phyEstimate: Phylogenetic estimation of traits for unobserved taxa

In picante: Integrating Phylogenies and Ecology

Description

Uses phylogenetic ancestral state reconstruction to estimate trait values for unobserved taxa.

Usage

phyEstimate(phy, trait, method="pic", ...)
phyEstimateDisc(phy, trait, best.state=TRUE, cutoff=0.5, ...)

Arguments

phy	phylo object
trait	vector or data.frame containing trait values
method	ancestral state estimation method used by ace (default="pic")
best.state	estimate best-supported trait state for discrete variables? (default=TRUE)
cutoff	support cutoff required to declare a best.state
...	Additional arguments passed to ace

Details

These functions use phylogenetic ancestral state estimation to infer trait values for novel taxa on a phylogenetic tree, for continuous (phyEstimate) and discrete (phyEstimateDisc) traits.

The required input is a phylogenetic tree object plus a vector or data.frame containing estimated trait values for a subset of the taxa in the phylogenetic tree. Trait values for taxa that are present in the tree but not the trait data will be estimated using ancestral state estimation (Garland and Ives 2000). Briefly, for each taxon present in the tree but not the trait data, the phylogeny is rerooted at the most recent common ancestor of the novel taxon and the rest of the phylogeny, and the trait value of the novel taxon is estimated from the reconstructed trait value at the root of the rerooted phylogeny.

For phyEstimateDisc, the state with the highest support will be reported if argument best.state=TRUE. If the best-supported state's support is less than the specified cutoff, no best state is reported and a NA value will be returned.

Value

phyEstimate produces a data frame with columns:

est	Estimated trait value
se	Standard error of estimated trait value

phyEstimateDisc produces a data frame with columns:

states 1..N	A column with statistical support is produced for each discrete trait state
estimated.state	If best.state=TRUE, a column with the state with the highest support
estimated.state.support	Statistical support for the state with the highest support

Author(s)

Steven Kembel <[e-mail]>

References

T. Garland Jr., and A.R. Ives. 2000. Using the past to predict the present: confidence intervals for regression equations in phylogenetic comparative methods. American Naturalist 155:346364.

S.W. Kembel, M. Wu, J.A. Eisen, and J.L. Green. 2012. Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance. PLoS Computational Biology 8(10):e1002743.

Examples

#generate random phylogeny
randtree <- rcoal(50)
#simulate trait evolution for a subset of taxa on phylogeny
randtraits <- sample(rTraitCont(randtree, sigma=10, root.value=100), 40)
#estimate trait values for "missing" taxa using PIC method
phyEstimate(randtree, randtraits, method="pic")

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
     estimate        se
t38  82.21203 1.1321776
t46  67.75518 0.5086305
t4   67.85972 0.4911713
t5   77.38010 0.6095390
t47  78.68098 0.5766860
t37  79.44457 0.1585342
t1   98.64342 0.3089327
t26 105.33306 0.4335564
t20 105.57074 0.4493353
t23 104.20200 1.0610661

picante documentation built on July 1, 2020, 10:57 p.m.