phylocomr (version 0.3.4)

ph_aot: aot

Description

AOT conducts univariate and bivariate tests of phylogenetic signal and trait correlations, respectively, and node-level analyses of trait means and diversification.

Usage

ph_aot(
  traits,
  phylo,
  randomizations = 999,
  trait_contrasts = 1,
  ebl_unstconst = FALSE
)

Value

a list of data.frames

Arguments

traits

(data.frame/character) trait data.frame or path to traits file. required. See Details.

phylo

(character/phylo) One of: phylogeny as a newick string (will be written to a temp file) - OR path to file with a newick string - OR a an ape phylo object. required.

randomizations

(numeric) number of randomizations. Default: 999

trait_contrasts

(numeric) Specify which trait should be used as 'x' variable for contrasts. Default: 1

ebl_unstconst

(logical) Use equal branch lengths and unstandardized contrasts. Default: FALSE

Taxon name case

In the traits table, if you're passing in a file, the names in the first column must be all lowercase; if not, we'll lowercase them for you. If you pass in a data.frame, we'll lowercase them for your. All phylo tip/node labels are also lowercased to avoid any casing problems

Details

See phylocomr-inputs for expected input formats

Examples

if (FALSE) {
traits_file <- system.file("examples/traits_aot", package = "phylocomr")
phylo_file <- system.file("examples/phylo_aot", package = "phylocomr")

# from data.frame
traitsdf_file <- system.file("examples/traits_aot_df",
  package = "phylocomr")
traits <- read.table(text = readLines(traitsdf_file), header = TRUE,
  stringsAsFactors = FALSE)
phylo_str <- readLines(phylo_file)
(res <- ph_aot(traits, phylo = phylo_str))

# from files
traits_str <- paste0(readLines(traits_file), collapse = "\n")
traits_file2 <- tempfile()
cat(traits_str, file = traits_file2, sep = '\n')
phylo_file2 <- tempfile()
cat(phylo_str, file = phylo_file2, sep = '\n')
(res <- ph_aot(traits_file2, phylo_file2))
}