Performs all the steps defined in a Recipe — prep • dar

For a Recipe with at least one preprocessing or DA operation run the steps in a convenient order.

Usage

prep(
  rec,
  parallel = TRUE,
  workers = future::availableCores(constraints = "connections-16"),
  force = FALSE
)

Arguments

rec: A Recipe object.
parallel: if FALSE, no palatalization. if TRUE, parallel execution using future and furrr packages.
workers: Number of workers for palatalization.
force: Force the reexecution of all steps. This remove previous results.

Value

A PrepRecipe object.

Examples

data(metaHIV_phy)
rec <- 
  recipe(metaHIV_phy, var_info = "RiskGroup2", tax_info = "Class") |>
  step_subset_taxa(tax_level = "Kingdom", taxa = c("Bacteria", "Archaea")) |>
  step_filter_taxa(.f = function(x) sum(x > 0) >= (0.03 * length(x))) |>
  step_maaslin()

da_results <- prep(rec)