RRphylo (version 3.0.0)

StableTraitsR: Run StableTraits from within R

Description

This function runs StableTraits and StableTraitsSum (Elliot and Mooers 2014) from within the R environment and returns its output into the workspace.

Usage

StableTraitsR(tree,y,path,output=NULL,aces=NULL,argST=NULL,argSTS=NULL)

Value

The function returns a 'list' containing the output of StableTraits and StableTraitsSum.

$progress a table reporting the DIC and PRSF diagnostics.

$rates_tree a copy of the original tree with branch lengths set to the evolutionary rate imputed by the stable reconstruction. Specifically, each branch length is equal to the absolute difference in the stable reconstruction occurring on that branch divided by the square root of the input branch length.

$rates the original branch lengths, evolutionary rates, node height and (optionally) scaled branch lengths.

$aces the median estimates of ancestral states and stable parameters along with the 95% credible interval.

$brownian_tree if "brownian" is TRUE in

argSTS, a copy of the original tree with branch lengths set such that the Brownian motion reconstruction of the character on this tree is approximately the same as the stable ancestral reconstruction.

$ace.prior.values if aces is specified, the function returns a dataframe containing the corresponding node number on the

RRphylo tree for each node, the original (preset) and the estimated values, and the 95% credible interval.

Arguments

tree

a phylogenetic tree. The tree needs not to be either ultrametric or fully dichotomous.

y

a named vector of phenotypic trait.

path

the folder path where the StableTraits output will be stored. Notice that the input tree and data (modified automatically if the original tree is not fully dichotomous or if aces are specified) will be stored in this folder as well.

output

name of the output to be returned, if unspecified it will be named "output".

aces

a named vector of ancestral character values at nodes specified in advance. Names correspond to the nodes in the tree.

argST

a list of further arguments passed to StableTraits. If the argument has no value (for example "brownian") it must be specified as TRUE.

argSTS

list of further arguments passed to StableTraitsSum. If the argument has no value (for example "brownian") it must be specified as TRUE.

Author

Silvia Castiglione, Carmela Serio, Pasquale Raia

Details

The StableTraits software is available at https://mickelliot.com/, along with instructions for compilation. Once it is installed, the user must set as R working directory the folder where the StableTraits software are installed. Further information about the arguments and outputs of StableTraits and StableTraitsSum can be found at https://mickelliot.com/. StableTraitsR automatically recognizes which Operating System is running on the computer (it has been tested successfully on MacOS and Windows machines).

References

Elliot, M. G., & Mooers, A. Ø. (2014). Inferring ancestral states without assuming neutrality or gradualism using a stable model of continuous character evolution. BMC evolutionary biology, 14: 226. doi.org/10.1186/s12862-014-0226-8

Examples

if (FALSE) {
library(ape)
library(phytools)

# Set as working directory the folder where StableTraits software are stored
# setwd("~/StableTraits")

dir.create("Analyses")
rtree(100)->tree
fastBM(tree)->y
c(1,2,3)->acev
sample(Ntip(tree)+seq(1:Nnode(tree)),3)->names(acev)
StableTraitsR(tree,y,path="Analyses/",output="my_output",aces=acev,
argST=list(iterations=500000,chains=4),argSTS=list(brownian=TRUE))->STr
}