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Calculate Species Co-occurrence Matrices Based on Time Slice Overlap

comp_slice_occ_cooccurr.Rd

This auxiliary function computes species-by-species co-occurrence matrices for each time slice based on shared site occupancy. Two species are considered to co-occur if they are found at the same site during the same time slice. The resulting matrices quantify how many sites each pair of species shares, which can be used to calculate trait distances among co-occurring species.

Usage

comp_slice_occ_cooccurr(
  spp_slice,
  df.occ,
  species = "species",
  Max.age = "Max.age",
  Min.age = "Min.age"
)

Arguments

spp_slice

A named list where each element contains a character vector of species names present in a given time slice. Names of list elements should be time slice identifiers (typically numeric values). Usually generated by calc_spp_slice().

df.occ

A data frame containing fossil occurrence records with at least four columns: species names, minimum age, maximum age, and site location ID. Each row represents a single occurrence record at a specific site. Column names should match the parameters below.

species

Character. The name of the column in df.occ containing species identifiers. Default is "species".

Max.age

Character. The name of the column in df.occ containing the maximum (oldest) age estimate for each occurrence record. Default is "Max.age".

Min.age

Character. The name of the column in df.occ containing the minimum (youngest) age estimate for each occurrence record. Default is "Min.age".

Value

A list with length equal to the number of time slices in spp_slice. Each element is a square matrix (species × species) where:

  • Row and column names are species names

  • Diagonal elements represent the number of sites where each species occurs

  • Off-diagonal elements represent the number of shared sites between pairs of species

  • Values of 0 indicate no site overlap between species pairs