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

In picante: R tools for integrating phylogenies and ecology

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)

Example output

Loading required package: ape
Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.5-4
Loading required package: nlme
[[1]]
           clump1   clump2a   clump2b    clump4      even
clump2a 0.6382979                                        
clump2b 0.6153846 0.6274510                              
clump4  0.5882353 0.6538462 0.6800000                    
even    0.5098039 0.5200000 0.5555556 0.7407407          
random  0.5769231 0.6037736 0.5185185 0.5490196 0.4800000

[[2]]
           clump1   clump2a   clump2b    clump4      even
clump2a 0.7450980                                        
clump2b 0.7083333 0.7307692                              
clump4  0.5090909 0.6274510 0.6274510                    
even    0.5555556 0.6296296 0.6274510 0.6538462          
random  0.5098039 0.5283019 0.5660377 0.5555556 0.6274510

[[3]]
           clump1   clump2a   clump2b    clump4      even
clump2a 0.7450980                                        
clump2b 0.7058824 0.6250000                              
clump4  0.5964912 0.7200000 0.6122449                    
even    0.5600000 0.5384615 0.4615385 0.7586207          
random  0.4680851 0.6037736 0.5000000 0.4897959 0.5660377

[[4]]
           clump1   clump2a   clump2b    clump4      even
clump2a 0.6538462                                        
clump2b 0.7142857 0.5714286                              
clump4  0.5283019 0.6800000 0.6909091                    
even    0.5000000 0.5769231 0.6785714 0.6909091          
random  0.5357143 0.5600000 0.5714286 0.5384615 0.5098039

[[5]]
           clump1   clump2a   clump2b    clump4      even
clump2a 0.7169811                                        
clump2b 0.7500000 0.7037037                              
clump4  0.6153846 0.6792453 0.8363636                    
even    0.5200000 0.5490196 0.5000000 0.7169811          
random  0.6071429 0.6153846 0.5769231 0.5000000 0.5283019

picante documentation built on May 2, 2019, 6:30 p.m.