Tip-based in-situ diversification metrics

Usage

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

Arguments

W: A species occurrence (assemblage) matrix. Rows represent assemblages (sites) and columns represent species.
tree: A phylogenetic tree object (class phylo).
ancestral.area: A one-column data frame indicating the ecorregion of occurrence of each node (rows).
biogeo: A data frame with one column indicating the ecoregion of each assemblage (row).
type: Character string indicating the type of evolutionary distinctiveness (ED) metric to be used. Options are "equal.splits" (default) or "fair.proportion".

Value

A named list containing the following elements (if available):

jetz_site_sp: Site-by-species matrix of DR diversification rates.
jetz_comm_mean: Harmonic mean of DR diversification rates per site.
insitu_site_sp: Site-by-species matrix of \(DR_in-situ\) diversification rates.
insitu_comm_mean: Harmonic mean of \(DR_in-situ\) diversification rates per site (ignoring zeros when specified).
prop_site_sp: Site-by-species matrix of proportional diversification rates.
prop_comm_mean: Arithmetic mean of proportional diversification rates per site.

Details

This function calculates three related diversification metrics:

Jetz diversification rate (DR_jetz): The inverse of the evolutionary distinctiveness (ED) metric for each species across the full phylogeny. This is the same as described in Jetz et al (2012)
```
    \deqn{
           DR_{i} = (\sum_{j=1}^{N_i}\cdot l_j \cdot 1/2^{j-1})^{-1}
        }
```
In-situ diversification rate (DR_insitu): In situ measure of diversification calculated as the inverse of ED, but restricted to the portion of a species' branches that diversified in the region (informed in biogeo argument) matching the assemblage.
Proportional diversification rate (DR_prop): The fraction of diversification that occurred in a given ecoregion (informed in biogeo argument), calculated as the proportion of ED in that region relative to the total ED, multiplied by the species’ total diversification rate (DR_jetz).

For assemblage-level summaries, site-by-species matrices are generated for each metric, and site-level means are calculated as:

Harmonic mean (Jetz and in-situ): computed across species in each assemblage. Zeros in the in-situ matrix are ignored in the harmonic mean calculation to account only for species with diversification in situ.
Arithmetic mean (proportional rates): used for proportional diversification rates.

Examples

if (FALSE) { # \dontrun{
# Example with a random tree and toy data
library(ape)
tree <- rcoal(5)
W <- matrix(c(1,0,1,1,1,0,1,1,0,1 ), nrow=2, byrow=TRUE,
            dimnames = list(c("site1","site2"), tree$tip.label))
biogeo <- data.frame(region=c("A","B"))
ancestral.area <- data.frame(region=rep("A", tree$Nnode))

res <- calc_insitu_diversification(W, tree, ancestral.area, biogeo)
str(res)
} # }