Compute Mean Pairwise Distances Between Species Cooccurring in Local Assemblages

Usage

assemblage_site_trait_distance_null(
  df.TS.TE,
  df.occ,
  time.slice,
  dist_matrix_trait,
  round.digits = 10,
  species = "species",
  TS = "TS",
  TE = "TE",
  Max.age = "Max.age",
  Min.age = "Min.age",
  site = "site",
  nearest.taxon = c("mpd", "mnnd"),
  nperm = 1000,
  fixedmar = "rows",
  mtype = "prab"
)

Arguments

df.TS.TE: Data frame object containing at least four columns. Species names, origination time, extinction time and a trait value for each species.
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.
time.slice: Numeric. The time interval (in the same units as TS and TE) between consecutive time slices for temporal binning.
dist_matrix_trait: A distance matrix object (class dist or matrix) containing pairwise trait distances between species. Row and column names must match species names in df.TS.TE. If NULL, distances will be computed from the trait column using Euclidean distance.
round.digits: Integer. The number of decimal places to round time slice values. Default is 1. This affects temporal binning precision.
species: Character. The name of the column in df.TS.TE and df.occ containing species identifiers. Default is "species".
TS: Character. The name of the column in df.TS.TE containing origination (first appearance) times for each species. Default is "TS".
TE: Character. The name of the column in df.TS.TE containing extinction (last appearance) times for each species. Default is "TE".
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".
site: Character. The name of the column in df.occ containing site location identifiers. Default is "site".
nearest.taxon: Character, indicating the mean distance to be used. If "mpd" mean pairwise distance will be calculated, if mnnd mean nearest neighbour distance will be computed, considering only the distant to the closest species in the morphospace.
nperm: A scalar, indicating the number of permutations to be used in the null model
fixedmar: Character, stating which row/column sums should be preserved in the assemblage composition matrix (sites in the rows and species in the columns). Options are "none", "rows", "columns" or "both".
mtype: Character, indicanting the type of null model to be performed. "prab" is the option for presence-absence (detection/non-detection) matrix and "count" for matrix with count data.