olap_tree_and_meta: Overlap a tree and metadata
In biobakery/anpan: Quantifying Microbial Strain-Host Associations

olap_tree_and_meta

R Documentation

Overlap a tree and metadata

Description

Overlap a tree's leaves with the observations in metadata, returning an intersected tree and metadata data.table.

Usage

olap_tree_and_meta(
  tree_file,
  meta_file,
  covariates,
  offset,
  outcome,
  omit_na = FALSE,
  ladderize = TRUE,
  trim_pattern = NULL,
  verbose = TRUE
)

Arguments

`tree_file`	either a path to a tree file readable by `ape::read.tree()` or an object of class "phylo" that is already read into R. Ignored if `cor_mat` is supplied.
`meta_file`	either a data frame of metadata or a path to file containing the metadata
`covariates`	covariates to account for (as a vector of strings)
`offset`	a variable to include as an offset
`outcome`	the name of the outcome variable
`omit_na`	logical indicating whether to omit incomplete cases of the metadata
`ladderize`	logical indicating whether to run `ape::ladderize()` on the tree before running the model
`trim_pattern`	optional pattern to trim from tip labels of the tree