pcd_pred: Predicted PCD with species pool

In phyr: Model Based Phylogenetic Analysis

Description

This function will calculate expected PCD from one or two sets of communities (depends on the species pool)

Usage

pcd_pred(comm_1, comm_2 = NULL, tree, reps = 10^3, cpp = TRUE)

Arguments

comm_1	A site by species dataframe or matrix, with sites as rows and species as columns.
comm_2	An optional second site by species data frame. It should have the same number of rows as comm_1. This can be useful if we want to calculate temporal beta diversity, i.e. changes of the same site over time. Because data of the same site are not independent, setting comm_2 will use both communities as species pool to calculate expected PCD.
tree	The phylogeny for all species, with "phylo" as class; or a var-cov matrix.
reps	Number of random draws, default is 1000 times.
cpp	Whether to use loops written with c++, default is TRUE. If you came across with errors, try to set cpp = FALSE. This normally will run without errors, but slower.

Value

A list with species richness of the pool, expected PSV, PSV of the pool, and unique number of species richness across sites.

phyr documentation built on Jan. 13, 2021, 5:40 p.m.