taxatree_models: Statistical modelling for individual taxa across multiple...

In david-barnett/microViz: Microbiome Data Analysis and Visualization

Statistical modelling for individual taxa across multiple ranks

Description

taxatree_models runs tax_model on every taxon at multiple taxonomic ranks (you choose which ranks with the plural ranks argument). It returns the results as a named nested list of models attached to a psExtra object. One list per rank, one model per taxon at each rank.

The result can then be used with taxatree_models2stats to extract a dataframe of statistics for use with taxatree_plots.

Usage

taxatree_models(
  ps,
  ranks = NULL,
  type = "lm",
  variables = NULL,
  formula = NULL,
  use_future = FALSE,
  checkVars = TRUE,
  checkNA = "warning",
  verbose = "rank",
  trans = "identity",
  trans_args = list(),
  ...
)

Arguments

ps	phyloseq object or psExtra
ranks	vector of rank names at which to aggregate taxa for modelling
type	name of regression modelling function, or the function itself
variables	vector of variable names, to be used as model formula right hand side. If variables is a list, not a vector, a model is fit for each entry in list.
formula	Right hand side of a formula, as a formula object or character string. Or a list of these. (alternative to variables argument, do not provide both)
use_future	if TRUE parallel processing with future is possible, see details of ?tax_model.
checkVars	check variance of variables?
checkNA	check variables for NAs?
verbose	message about progress: "rank" only notifies which rank is being processed; TRUE notifies you about each taxon being processed; FALSE for no messages.
trans	name of tax_transform transformation to apply to aggregated taxa before fitting statistical models
trans_args	named list of any additional arguments to tax_transform e.g. list(zero_replace = "halfmin")
...	extra arguments are passed directly to modelling function

See Also

tax_model for more details and examples

taxatree_plots for how to plot the output of taxatree_models

david-barnett/microViz documentation built on April 17, 2025, 4:25 a.m.