step_taxonomy: Taxonomic clades feature generator

In scimo: Extra Recipes Steps for Dealing with Omics Data

Taxonomic clades feature generator

Description

Extract clades from a lineage, as defined in the {yatah} package.

Usage

step_taxonomy(
  recipe,
  ...,
  role = "predictor",
  trained = FALSE,
  rank = NULL,
  res = NULL,
  keep_original_cols = FALSE,
  skip = FALSE,
  id = rand_id("taxonomy")
)

## S3 method for class 'step_taxonomy'
tidy(x, ...)

Arguments

recipe	A recipe object. The step will be added to the sequence of operations for this recipe.
...	One or more selector functions to choose variables for this step. See selections() for more details.
role	For model terms created by this step, what analysis role should they be assigned? By default, the new columns created by this step from the original variables will be used as predictors in a model.
trained	A logical to indicate if the quantities for preprocessing have been estimated.
rank	The desired ranks, a combinaison of "kingdom", "phylum", "class", "order", "family", "genus", "species", or "strain". See yatah::get_clade() for more details.
res	This parameter is only produced after the recipe has been trained.
keep_original_cols	A logical to keep the original variables in the output. Defaults to FALSE.
skip	A logical. Should the step be skipped when the recipe is baked by bake()? While all operations are baked when prep() is run, some operations may not be able to be conducted on new data (e.g. processing the outcome variable(s)). Care should be taken when using skip = TRUE as it may affect the computations for subsequent operations.
id	A character string that is unique to this step to identify it.
x	A step_taxonomy object.

Value

An updated version of recipe with the new step added to the sequence of any existing operations.

Author(s)

Antoine Bichat

Examples

data("cheese_taxonomy")
rec <-
  cheese_taxonomy %>%
  select(asv, lineage) %>%
  recipe(~ .) %>%
  step_taxonomy(lineage, rank = c("order", "genus")) %>%
  prep()
rec
tidy(rec, 1)
bake(rec, new_data = NULL)

scimo documentation built on June 24, 2024, 5:17 p.m.