Diversification-based PD and PE

Usage

calc_insitu_metrics(W, tree, ancestral.area, biogeo, PD = TRUE, PE = TRUE)

Arguments

W: Occurrence matrix, rows are assemblages and columns are species
tree: Phylogenetic hipothesis in newick format
ancestral.area: One column data frame with nodes in rows and one column indicating the occurrence area of nodes
biogeo: One columns data frame with rows indicating assemblages and one column indicating the biome/ecoregion of each assemblage
PD: Logical, if TRUE (default) PD~in-situ~ will be computed
PE: Logical, if TRUE (default) PE~in-situ~ will be computed

Value

A data frame containing the values of original PD and PE and also their in-situ diversification based version

Details

This function computes two modified versions of Phylogenetic Diversity (PD) and Phylogenetic endemism by considering in the calculation the in-situ diversification. the PD~in-situ~ and PE~in-situ~ are calculated by coupling in the calculation an ancetral area reconstruction that divide the phylogenetic tree in two parts, one that correspond to dispersion events and another that correspond to in-situ diversification events. We use the in-situ diversification part to calculate both Db-PD and Db-PE

Author

Gabriel Nakamura gabriel.nakamura.souza@gmail.com

Examples

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")
 biogeo_toy <- data.frame(Ecoregion= c("A", "B", "C"))
 ancestral_area_toy <- data.frame(state= c("ABC", "B", "C", "ABC"))
 assemblage_phylo_metrics <- calc_insitu_metrics(W_toy,
      toy_treeEx,
      ancestral_area_toy, 
      biogeo_toy)