CpD: Calculates the rate of accumulation of phylogenetic diversity...

In treesliceR: To Slice Phylogenetic Trees and Infer Evolutionary Patterns Over Time

Calculates the rate of accumulation of phylogenetic diversity (CpD) over time slices

Description

This function estimates the rates of accumulation of phylogenetic diveristy (CpD) over time for inputted assemblages.

Usage

CpD(tree, n, mat, criterion = "my", pDO = 5, ncor = 0)

Arguments

tree	phylo. An ultrametric phylogenetic tree in the "phylo" format.
n	numeric. A numeric value indicating the number of temporal slices (method = 1) or the time interval in million years (or phylogenetic diversity) among the tree slices (method = 2). Default is 1.
mat	matrix. A presence/absence matrix containing all studied species and sites.
criterion	character string. The method for cutting the tree. It can be either "my" (million years) or "PD" (accumulated phylogenetic diversity). Default is "my".
pDO	numeric. A value indicating the numeric proportion to define the temporal origin at which the phylogenetic diversity (PD) started to accumulate in a given assemblage. Default is 5%.
ncor	numeric. A value indicating the number of cores the user wants to parallelize. Default is 0.

Details

Parallelization

Users are advised to check the number of available cores within their machines before running parallel programming.

Value

The function returns a data frame containing the assemblages' rates of cumulative phylogenetic diversity (CpD), their total phylogenetic diversity (PD), and their PD origin (pDO).

Author(s)

Matheus Lima de Araujo [e-mail]

See Also

Other cumulative phylogenetic rates analysis: CpE(), CpB(), CpB_RW()

Examples

# Generate a random tree
tree <- ape::rcoal(20)

# Create a presence-absence matrix
mat <- matrix(sample(c(1,0), 20*10, replace = TRUE), ncol = 20, nrow = 10)
colnames(mat) <- tree$tip.label

# Calculate the CpD for 100 tree slices
CpD(tree, n = 100, mat = mat)

treesliceR documentation built on Sept. 11, 2024, 8:47 p.m.