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Calculate Regional Individual Species Coexistence Across Time Slices

IndivSpec_regional_coex.Rd

This function computes the number of coexisting species at each time slice in a regional scale analysis. It divides the temporal range into discrete intervals and counts how many species overlap in each interval based on their origination (TS) and extinction (TE) times.

Usage

IndivSpec_regional_coex(
  df.TS.TE,
  time.slice,
  round.digits = 1,
  species = "species",
  TS = "TS",
  TE = "TE"
)

Arguments

df.TS.TE

A data frame containing species temporal data with at least three columns: species names, origination times, and extinction times.

time.slice

Numeric. The time interval (in the same units as TS and TE) between consecutive time slices.

round.digits

Integer. The number of decimal places to round time slice values. Default is 1. This affects the precision of temporal binning.

species

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

TS

Character. The name of the column in df.TS.TE containing origination (start) times for each species. Default is "TS".

TE

Character. The name of the column in df.TS.TE containing extinction (end) times for each species. Default is "TE".

Value

A data frame with three columns:

time.slice

Numeric. The time point representing each slice.

species

Character. The name of each species.

n.coexistence

Numeric. The number of species coexisting in each time slice for all species.

Examples

# Example with fossil data
df <- data.frame(
  species = c("sp1", "sp2", "sp3"),
  TS = c(100, 90, 80),
  TE = c(50, 40, 30)
)
IndivSpec_regional_coex(df, time.slice = 10)
#>   time.slice species n.coexistence
#> 1        100     sp1             0
#> 2         90     sp1             1
#> 3         90     sp2             1
#> 4         40     sp2             1
#> 5         40     sp3             1
#> 6         30     sp3             0