Compute mean distance for individual species cooccurring in sites

Usage

IndivSpec_site_distance(
  df.TS.TE,
  df.occ,
  time.slice,
  dist.trait,
  nearest.taxon,
  group = NULL,
  group.focal.compare = NULL,
  type.comparison = NULL,
  trait = NULL,
  round.digits = 1,
  species = "species",
  TS = "TS",
  TE = "TE",
  Max.age = "Max.age",
  Min.age = "Min.age",
  site = "site"
)

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 object containing the occurrence records for each species. This must have at least a column indicating the name of species, its minimum and maximum age estimate, and its site location ID.
time.slice: Scalar indicating the time interval between consecutive time slices.
dist.trait: A dist object containing the clade pairwise distance matrices. The name of the clades in this object must be equal to the name of the clades in df.TS.TE data frame.
nearest.taxon: A scalar indicating the number of nearest species/genus that will be used. 1 computes mnnd metric and the option "all" computes mpd.
group: Character indicating the name of the column that contain the groups that will be used in comparison.
group.focal.compare: Character vector indicating the focal (first element) and comparison (second element) groups used in the calculation. If NULL, the default, the metrics will be calculated using all clades.
type.comparison: Character. It can be "between" to compute distances only between species/genus of two groups or "within" to calculate distance only inside the focal group. If null the distance is computed considering all clades together
trait: Character indicating the name of the column containing values of the traits for each species. If NULL, the default, the user must provide a distance matrix.
round.digits: Scalar indicating the precision of time slices.
species: Character indicating the name of the column of the data frame containing the species name information.
TS: haracter indicating the name of the columns of the data frame containing the information on origination time.
TE: Character indicating the name of the column of the data frame containing the information on extinction time.
Max.age: Character indicating the name of the column containing the upper age limit for occurrence record.
Min.age: Character indicating the name of the column containing the lower age limit for occurrence record.
site: Character indicating the name of the column containing the information on site location.