with bootstrap support using any distance applicable to genind or genclone objects.
addhierarchy Access and manipulate the population hierarchy for genclone objects.
addhierarchy-method Access and manipulate the population hierarchy for genclone objects.
addhierarchy<- Access and manipulate the population hierarchy for genclone objects.
addhierarchy<--method Access and manipulate the population hierarchy for genclone objects.
Aeut Oomycete root rot pathogen _Aphanomyces euteiches_ AFLP data
amova Perform Analysis of Molecular Variance (AMOVA) on genind or genclone objects.
as.genclone Create a genclone object from a genind object.
as.genclone-method Create a genclone object from a genind object.
bootstrap Calculate a dendrogram with bootstrap support using any distance applicable to genind or genclone objects.
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.
clonecorrect Remove potential bias caused by cloned genotypes in genind or genclone object.
diss.dist Calculate a distance matrix based on relative dissimilarity
edwards.dist Calculate Genetic Distance for a genind or genclone object.
genclone Genclone class
genclone-class Genclone class
genind2genalex Exporting 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.
gethierarchy Access and manipulate the population hierarchy for genclone objects.
gethierarchy-method Access and manipulate the population hierarchy for genclone objects.
greycurve Display a greyscale gradient adjusted to specific parameters
ia Index of Association
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.genclone Check for validity of a genclone object
locus_table Create a table of summary statistics per locus.
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.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.
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.
namehierarchy Access and manipulate the population hierarchy for genclone objects.
namehierarchy-method Access and manipulate the population hierarchy for genclone objects.
namehierarchy<- Access and manipulate the population hierarchy for genclone objects.
namehierarchy<--method Access and manipulate the population hierarchy for genclone objects.
nei.dist Calculate Genetic Distance for a genind or genclone object.
partial_clone Simulated data illustrating a Minimum Spanning Network based on Bruvo's Distance
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.
popsub Subset a 'genclone' or 'genind' object by population
private_alleles Tabulate alleles the occur in only one population.
provesti.dist Calculate Genetic Distance for a genind or genclone object.
read.genalex Importing data from genalex formatted *.csv files.
recode_polyploids Recode polyploid microsatellite data for use in frequency based statistics.
reynolds.dist Calculate Genetic Distance for a genind or genclone object.
rogers.dist Calculate Genetic Distance for a genind or genclone object.
sethierarchy Access and manipulate the population hierarchy for genclone objects.
sethierarchy-method Access and manipulate the population hierarchy for genclone objects.
sethierarchy<- Access and manipulate the population hierarchy for genclone objects.
sethierarchy<--method Access and manipulate the population hierarchy for genclone objects.
setpop Manipulate the population factor of genclone objects.
setpop-method Manipulate the population factor of genclone objects.
setpop<- Manipulate the population factor of genclone objects.
setpop<--method Manipulate the population factor of genclone objects.
shufflepop Shuffle individuals in a 'genclone' or 'genind' object independently over each locus.
splitcombine Split a or combine items within a data frame in 'genind' objects (DEPRECATED).
splithierarchy Access and manipulate the population hierarchy for genclone objects.
splithierarchy-method Access and manipulate the population hierarchy for genclone objects.
splithierarchy<- Access and manipulate the population hierarchy for genclone objects.
splithierarchy<--method Access and manipulate the population hierarchy for genclone objects.