mmodely (version 0.2.5)

get.pgls.coefs: Get coeficients from a list of PGLS model-fits (from each selected subset)

Description

Post PGLS model selection, the list of all possible PGLS model fits can be subset and passed to this function, which harvests out the coefficients or t-values for each model into bins for the coefficients

Usage

get.pgls.coefs(pgls.fits, est=c("t value","Estimate","Pr(>|t|)")[1])

Value

A list of PGLS coeficients (lists of estimates and t-values) organized by coeficient-named bins

Arguments

pgls.fits

a list of PGLS models output from 'pgls' or 'pgls.report'

est

a character string indicating if Estimate or t value should be used as data points in the plot, default is 'Estimate'

Examples

data.path <- system.file("extdata","primate-example.data.csv", package="mmodely")
data <- read.csv(data.path, row.names=1)
pvs <- names(data[3:5])
data$gn_sp <- rownames(data)

tree.path <- system.file("extdata","primate-springer.2012.tre", package="mmodely")
phyl <- ape::read.tree(tree.path)[[5]]

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

mods <- get.model.combos(predictor.vars=pvs, outcome.var='OC', min.q=2)

PGLSi <- pgls.iter(models=mods, phylo=phyl, df=data, k=1,l=1,d=1) 

coefs.objs <- get.pgls.coefs(PGLSi$fits, est='Estimate')