treesliceR (version 1.0.3)

r_phylo: Calculates the relative value of a phylogenetic index in a temporal sequence of phylogenetic slices.

Description

This function estimates the relative value of a phylogenetic index in a sequence of multiple phylogenetic slices cut from roots to tips.

Usage

r_phylo(tree, n, mat, adj, index = NULL, comp, method, criterion = "my", ncor = 0)

Value

The function returns a list where each object contains a vector (of length "n") with the relative phylogenetic index, from the phylogeny root to the tips, from the inputted assemblage.

Arguments

tree

phylo. An ultrametric phylogenetic tree in the "phylo" format.

n

numeric. A numeric value indicating either 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.

adj

matrix. A square adjacency matrix containing the presence/absence information of all sites and their spatially adjacent ones.

index

character string. The phylogenetic index to be calculated over the phylogenetic slices. It can be set as "PD" (phylogenetic diversity), "PE" (phylogenetic endemism), "PB" (phylogenetic B-diversity), or "PB_RW" (phylogenetic B-diversity range-weighted).

comp

character string. The component of phylogenetic beta-diversity to obtain the relative value. It can be "sorensen", "turnover", or "nestedness". Default is "sorensen".

method

character string. The method for calculating phylogenetic beta-diversity. It can be obtained through a "pairwise" or "multisite" approach. Default is "multisite".

criterion

character string. The method for cutting the tree. It can be either "my" (million years) or "PD" (accumulated phylogenetic diversity). Default is "my".

ncor

numeric. A value indicating the number of cores the user wants to parallel. Default is 0.

Author

Matheus Lima de Araujo

Details

The "adj" argument

Must be filled only for phylogenetic B-diversity ("PB") or it's range weight version ("PB_RW", defined in "index").

Parallelization

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

See Also

Other cumulative phylogenetic rates analysis: CpD(), 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

# Create a random adjacency matrix
adj <- matrix(sample(c(1,0), 10*10, replace = TRUE), ncol = 10, nrow = 10)

# Fill the diagonals with 1
diag(adj) <- 1

# Calculate the relative PD for 100 slices
rPD <- r_phylo(tree, n = 100, mat = mat, index = "PD")
# Plot the relative PD of the first assemblage
plot(rPD[[1]])

# Calculate the relative PE for 100 slices
rPE <- r_phylo(tree, n = 100, mat = mat, index = "PE")
# Plot the relative PE of the first assemblage
plot(rPE[[1]])

# Calculate the relative PB for 100 slices
rPB <-  r_phylo(tree, n = 100, mat = mat, adj = adj, index = "PB")
# Plot the relative PB of the first assemblage
plot(rPB[[1]])

# Calculate the relative PB_RW for 100 slices
rPB_RW <- r_phylo(tree, n = 100, mat = mat, adj = adj, index = "PB_RW")
# Plot the relative PB_RW of the first assemblage
plot(rPB_RW[[1]])