trait.asm: Produces simulated communities based on species attributes

In pez: Phylogenetics for the Environmental Sciences

Produces simulated communities based on species attributes

Description

trait.asm calculates phylogenetic biodiversity metrics

Usage

trait.asm(
  a,
  m = 1000,
  meanSR = NULL,
  interval = c(0.001, 10),
  exponential = TRUE,
  Pscale = 1
)

Arguments

a	species attributes (e.g., traits like body size)
m	number of communities to be simulated
meanSR	target mean species richness across simulated communities
interval	adjust to obtain meanSR
exponential	use the exponential distribution when simulating communities
Pscale	adjust this value when not using the exponential distribution in order to scale the species richnesses in the simulated communities

Details

Simulates a set of communties based on the supplied attribute (trait) where larger values make it more likely for species to be in the communities.

Value

Y presence/absence matrix

P probabilities

a the supplied trait

exponential if the exponential distribution was used

meanSR supplied meanSR value

std estimated sd

Author(s)

M.R. Helmus

References

Helmus M., Mercado-Silva N. & Vander Zanden M.J. (2013). Subsidies to predators, apparent competition and the phylogenetic structure of prey communities. Oecologia, 173, 997-1007.

Examples

## Not run: 
 data(laja)
 trait.asm(laja$fish.pref)

## End(Not run)

pez documentation built on Aug. 29, 2025, 5:33 p.m.