CpR_sensitivity {treesliceR} | R Documentation |
Runs a sensitivity analysis for rates of accumulation of a given phylogenetic index
Description
This function allows the evaluation of the sensitivity of the estimated rates of accumulation of a given phylogenetic index (e.g., CpD()
, CpE()
, CpB()
, CpB_RW()
) to the number of slices inputted by the user.
Usage
CpR_sensitivity(tree, vec, mat, adj, rate, samp, comp, method, criterion, ncor)
Arguments
tree |
phylo. An ultrametric phylogenetic tree in the "phylo" format. |
vec |
numeric vector. A numeric vector containing a series of numbers of slices. |
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. |
rate |
character string. The desired cumulative phylogenetic rate to be assessed, which can be the phylogenetic diversity (CpD), phylogenetic endemism (CpE), phylogenetic B-diversity (CpB), or phylogenetic B-diversity range-weighted (CpB_RW). Default is NULL, but must be filled with "CpD", "CPE", "CpB_RW", or "CpB". |
samp |
numeric. The number of assemblages, or sites, to be sampled to make the sensitivity analysis. |
comp |
character string. The component of beta-diversity that the user wants to calculate the CpB. It can be either "sorensen", turnover" or "nestedness". This argument works only when "rate = CpB". Default is "sorensen". |
method |
character string. The method for calculating the CpB-rate. It can be either "pairwise" or "multisite". This argument works only when the argument "rate" is set to run for "CpB" or "CpB_RW". 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 parallelize. Default is 0. |
Details
Parallelization
Users are advised to check the number of available cores within their machines before running parallel programming.
Plotting
For plotting the sensitivity analysis output users can use CpR_sensitivity_plot()
.
Value
This function returns a data frame containing the sensitivity analysis for a given rate of accumulation of a phylogenetic index. This outputted data frame contains, for each row or assemblage, a column with the rate value assessed for each inputted number of slices.
Author(s)
Matheus Lima de Araujo matheusaraujolima@live.com
References
See the tutorial on how to use this function on our website.
See Also
Other cumulative phylogenetic index rate 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
# Calculate the CpD for 100 tree slices
CpD(tree, n = 100, mat = mat)
# Create a vector of number of slices
vec <- c(25, 50, 75, 100, 125, 150)
# Calculate the sensitivity of the CpD
CpR_sensitivity(tree, vec, mat, rate = "CpD", samp = 5)