Statistical modelling for individual taxa across multiple ranks

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.

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

Statistical modelling for individual taxa across multiple ranks

Arguments

See also