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. |