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Generate an HTML imputation report from a pigauto fit

Source: R/report.R
pigauto_report.Rd

Produces an HTML file with interactive charts (loading Chart.js from its public CDN). For fits created with the default gnn = FALSE, the report describes baseline-only imputation. For fits created with gnn = TRUE, it also compares the GNN against the phylogenetic baseline and includes training history. Per-trait metrics, gate values, and held-out diagnostic conformal coverage are included when available.

Usage

pigauto_report(
  fit,
  data = NULL,
  splits = NULL,
  output_path = "pigauto_report.html",
  title = "pigauto Imputation Report",
  open = TRUE
)

Arguments

fit

A pigauto_fit object (or a pigauto_result from impute).

data

Optional pigauto_data object. Extracted automatically when fit is a pigauto_result. When supplied it must match the fit (species and traits).

splits

Optional splits object from make_missing_splits. Extracted automatically when fit is a pigauto_result. When supplied it must match the fit.

output_path

Character of length 1. File path for the HTML report (default "pigauto_report.html" in the working directory).

title

Character of length 1. Report title (HTML-escaped on write).

open

Logical of length 1. Open the report in a browser when done (default TRUE).

Value

The output path (invisibly).

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
traits$Mass[seq_len(3L)] <- NA_real_
result <- impute(traits, tree, epochs = 5L, verbose = FALSE)
#> Warning: Small validation set for 2 trait(s): Mass (n=4), Wing.Length (n=3). Calibrated gate and conformal scores will be noisy for these trait(s). 95% split-conformal coverage is NOT achievable for 2 trait(s) with fewer than 19 validation cells (Mass (n=4), Wing.Length (n=3)): the achievable ceiling is n_val / (n_val + 1), which only reaches 0.95 at n_val >= 19. See `?fit_pigauto` under 'Calibration at small n' for smoothing options.
pigauto_report(result, output_path = tempfile(fileext = ".html"),
               open = FALSE)
# }