allele_divtables-class: List of divtables holding allele diversity data

In douglasgscofield/dispersalDiversity: Analyse individual and genetic diversity of dispersal processes in biological populations

Description

An object of class allele_divtables is a list of divtable objects, each representing sites-by-allele counts data for a single genetic locus. Row and column names are the site names and individual alleles, respectively. This is the basic data object for analysis of genetic data using the dispersalDiversity package. It is accepted by the function diversity, which generates descriptive statistics, and the functions alphaDiversityTest, gammaContrastTest and others that test for differences in the structure of genetic diversity.

Details

Assembling an allele_divtables by hand is labourious. More typically, genotype data will be in a class genalex object and then converted to allele_divtables using createAlleleTables. The createAlleleTables and as.allele_divtables functions will attempt to convert non-genalex objects using to genalex format using as.genalex, but this may not be successful.

Examples

## One possible way to plot an \code{allele_divtables} object, plotting
## each locus as a separate divtable in a two-column format

data(Qagr_pericarp_genotypes)
pal <- createAlleleTables(Qagr_pericarp_genotypes)
par(mfrow = c(round(length(pal) / 2), 2))
lapply(names(pal), function(n) plot(pal[[n]], main = n, l2 = NULL, las = 2))

douglasgscofield/dispersalDiversity documentation built on March 30, 2021, 9:50 a.m.