Calculate 3d overlap of predator groups with their prey over time using Schoener Index.

calculate_spatial_overlap(biomass_spatial, dietmatrix, agemat)

Arguments

biomass_spatial	Biomass timeseries of each group and ageclass per polygon and layer. This dataframe should be generated with `calculate_biomass_spatial`.
dietmatrix	Availability matrix given in the biological parameter file. This dataframe should be generated with `load_dietmatrix`. Please make sure to use `convert_names = TRUE` in `load_dietmatrix`.
agemat	First mature age class for age structured groups. This dataframe should be generated with `prm_to_df` using "age_mat" as parameter.

Value

List of Schoener's similarity indices ranging from 1 (perfect overlap) to 0 (zero overlap). Dataframe in first listentry gives pred, pred agecl, prey, preyageclass specific index. Dataframe in second listentry gives index per pred, pred agecl. Si is calculated as weighted mean with the availabilities as weights.

Examples

# Using built in datasets.
d <- system.file("extdata", "setas-model-new-trunk", package = "atlantistools")
prm_biol <- file.path(d, "VMPA_setas_biol_fishing_Trunk.prm")
fgs <- file.path(d, "SETasGroupsDem_NoCep.csv")

dietmatrix <- load_dietmatrix(prm_biol, fgs, convert_names = TRUE)
#> `.cols` has been renamed and is deprecated, please use `.vars`
agemat <- prm_to_df(prm_biol = prm_biol, fgs = fgs,
                    group = get_age_acronyms(fgs = fgs),
                    parameter = "age_mat")

sp_overlap <- calculate_spatial_overlap(biomass_spatial = ref_bio_sp,
                                        dietmatrix = dietmatrix,
                                        agemat = agemat)