basic.stats: Basic diversity and differentiation statistics

Description

Estimates individual counts, allelic frequencies, observed heterozygosities and genetic diversities per locus and population. Also Estimates mean observed heterozygosities, mean gene diversities within population Hs, Gene diversities overall Ht and corrected Htp, and Dst, Dstp. Finally, estimates Fst and Fstp as well as Fis following Nei (1987) per locus and overall loci

Usage

basic.stats(data,diploid=TRUE,digits=4)
# S3 method for basic.stats
print(x,...)
Hs(data,...)
Ho(data,...)

Arguments

data

a data frame where the first column contains the population to which the different individuals belong, and the following columns contain the genotype of the individuals -one locus per column-

diploid

Whether individuals are diploids (default) or haploids

digits

how many digits to print out in the output (default is 4)

an object of class basic.stats

...

further arguments to pass to print.bas.stats

Value

n.ind.samp

A table --with np (number of populations) columns and nl (number of loci) rows-- of genotype counts

pop.freq

A list containing allele frequencies. Each element of the list is one locus. For each locus, Populations are in columns and alleles in rows

A table --with np (number of populations) columns and nl (number of loci) rows-- of observed heterozygosities

A table --with np (number of populations) columns and nl (number of loci) rows-- of observed gene diversities

Fis

A table --with np (number of populations) columns and nl (number of loci) rows--of observed Fis

perloc

A table --with as many rows as loci-- containing basic statistics Ho, Hs, Ht, Dst, Ht', Dst', Fst, Fst' ,Fis, Dest

overall

Basic statistics averaged over loci

References

Nei M. (1987) Molecular Evolutionary Genetics. Columbia University Press

Jost L (2008) GST and its relatives do not measure differentiation. Molecular Ecology, 17, 4015-4026.

Nei M, Chesser R (1983) Estimation of fixation indexes and gene diversities. Annals of Human Genetics, 47, 253-259.

Examples

Run this code

# NOT RUN {
data(gtrunchier)
basic.stats(gtrunchier[,-1])
Hs(gtrunchier[,-2])
Ho(gtrunchier[,-2])
# }