get.phylo.stats | R Documentation |
This function uses Pagel's lambda, Blombergs k, and Ancestral Character Estimation [ACE] to calculate statistics on a tree given a specified trait.
get.phylo.stats(phylo, data, trait.clmn, gs.clmn='gn_sp',
ace.method='REML',ace.scaled=TRUE, ace.kappa=1)
phylo |
PARAMDESCRIPTION |
data |
PARAMDESCRIPTION |
trait.clmn |
PARAMDESCRIPTION |
gs.clmn |
PARAMDESCRIPTION |
ace.method |
PARAMDESCRIPTION |
ace.scaled |
PARAMDESCRIPTION |
ace.kappa |
PARAMDESCRIPTION |
statistics on a particular trait within a tree (Pagel's lambda, Blomberg's k, and the most ancestral ACE estimate)
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")
phyl <- ape::read.tree(tree.path)[[5]]
get.phylo.stats(phylo=phyl, data=data, trait.clmn='OC',
gs.clmn='gn_sp', ace.method='REML',ace.scaled=TRUE, ace.kappa=1)
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