pgls.wrap: A Wrapper for PGLS model

In mmodely: Modeling Multivariate Origins Determinants - Evolutionary Lineages in Ecology

A Wrapper for PGLS model

Description

Print the results of an unfit PGLS model

Usage

pgls.wrap(cd,f,b,l,k,d,all.vars=names(cd$data)[-1], 
           model.no=NA, mtx.out=NA, write=TRUE,print=FALSE)

Arguments

cd	a 'comparative data' object, here created by 'comp.data(phylo, df, gs.clmn)'
f	the model formula (as acharacter string)
b	a list of vectors of upper and lower bounds for kappa, lambda, and delta
l	the fixed or 'ML' value for lambda
k	the fixed or 'ML' value for kappa
d	the fixed or 'ML' value for delta
all.vars	the names of all the variables to be reported
model.no	the model number (can be the order that models were run
mtx.out	should a matrix of the tabular summary results be returned
write	should the matrix of summary results be written to disk?
print	should the matrix of summary results be printed to screen?

Value

A matrix of summary results of a fit PGLS model

Examples

data.path <- system.file("extdata","primate-example.data.csv", package="mmodely")
data <- read.csv(data.path, row.names=1)
data$gn_sp <- rownames(data)

tree.path <- system.file("extdata","primate-springer.2012.tre", package="mmodely")
#5. RAxML phylogram based on the 61199 bp concatenation of 69 nuclear and ten mitochondrial genes.
phyl <- ape::read.tree(tree.path)[[5]]

phyl <- trim.phylo(phylo=phyl, gs.vect=data$gn_sp)

comp <- comp.data(phylo=phyl, df=data)

model <- 'OC ~ mass.Kg + group.size'

pgls.wrap(cd=comp,f=model,b=list(kappa=c(.3,3),lambda=c(.3,3),delta=c(.3,3)), 
           l=1,k=1,d=1,all.vars=names(cd.obj$data)[-1])

mmodely documentation built on May 31, 2023, 6:47 p.m.