Tip-based in-situ diversification metrics

Usage

calc_insitu_diversification(
  W,
  tree,
  ancestral.area,
  biogeo,
  diversification = "jetz",
  type = "equal.splits"
)

Arguments

W: Assemblage occurrence matrix, rows are assemblages and columns are species
tree: Phylogenetic tree in newick format
ancestral.area: One column data frame indicating the Ecoregion of occurrence of each node (rows)
biogeo: Data frame with one column indicating the Ecoregion of each assemblage
diversification: Character indicating the tip-based diversification metric to be calculated. Default is "jetz"
type: Character indicating the type of calculation to be used in the calculation of tip-based metric, "equal-splits" is the default

Value

A list with the following objects:

Jetz_per_sppJetz tip-based metric of diversification for each species
Jetz_species_siteMatrix containing the values of Jetz tip-based diversification metric for each assemblage
Jetz_harmonic_mean_siteHarmonic mean of Jetz tip-based diversification metric
insitu_Jetz_species_sitesMatrix with model-based Jetz metric for each species in each assemblage
insitu_Jetz_harmonic_mean_siteHarmonic mean of model-based Jetz diversification

Details

model-based measure of diversification is calculated as the proportion of total tip-based diversification metric corresponded only to the branches of a given species that diversified in the current area of occurrence of that species $$Jetz_total \times (ED_div/ED_total)$$

Author

Gabriel Nakamura gabriel.nakamura.souza@gmail.com and Arthur V Rodrigues

Examples

if (FALSE) {
W_toy <- matrix(c(0, 1, 1, 0, 1, 
    1, 0, 1, 0, 1, 
    0, 0, 1, 0, 0),nrow= 3,
    ncol= 5,dimnames=list(c("Comm 1", "Comm 2", "Comm 3"),
                          c(paste("s", 1:5, sep=""))))
data("toy_treeEx")
toy_treeEx                   
biogeo_toy <- data.frame(Ecoregion= c("A", "B", "C"))
ancestral_area_toy <- data.frame(state= c("ABC", "B", "C", "ABC"))
plot(toy_treeEx, show.node.label = TRUE)
calc_insitu_diversification(W = W_toy,
                            tree = toy_treeEx, 
                            ancestral.area = ancestral_area_toy,
                             biogeo = biogeo_toy)
}