Get abundance matrix

This function constructs an abundance matrix based on the space sites.

Usage

get_abundance_matrix(
  species_list,
  space = NULL,
  xy = FALSE,
  empty_sites = FALSE
)

Arguments

species_list

a list of species to include in the calculations.

space

the space to calculate over.

xy

if TRUE, site coordinates are returned as matrix columns. Default is FALSE.

empty_sites

if TRUE, sites with no species will be included in the matrix. Default is FALSE.

Value

an abundance matrix with sites as rows and species as columns.

See also

vignette("h-support-functions", package = "gen3sis2")

Examples

if (FALSE) { # \dontrun{
  # mock simulation state
  space <- system.file("extdata/SouthAmerica/species_and_spaces/space_t_2.rds", package = "gen3sis2") |> readRDS()
  
  all_species <- system.file("extdata/SouthAmerica/species_and_spaces/species_t_2.rds", package = "gen3sis2") |> readRDS()
  
  data <- list(
    space = space,
    all_species = all_species
  )
  
  get_abundance_matrix(data$all_species)[1:5,]
} # }