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Generate a LaTeX summary table of incubation period estimates

Source: R/table_utils.R
generate_results_table.Rd

Produces a booktabs-style LaTeX table with one row per pathogen and (optionally) indented italic sub-rows for each subgroup analysis.

Usage

generate_results_table(
  all_results,
  pathogens = NULL,
  model_weights = NULL,
  show_subgroups = TRUE,
  rhat_threshold = 1.05,
  ci_prob = 0.95,
  pathogen_labels = NULL,
  caption =
    paste0("Incubation period estimates by pathogen, grouped by epidemiological category. ",
    "Values are posterior medians with 95\\% credible intervals (CI). ",
    "$\\tau$ is the between-study heterogeneity SD. ",
    "Subgroup analyses are shown in italics beneath each pathogen."),
  label = "tab:incubation_periods"
)

Arguments

all_results

Nested list produced by analysis/main_analysis.R.

model_weights

Pre-computed output from compute_pathogen_model_bayes_factors(). Computed internally if NULL (slow — pre-compute and cache).

show_subgroups

Logical. Include subgroup sub-rows (default TRUE).

rhat_threshold

Numeric. Maximum acceptable Rhat for convergence; fits with max Rhat above this are skipped (default 1.05).

ci_prob

Numeric. Width of the credible interval, e.g. 0.95 gives a 2.5%–97.5% interval (default 0.95).

pathogen_labels

Optional named character vector overriding the display names used in the table rows.

caption

LaTeX \caption{} string.

label

LaTeX \label{} string.

Value

A single character string containing the complete LaTeX table environment, ready to paste into an Overleaf document.

Details

For every row the table reports:

  • the best-fitting distribution (selected with the same convergence-filtered LOO-weight logic as plot_main_figure());

  • the posterior predictive median with 95% credible interval;

  • the posterior predictive 95th percentile (\(p_{95}\)) with 95% CI;

  • the population-level location parameter \(\mu_0\) with 95% CI;

  • the shape parameter \(\phi\) with 95% CI;

  • the second shape parameter \(\kappa\) with 95% CI (Burr XII and Generalised Gamma only; shown as \(-\) for other families).

All intervals are formatted as median (lower, upper).

The table requires the LaTeX packages booktabs and multirow in the preamble.

See also

compute_pathogen_model_bayes_factors(), plot_main_figure()