Compute mean pairwise distance for each species co-occurring in sites and time slices

Usage

IndivSpec_site_mpd(
  df.TS.TE,
  df.occ,
  time.slice,
  trait,
  round.digits = 1,
  species = "species",
  TS = "TS",
  TE = "TE",
  Max.age = "Max.age",
  Min.age = "Min.age",
  site = "site"
)

Arguments

df.TS.TE: a data frame object containing at least three columns. Species names, origination time and extinction time 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.
trait: Numeric indicating the values of the traits for each species
round.digits: scalar indicating the number of digits for time of origination and time for extinction.
species: character indicating the name of the column of the data frame containing the species name information.
TS: character 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 in df.occ containing the upper age limit for occurrence record.
Min.age: character indicating the name of the column in df.occ containing the lower age limit for occurrence record.
site: character indicating the name of the column in df.occ containing the information on site location.

Value

A data frame containing the name of species, its mean mpd value calculated by each time slice considering all sites in which the species occur in that time slice