mv.Precalc {mvMORPH}

Model parameterization for the various mvMORPH functions

Description

This function allows computing the fixed parameters or objects needed by the mvMORPH functions. This could be useful for bootstrap-like computations (see exemple)

Usage

mv.Precalc(tree, nb.traits = 1, scale.height = FALSE, param = list(pivot = "MMD",
            method = c("sparse"), smean = TRUE, model = "OUM"))

Arguments

tree

A "phylo" (or SIMMAP like) object representing the tree for which we want to precalculate parameters.

nb.traits

The number of traits involved in the subsequent analysis.

scale.height

Whether the tree should be scaled to unit length or not.

param

A list of parameters used in the computations (see details)

Details

The mv.Precalc function allows the pre-computation of the fixed parameters required by the different mvMORPH models (e.g., the design matrix, the vcv matrix, the sparsity structure...). In the "param" list you should provide the details about the model fit:

-model name (e.g., "OUM", "OU1")

-method (which kind of algorithm is used for computing the log-likelihood).

-smean (whether there is one ancestral state per trait or per selective regimes - for mvBM only).

Additional parameters can be fixed:

-root (estimation of the ancestral state for the Ornstein-Uhlenbeck model; see ?mvOU).

-pivot (pivot method used by the "sparse" matrix method for computing the log-likelihood; see ?spam).

Value

An object of class "mvmorph.precalc" which can be used in the "precalc" argument of the various mvMORPH functions.

Note

This function is mainly used internally; it is still in development. A misuse of this functions can result in a crash of the R session.

Author(s)

Julien Clavel

See Also

mvMORPH mvOU mvEB mvBM mvSHIFT mvLL

Examples

set.seed(14)
# Generating a random tree
tree<-pbtree(n=50)

# Simulate two correlated traits evolving along the phylogeny according to a
# Ornstein-Uhlenbeck process
alpha<-matrix(c(2,1,1,1.3),2,2)
sigma<-matrix(c(1,0.5,0.5,0.8),2,2)
theta<-c(3,1)
nsim<-50
simul<-mvSIM(tree,param=list(sigma=sigma, alpha=alpha, ntraits=2, theta=theta,
             names_traits=c("head.size","mouth.size")), model="OU1", nsim=nsim)

# Do the pre-calculations
precal<-mv.Precalc(tree,nb.traits=2, param=list(method="sparse",model="OU1", root=FALSE))

mvOU(tree, simul[[1]], method="sparse", model="OU1", precalc=precal,
    param=list(decomp="cholesky"))

### Bootstrap

# Fit the model to the "nsim" simulated datasets
 results<-lapply(1:nsim,function(x){
 mvOU(tree, simul[[x]], method="sparse", model="OU1", precalc=precal,
    param=list(decomp="cholesky"),
    echo=FALSE, diagnostic=FALSE)
 })

### Use parallel package
 library(parallel)
if(.Platform$OS.type == "unix"){
  number_of_cores<-2L # Only working on Unix systems
}else{
  number_of_cores<-1L
} 

 results<-mclapply(simul, function(x){
    mvOU(tree, x, method="sparse", model="OU1", precalc=precal,
       param=list(decomp="cholesky"), echo=FALSE, diagnostic=FALSE)
 }, mc.cores = getOption("mc.cores", number_of_cores))


# Summarize (we use the generic S3 method "logLik" to extract the log-likelihood)
loglik<-sapply(results,logLik)
hist(loglik)