generate_gpmap: Function for creating genotype-phenotype (GP) maps
In gpmap: Analysing and Plotting Genotype-Phenotype Maps

Description Usage Arguments Details Value Author(s) References Examples

Function for creating a gpmap object representing a genotype-phenotype (GP) map for N biallelic loci or more generally K such maps, from a matrix of genotypic values.

1	generate_gpmap(y, locinames = NULL, allelenames = NULL, mapnames = NULL)

`y`	A (3^NxK) matrix or numeric with each column specifying the 3^N genotypic values for K GP maps
`locinames`	An optional character vector with N names of loci
`allelenames`	An optional character object specifying allele names
`mapnames`	An optional character vector with K names of GP maps / phenotypes

Arguments locinames and allelenames are passed on to enumerate_genotypes, and the genotypic values in y should be given in the same sequence as the sequence of genotypes returned by enumerate_genotypes. If mapnames is not specified then the GP maps will be named "GPmap_1", "GPmap_2",..,"GPmap_K".

The function returns an object of class gpmap containing the following components

`values`	The vector or matrix of genotypic values
`nloci`	The number of loci in the map
`genotypes`	Data frame with enumeration of genotypes
`locinames`	Character vector with names for all loci
`mapname`	The name(s) of the GP map

Arne B. Gjuvsland <arne.gjuvsland@nmbu.no> and Yunpeng Wang <yunpeng.wng@gmail.com>

Gjuvsland AB, Vik JO, Woolliams JA, Omholt SW (2011) Order-preserving principles underlying genotype-phenotype maps ensure high additive proportions of genetic variance. Journal of Evolutionary Biology 24(10):2269-2279 [link]

#inter- and intra-locus additive GPmap with two loci 
generate_gpmap(c(-2,1,0,-1,0,1,0,1,2),mapnames="Additive") 

#two-locus GP map with AxA epistasis for loci named A and B
generate_gpmap(c(-1,0,1,0,0,0,1,0,-1),locinames=c("A","B"),mapnames="AxA")

#random GP map with 3 loci
set.seed(0)
generate_gpmap(rnorm(27))