comp.data {mmodely} | R Documentation |
Comparative Data
Description
This is a shortcut function that wraps around "comparative.data" for use in the PGLS function.
Usage
comp.data(phylo,df,gn_sp='gn_sp')
Arguments
phylo |
a tre file of the format phylo |
df |
a data.frame with row names matching number and tip labels of 'tree' |
gn_sp |
the column name (e.g. "gn_sp") that indicates how to match df with tree |
Value
a "comparative data" table for use in PGLS modeling
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)
[Package mmodely version 0.2.5 Index]