Genetic Analysis of Populations with Mixed Reproduction

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.