Compare BM baseline and pigauto methods across replicates

Runs a full comparison of the BM baseline and pigauto (with attention + calibration) over multiple random seeds. Returns a tidy data.frame suitable for plotting or downstream analysis.

Usage

compare_methods(
  data,
  tree,
  splits = NULL,
  seeds = NULL,
  epochs = 500L,
  verbose = TRUE,
  ...
)

Arguments

data: pigauto_data object.
tree: phylo object.
splits: pre-computed splits (applied to all reps) or NULL to create fresh splits per seed.
seeds: optional integer vector of random seeds for replication. The default NULL performs one run using the current RNG stream.
epochs: number of training epochs.
verbose: logical.
...: additional arguments passed to fit_pigauto.

Value

A data.frame with columns: method, trait, type, metric, value, rep.

Details

For each seed the function:

Creates train/val/test splits.
Fits the phylogenetic BM baseline.
Fits pigauto (with attention and calibration enabled by default).
Evaluates both methods on the test split.
Collects results into a single data.frame.

Examples

# \donttest{
data(avonet300, tree300)
tree <- ape::keep.tip(tree300, tree300$tip.label[seq_len(30L)])
traits <- avonet300[match(tree$tip.label, avonet300$Species_Key),
                     c("Mass", "Wing.Length"), drop = FALSE]
rownames(traits) <- tree$tip.label
cmp <- compare_methods(preprocess_traits(traits, tree), tree, seeds = 1L,
                       epochs = 5L, verbose = FALSE)
#> Error: Lantern is not loaded. Please use `install_torch()` to install additional dependencies.
aggregate(value ~ method + trait + metric, data = cmp, FUN = mean)
#> Error in eval(m$data, parent.frame()): object 'cmp' not found
# }