lengthNonZeros: Calculate the species richness of a community
In eliotmiller/labAnalysis: Utility functions for UMSL Plant Biology

Description Usage Arguments Details Value References Examples

Given a vector of abundances or presence/absences from a community data matrix, will calculate the species richness of that community.

1	lengthNonZeros(input.vector)

input.vector

A vector from a community data matrix of abundances.

An internal function to calculate richness of a cdm.

A named vector of species richness.

Miller, Trisos and Farine.

library(geiger)
library(picante)

#simulate tree with birth-death process
tree <- sim.bdtree(b=0.1, d=0, stop="taxa", n=50)

sim.abundances <- round(rlnorm(5000, meanlog=2, sdlog=1))

cdm <- simulateComm(tree, min.rich=10, max.rich=25, abundances=sim.abundances)

#note that with this example, each community in the cdm will be labeled by its richness
apply(cdm, 1, lengthNonZeros)