Standardized effect size of PD
Standardized effect size of phylogenetic diversity (Faith's PD) in communities.
ses.pd(samp, tree, null.model = c("taxa.labels", "richness", "frequency",
"sample.pool", "phylogeny.pool", "independentswap", "trialswap"),
runs = 999, iterations = 1000, include.root=TRUE) samp |
Community data matrix |
tree |
Phylogeny (phylo object) |
null.model |
Null model to use (see Details section for description) |
runs |
Number of randomizations |
iterations |
Number of iterations to use for each randomization (for independent swap and trial null models) |
include.root |
Include distance to root node in calculation of PD (see documentation in |
Currently implemented null models (arguments to null.model):
Shuffle taxa labels across tips of phylogeny (across all taxa included in phylogeny)
Randomize community data matrix abundances within samples (maintains sample species richness)
Randomize community data matrix abundances within species (maintains species occurence frequency)
Randomize community data matrix by drawing species from pool of species occurring in at least one community (sample pool) with equal probability
Randomize community data matrix by drawing species from pool of species occurring in the phylogeny (phylogeny pool) with equal probability
Randomize community data matrix with the independent swap algorithm (Gotelli 2000) maintaining species occurrence frequency and sample species richness
Randomize community data matrix with the trial-swap algorithm (Miklos & Podani 2004) maintaining species occurrence frequency and sample species richness
A data frame of results for each community
ntaxa |
Number of taxa in community |
pd.obs |
Observed PD in community |
pd.rand.mean |
Mean PD in null communities |
pd.rand.sd |
Standard deviation of PD in null communities |
pd.obs.rank |
Rank of observed PD vs. null communities |
pd.obs.z |
Standardized effect size of PD vs. null communities (= (pd.obs - pd.rand.mean) / pd.rand.sd) |
pd.obs.p |
P-value (quantile) of observed PD vs. null communities (= mpd.obs.rank / runs + 1) |
runs |
Number of randomizations |
Steven Kembel <steve.kembel@gmail.com>
Webb, C.O., Ackerly, D.D., and Kembel, S.W. 2008. Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Version 4.0.1. http://www.phylodiversity.net/phylocom/.
Proches, S., Wilson, J.R.U. and Cowling, R.M. 2006. How much evolutionary history in a 10 x 10m plot? Proceedings of Royal Society of London B, Biological Sciences 273:1143-1148.
data(phylocom) ses.pd(phylocom$sample, phylocom$phylo, null.model="taxa.labels", runs=99)
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