phylosor.rnd: Null PhyloSor values of phylogenetic beta-diversity

In skembel/picante: Integrating Phylogenies and Ecology

Null PhyloSor values of phylogenetic beta-diversity

Description

PhyloSor values obtained by randomization for different choices of null models

Usage

phylosor.rnd(samp,tree, cstSor=TRUE, null.model=c("taxa.labels",
    "frequency","richness","independentswap","trialswap"),
    runs=999, iterations=1000)

Arguments

samp	Community data matrix
tree	Object of class phylo - a rooted phylogeny
cstSor	TRUE if the Sorensen similarity should be kept constant across communities. FALSE otherwise
null.model	Null model to use (see Details section)
runs	Number of randomizations
iterations	Number of iterations to use for each randomization (for independent swap and trial null models)

Details

Currently implemented null models (arguments to null.model):

taxa.labels

Shuffle community data matrix labels. Maintains species richness in each community and species shared between communities. Should be used with cstSor=TRUE

frequency

Randomize community data matrix abundances within species (maintains species occurence frequency). Does not maintain species richness in communities nor species shared between communities. Can only be used with cstSor=FALSE

richness

With cstSor=TRUE: For each pair of community, maintains species richness in each community and species shared between communities. Sample in the species pool with equal probability; With cstSor=FALSE: Maintains species richness in each community, does not maintain species shared between communities. Sample in the species pool with equal probability

independentswap

Randomize community data matrix with the independent swap algorithm (Gotelli 2000) maintaining species occurrence frequency and sample species richness. Can only be used with cstSor=FALSE

trialswap

Randomize community data matrix with the trial-swap algorithm (Miklos & Podani 2004) maintaining species occurrence frequency and sample species richness. Can only be used with cstSor=FALSE

Value

A list of length the number of runs. Each element of the list is a distance matrix containing the PhyloSor values of phylogenetic beta-diversity obtained by randomization

Author(s)

Helene Morlon <[e-mail]> and Steven Kembel <[e-mail]>

References

Bryant, J.B., Lamanna, C., Morlon, H., Kerkhoff, A.J., Enquist, B.J., Green, J.L. 2008. Microbes on mountainsides: Contrasting elevational patterns of bacterial and plant diversity. Proceedings of the National Academy of Sciences 105 Supplement 1: 11505-11511

See Also

phylosor, randomizeMatrix

Examples

data(phylocom)
phylosor.rnd(phylocom$sample,phylocom$phylo,cstSor=TRUE,null.model="richness",runs=5)

skembel/picante documentation built on July 19, 2023, 7:27 a.m.