DESin: Create Input Files for DES-PyRate

In azizka/speciesgeocodeR: Prepare Species Distributions for the Use in Phylogenetic Analyses

Create Input Files for DES-PyRate

Description

Create the input for the DES model implemented in PyRate from tables of fossil and current species distributions.

Usage

DESin(x, recent, bin.size, reps = 3, verbose = FALSE)

Arguments

x	a data.frame or the path to a tab delimited table with the fossil data. Column names follow the darwinCore standard: scientificName, earlistAge, latestAge, higherGeography. Each row represents a single fossil with scientificName = taxon name, earliestAge = maximum fossil age, latestAge = minimum fossil age, higherGeography = the area of interest for the DES analyses.
recent	a data.frame or the path to a tab delimited table with the recent distribution data. Column names follow the darwinCore standard: scientificName, higherGeography. Each row represents a taxon with scientificName = taxon name and higherGeography = the area of interest for the DES analyses. If a taxon occurs in both areas, two separated rows are needed, one for each area.
bin.size	numeric. The size of the DES-time bins in the same unit as fossil ages, but usually million years.
reps	numeric. The number of replicated output files. Replication arises from the uncertainty in fossil age. For each replicate the age of the fossil is sampled from a uniform distribution between the earliestAge and the latestAge.
verbose	logical. If TRUE, the progress is reported

Value

An object of the class DESin, which is a list containing the input and output data

Note

See https://github.com/azizka/speciesgeocodeR/wiki for more details and tutorials and

See Also

plot.DESin, summary.DESin, write.DESin

Examples

fos <- data.frame(species= rep(letters[1:4],25),
                  earliestAge = runif(100, min = 60, max = 100),
                  latestAge = runif(100, min = 0, max = 60),
                  area = sort(rep(c("A", "B"), 50)))

rec <- data.frame(species = c(letters[1:4], letters[1:2]),
                  area = c(rep("A",4), rep("B", 2)))

exp1 <- DESin(fos, rec, bin.size = 2, reps = 3)

summary(exp1)
#plot(exp1)

## Not run: 
write.DES.in(exp1, file = "Example1_DES_in")

## End(Not run)

azizka/speciesgeocodeR documentation built on Sept. 5, 2023, 3:45 a.m.