random.evolvability.test: Randomization test for phylogenetic structuring in...

In RRphylo: Phylogenetic Ridge Regression Methods for Comparative Studies

Randomization test for phylogenetic structuring in evolvability

Description

The function is a wrapper around the function MeanMatrixStatistics from the package evolqg (Melo et al. 2015). It estimates ancestral character at internal nodes either according to Brownian Motion or by means of RRphylo (see the argument node.estimation), then performs MeanMatrixStatistics to calculate: Mean Squared Correlation, ICV, Autonomy, ConditionalEvolvability, Constraints, Evolvability, Flexibility, Pc1Percent, and Respondability. To assess the importance of phylogenetic structuring (signal) on Respondability Evolvability, and Flexibility. The function performs a randomization test by randomly shuffling the species on tree and replicating the analyses nsim times. A p-value is computed by contrasting the real metrics to the ones derived by randomization.

Usage

random.evolvability.test(tree,data,node.estimation=c("RR","BM"),
  aces=NULL,iterations=1000,nsim=100,clus=0.5)

Arguments

tree	a phylogenetic tree. The tree needs not to be ultrametric or fully dichotomous.
data	a matrix or data.frame of phenotypic data having species as rownames
node.estimation	specify the method to compute ancestral character at nodes. It can be one of "RR", to compute ancestral states by mean of RRphylo, or "BM", to use phytools' function fastAnc (Paradis & Schliep 2019) to estimate ancestral characters at nodes according to Brownian Motion.
aces	a named matrix of known ancestral character values at nodes. Names correspond to the nodes in the tree.
iterations	the iterations argument to be indicated in MeanMatrixStatistics
nsim	the number of simulations to be performed for the randomization test, by default nrep is set at 100.
clus	the proportion of clusters to be used in parallel computing. To run the single-threaded version of NOME set clus = 0.

Value

The function returns a list object including ($means) the mean values for all statistics as produced by MeanMatrixStatistics and ($means) the significance levels for Respondability, Evolvability, and Flexibility.

Author(s)

Silvia Castiglione, Gabriele Sansalone, Pasquale Raia

References

Melo, D., Garcia, G., Hubbe, A., Assis, A. P., & Marroig, G. (2015). EvolQG-An R package for evolutionary quantitative genetics. F1000Research, 4.

Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods in Ecology and Evolution, 3, 217-223.

See Also

RRphylo vignette

Examples

 ## Not run: 
 library(ape)
 library(phytools)

 rtree(30)->tree
 fastBM(tree,nsim=4)->y

 random.evolvability.test(tree=tree,data=y,node.estimation="RR")->rEvTest

    
## End(Not run)

RRphylo documentation built on June 7, 2023, 5:49 p.m.