get.pgls.coefs | R Documentation |
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
get.pgls.coefs(pgls.fits, est=c("t value","Estimate","Pr(>|t|)")[1])
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' |
A list of PGLS coeficients (lists of estimates and t-values) organized by coeficient-named bins
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')
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