181: pre-assign sizes to variables (#182)

* Revert "177: use `num_elements` instead of `size` (#178)"

This reverts commit 2cfa802.

* assign sizes to variables

* rename variables to match data

DESCRIPTION

@@ -19,7 +19,7 @@ Authors@R:
            comment = c(ORCID = "0000-0003-2386-4031")),
     person(given = "Sebastian",
            family = "Funk",
-           role = c("ctb"),
+           role = c("aut"),
            email = "[email protected]",
            comment = c(ORCID = "0000-0002-2842-3406")))
 Description: Provides functions for working with primary

NEWS.md

@@ -11,7 +11,7 @@ Development release.
 ## Bug fixes
 
 - Added a missing `@family` tag to the `pcens` functions. This omission resulted in the Weibull analytical solution not being visible in the package documentation.
-- Changed a call to `size()` to use `num_elements()` instead as an underlying type conversion was causing issues on some platforms.
+- Added precalculation of vector sizes to the `primarycensored_cdf()` stan function, avoiding errors on some platforms due to narrowing conversions in aggregate initialisation. 
 - Changed `D` to be of type real in `pcens_model.stan` in order to support infinite `relative_obs_time`.
 
 # primarycensored 1.0.0

inst/WORDLIST

@@ -63,6 +63,7 @@ pcd
 pcens
 pdist
 pprimarycensored
+precalculation
 primaryeventdistributions
 propto
 pwindow

inst/stan/functions/primarycensored.stan

@@ -37,8 +37,10 @@ real primarycensored_cdf(data real d, int dist_id, array[] real params,
   } else {
     // Use numerical integration for other cases
     real lower_bound = max({d - pwindow, 1e-6});
-    array[num_elements(params) + num_elements(primary_params)] real theta = append_array(params, primary_params);
-    array[4] int ids = {dist_id, primary_id, num_elements(params), num_elements(primary_params)};
+    int n_params = size(params);
+    int n_primary_params = size(primary_params);
+    array[n_params + n_primary_params] real theta = append_array(params, primary_params);
+    array[4] int ids = {dist_id, primary_id, n_params, n_primary_params};
 
     vector[1] y0 = rep_vector(0.0, 1);
     result = ode_rk45(primarycensored_ode, y0, lower_bound, {d}, theta, {d, pwindow}, ids)[1, 1];