get_divergence_matrix {gen3sis}

Returns the full divergence matrix for a given species (site x site).

Description

Returns the full divergence matrix for a given species (site x site).

Usage

get_divergence_matrix(species)

Arguments

species

the species for which the divergence matrix should be produced

Details

The functions allows to extract the full divergence matrix representing the accumulated differentiation between all the sites that are occupied by the species. The input is a species object for any time step.

Value

the full decompressed divergence matrix

Examples

# get path containing example rasters
datapath <- system.file(file.path("extdata", "WorldCenter"), package="gen3sis")
# get species at t0
species_t_0 <- readRDS(file.path(datapath, "output/config_worldcenter/species/species_t_0.rds"))
# get divergence matrix from species 1
divergence_sp1_t0 <- get_divergence_matrix(species_t_0[[1]])
# get divergence matrix from species 12
divergence_sp12_t0 <- get_divergence_matrix(species_t_0[[12]])
# note that species 1 has no divergence between it's populations, while 12 has.