Refactor internal parameter cleaning

R/accessors.R

@@ -51,8 +51,10 @@ get_parameters.epidist <- function(x, ...) {
     }
 
     # convert to meanlog and sdlog names
-    class(params) <- family(x)
-    params <- clean_epidist_params(prob_dist_params = params)
+    params <- .clean_epidist_params(
+      prob_dist = family(x),
+      prob_dist_params = params
+    )
   } else {
     return(NA)
   }

R/epidist.R

@@ -62,18 +62,17 @@ new_epidist <- function(disease = character(),
         identical(names(prob_dist_params), names(uncertainty))
   )
 
+  # TODO: formalise if statement below or remove
   # include mean in prob_dist_params
-  if (!is.null(summary_stats$mean) && !is.na(summary_stats$mean)) {
-    prob_dist_params <- c(
-      prob_dist_params[!is.na(prob_dist_params)],
-      mean = summary_stats$mean
-    )
+  if (!is.null(summary_stats$mean) && !is.na(summary_stats$mean) &&
+      prob_dist %in% c("nbinom", "geom", "pois", "norm")) {
+    prob_dist_params["mean"] <- summary_stats$mean
   }
 
   if (is_epidist_params(prob_dist, prob_dist_params)) {
     # standardise common distribution parameters
-    class(prob_dist_params) <- prob_dist
-    prob_dist_params <- clean_epidist_params(
+    prob_dist_params <- .clean_epidist_params(
+      prob_dist = prob_dist,
       prob_dist_params = prob_dist_params
     )
   } else if (auto_calc_params) {
@@ -728,8 +727,8 @@ discretise.epidist <- function(x, ...) {
     }
 
     # standardise distribution parameter names
-    class(prob_dist_params) <- prob_dist
-    prob_dist_params <- clean_epidist_params(
+    prob_dist_params <- .clean_epidist_params(
+      prob_dist = prob_dist,
       prob_dist_params = prob_dist_params
     )