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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 charts. Baseline-only figures are embedded as SVG and work offline; GNN charts load Chart.js from its public CDN. The report compares the fitted baseline with the calibrated blend, which may include the neural component and other baseline contributions. This is not a comparison isolating the neural component. With gnn = FALSE, no neural network is fitted. 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, or reconstructed from a fit that retains its scaled observations. When supplied it must match the fit (species and traits).

splits

Optional splits object from make_missing_splits. Extracted automatically from the result or fit when available. 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)
# }