make.contrasts: Calculate contrasts required by the function
Description
Calculates the contrasts that hwde uses in fitting models
for genotypic disequilibrium. At present these are limited to
first order interaction terms between the distinct loci,
possibly with distinct values foe each different level of a
grouping factor.
Data frame, with one column per locus, and as
many rows as there are observations. Genotypes are represented
using a two-letter code, e.g., AA, Aa, aa
allele.chars
By default the letters "a", "b", ...,
one for each locus, are used.
Value
contrasts.dfData frame whose columns hold the contrasts that
will be explanatory variables for the Poisson regression model.
list.columnsList in which each element is a text string
that holds the codes for a sequence of model terms.
Details
Any pair of letters can be used for the two alleles. The setting
of allele.chars determines the coding used in the model
formulae. This function is called by hwde