Refactor estimate_truncation to use S3 class pattern

NAMESPACE

@@ -3,22 +3,28 @@
 S3method("!=",dist_spec)
 S3method("$",epinow)
 S3method("$",estimate_secondary)
+S3method("$",estimate_truncation)
 S3method("+",dist_spec)
 S3method("==",dist_spec)
 S3method("[[",epinow)
+S3method("[[",estimate_truncation)
 S3method(c,dist_spec)
 S3method(collapse,dist_spec)
 S3method(collapse,multi_dist_spec)
 S3method(discretise,dist_spec)
 S3method(discretise,multi_dist_spec)
 S3method(fix_parameters,dist_spec)
 S3method(fix_parameters,multi_dist_spec)
+S3method(get_delay,default)
+S3method(get_delays,epinowfit)
 S3method(get_predictions,estimate_infections)
 S3method(get_predictions,estimate_secondary)
+S3method(get_predictions,estimate_truncation)
 S3method(get_predictions,forecast_infections)
 S3method(get_predictions,forecast_secondary)
 S3method(get_samples,estimate_infections)
 S3method(get_samples,estimate_secondary)
+S3method(get_samples,estimate_truncation)
 S3method(get_samples,forecast_infections)
 S3method(get_samples,forecast_secondary)
 S3method(is_constrained,dist_spec)
@@ -35,12 +41,14 @@ S3method(plot,forecast_infections)
 S3method(plot,forecast_secondary)
 S3method(print,dist_spec)
 S3method(print,epinowfit)
+S3method(print,summary.estimate_truncation)
 S3method(sd,default)
 S3method(sd,dist_spec)
 S3method(sd,multi_dist_spec)
 S3method(summary,epinow)
 S3method(summary,estimate_infections)
 S3method(summary,estimate_secondary)
+S3method(summary,estimate_truncation)
 S3method(summary,forecast_infections)
 export(Fixed)
 export(Gamma)
@@ -86,6 +94,8 @@ export(forecast_infections)
 export(forecast_opts)
 export(forecast_secondary)
 export(generation_time_opts)
+export(get_delay)
+export(get_delays)
 export(get_distribution)
 export(get_parameters)
 export(get_pmf)

NEWS.md

@@ -39,6 +39,15 @@ The function interface remains unchanged.
   - The `output` argument now controls what is saved to disk, not the return structure.
   - **Deprecated**: The previous return structure with `$estimates`, `$estimated_reported_cases`, `$summary`, `$plots`, and `$estimate_infections` elements is deprecated. Backward compatibility is provided via `$` and `[[` operators with deprecation warnings.
 - `plot.estimate_infections()` and `plot.forecast_infections()` now accept a `CrIs` argument to control which credible intervals are displayed.
+- Refactored `estimate_truncation()` to return a proper S3 object with a simplified structure.
+  - Renamed return elements: `obs` → `observations`, `data` → `args`.
+  - Removed elements: `last_obs` (now included in `observations`), `cmf` and `dist`.
+  - Use `get_delays(object)$truncation` to extract the estimated truncation distribution for use in `epinow()` or `estimate_infections()`.
+  - Use `get_predictions(object)` to extract truncation-adjusted (nowcast) estimates that can be compared to observed data.
+  - Use `get_samples(object)` to extract posterior samples.
+  - Use `summary(object)` to get parameter estimates as a data.table.
+  - **Deprecated**: Accessing `$dist` via `$` or `[[` triggers deprecation warnings. Use `get_delays()$truncation` instead.
+- Added `get_delays()` generic function to extract delay distributions from fitted models as a named list of `dist_spec` objects. Works with `estimate_infections()`, `estimate_secondary()`, and `estimate_truncation()`. Also added `get_delay(object, type)` as a convenience function to extract a single delay by name (e.g., `get_delay(fit, "truncation")`).
 - Added a `style` argument to `plot_estimates()` and related plot methods to display credible intervals as error bars (`"linerange"`) instead of the default ribbons (`"ribbon"`). Error bars can be clearer for weekly or aggregated data.
 - **Internal**: Stan model delay identifiers have been renamed for semantic clarity (`delay_id` → `delay_id_reporting`, `gt_id` → `delay_id_generation_time`, `trunc_id` → `delay_id_truncation`). This may affect users who access Stan models directly.
 - **Internal**: Stan model parameter names have been renamed for clarity (`dispersion` → `reporting_overdispersion`, `frac_obs` → `fraction_observed`). This simplifies internal code by removing post-hoc parameter renaming. This may affect users who access Stan models directly or use custom priors with the old parameter names.

R/create.R

@@ -775,7 +775,7 @@ create_stan_delays <- function(..., time_points = 1L) {
   ret$weight <- array(rep(1, ret$n_p))
   ret$weight[weight_priors] <- time_points
   ## assign distribution
-  ret$dist <- array(match(distributions, c("lognormal", "gamma")) - 1L)
+  ret$dist <- array(match(distributions, dist_spec_distributions()) - 1L)
 
   names(ret) <- paste("delay", names(ret), sep = "_")
   ret <- c(ret, as.list(delay_ids))

R/dist_spec.R

@@ -1123,6 +1123,22 @@ natural_params <- function(distribution) {
   )
 }
 
+#' Get parametric distribution types
+#'
+#' @description `r lifecycle::badge("experimental")`
+#' Returns the mapping of Stan integer codes to distribution names.
+#' Stan uses 0 for lognormal, 1 for gamma.
+#' @return A character vector of distribution names in Stan order.
+#' @keywords internal
+#' @examples
+#' \dontrun{
+#' dist_spec_distributions()
+#' dist_spec_distributions()[1]  # "lognormal"
+#' }
+dist_spec_distributions <- function() {
+  c("lognormal", "gamma")
+}
+
 #' Get the lower bounds of the parameters of a distribution
 #'
 #' @description `r lifecycle::badge("experimental")`

R/estimate_infections.R

@@ -295,6 +295,6 @@ estimate_infections <- function(data,
   )
 
   ## Join stan fit if required
-  class(ret) <- c("epinowfit", "estimate_infections", class(ret))
+  class(ret) <- c("estimate_infections", "epinowfit", class(ret))
   ret
 }

R/estimate_secondary.R

@@ -273,7 +273,7 @@ estimate_secondary <- function(data,
     observations = reports
   )
 
-  class(ret) <- c("epinowfit", "estimate_secondary", class(ret))
+  class(ret) <- c("estimate_secondary", "epinowfit", class(ret))
   ret
 }