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Check whether traits and a tree are ready for pigauto

Source: R/check_pigauto.R
check_pigauto.Rd

Inspect declared inputs without constructing a phylogenetic graph or fitting a model. The check is intended to make input problems and likely compute scale visible before calling impute(). Its fingerprint identifies the declared input object for comparison within a workflow; it is not a security hash.

Usage

check_pigauto(
  traits,
  tree,
  species_col = NULL,
  trait_types = NULL,
  multi_proportion_groups = NULL,
  covariates = NULL,
  gnn = FALSE
)

Arguments

traits

A data.frame of traits, with row names or a species column.

tree

A phylo tree.

species_col

Optional column naming species identities.

trait_types

Optional named type overrides passed to preprocess_traits().

multi_proportion_groups

Optional named composition groups passed to preprocess_traits().

covariates

Optional environmental covariates passed to preprocess_traits(). Non-finite values are an error.

gnn

Whether the planned imputation will use the graph neural network. The default FALSE skips the torch runtime probe, matching impute()'s default. Set TRUE to include the torch runtime in the preflight.

Value

A list of class pigauto_check containing a schema version, status, stable input fingerprint, input summaries, and structured messages.

Examples

# \donttest{
tree <- ape::read.tree(text = "((a:1,b:1):1,c:2);")
traits <- data.frame(x = c(1, NA, 3), row.names = tree$tip.label)
check_pigauto(traits, tree)
#> pigauto input check: ready 
# }