review comments

R/epidist.R

@@ -14,9 +14,11 @@
 #' reexported as part of `epidist`.
 #' @param prior One or more `brmsprior` objects created by [brms::set_prior()]
 #' or related functions. These priors are passed to [epidist_prior()] in the
-#' `prior` argument.
-#' @param merge_priors If `TRUE` then merge new priors with existing ones, if
-#' `FALSE` only use new priors. Defaults to `TRUE`. This may be useful if
+#' `prior` argument. Some models have default priors that are automatically
+#' added (see [epidist_model_prior()]). These can be merged with user-provided
+#' priors using the `merge_priors` argument.
+#' @param merge_priors If `TRUE` then merge user priors with default priors, if
+#' `FALSE` only use user priors. Defaults to `TRUE`. This may be useful if
 #' the built in approaches for merging priors are not flexible enough for a
 #' particular use case.
 #' @param fn The internal function to be called. By default this is

R/family.R

@@ -90,7 +90,14 @@ epidist_family_param.default <- function(family, ...) {
   )
   lpdf_match <- regexpr(lpdf_pattern, dummy_mdl)
   reparam <- if (lpdf_match > 0) {
-    match_str <- regmatches(dummy_mdl, lpdf_match)[[1]]
+    matches <- unlist(regmatches(dummy_mdl, lpdf_match))
+    mu_matches <- matches[grepl("mu", matches, fixed = TRUE)]
+    if (length(mu_matches) > 1) {
+      cli_abort("Multiple Stan parameterisations found with 'mu' parameter.")
+    } else if (length(mu_matches) == 0) {
+      cli_abort("No Stan parameterisation found with 'mu' parameter.")
+    }
+    match_str <- mu_matches[1]
     param <- sub(
       paste0(
         "target \\+= ", family_name, "_(lpdf|lpmf)\\(Y \\| " # nolint

R/gen.R

@@ -35,7 +35,7 @@ epidist_gen_log_lik <- function(family) {
     swindow <- prep$data$vreal3[i]
 
     # make the prep object censored
-    # 1 here is equivalent  to right censored in brms
+    # -1 here is equivalent to right censored in brms
     prep$data$cens <- -1
 
     # Calculate density for each draw using primarycensored::dpcens()

R/latent_model.R

@@ -112,7 +112,6 @@ epidist_family_model.epidist_latent_model <- function(
 #' @export
 epidist_formula_model.epidist_latent_model <- function(
     data, formula, ...) {
-  # Update main formula
   formula <- stats::update(
     formula, delay | vreal(relative_obs_time, pwindow, swindow) ~ .
   )
@@ -193,7 +192,7 @@ epidist_stancode.epidist_latent_model <- function(
     stanvar(
       block = "data",
       scode = "array[wN] int woverlap;",
-      x = as.integer(filter(data, woverlap > 0)$.row_id),
+      x = filter(data, woverlap > 0)$.row_id,
       name = "woverlap"
     )