Almost working with "import all functions" strategy

inst/cohort-scratch.R

@@ -49,17 +49,13 @@ summary(fit_direct_weighted)
 
 lognormal <- brms::lognormal()
 
-primarycensored_lognormal_uniform_lcdf <- brms::custom_family(
-  "primarycensored_lognormal_uniform_lcdf",
+primarycensored_lognormal_uniform_lpmf <- brms::custom_family(
+  "primarycensored_lognormal_uniform",
   dpars = lognormal$dpar,
   links = c(lognormal$link, lognormal$link_sigma),
-  type = lognormal$type,
+  type = "int",
   loop = TRUE,
-  vars = c("pwindow", "vreal1[n]")
-)
-
-primarycensored_lognormal_uniform_lcdf_file <- file.path(
-  tempdir(), "primarycensored_lognormal_uniform_lcdf.stan"
+  vars = c("vreal1[n]", "pwindow[n]")
 )
 
 data <- cohort_obs |>
@@ -68,14 +64,10 @@ data <- cohort_obs |>
     pwindow = 1,
     q = pmax(d - pwindow, 0)
   )
-
-pcd_function <- pcd_load_stan_functions("primarycensored_lognormal_uniform_lcdf")
-pcd_function <- sub(pattern = "array\\[\\] real params", "real mu, real sigma", pcd_function)
-pcd_function <- gsub("\\s*real mu = params\\[1\\];\\n\\s*real sigma = params\\[2\\];\\n", "", pcd_function)
 
 stanvars_functions <- brms::stanvar(
   block = "functions",
-  scode = pcd_function
+  scode = .stan_chunk("cohort_model/primarycensored-edit.stan")
 )
 
 # stanvars_tparameters <- brms::stanvar(
@@ -98,16 +90,19 @@ stanvars_data <- brms::stanvar(
 
 stanvars_all <- stanvars_functions + stanvars_data
 
-brms::make_stancode(
+stancode <- brms::make_stancode(
   formula = d | weights(n) + vreal(q) ~ 1,
-  family = primarycensored_lognormal_uniform_lcdf,
+  family = primarycensored_lognormal_uniform_lpmf,
   data = data,
   stanvars = stanvars_all,
 )
 
+model <- rstan::stan_model(model_code = stancode)
+
 fit_pcd <- brms::brm(
-  formula = d | weights(n), vreal(q) ~ 1,
-  family = primarycensored_lognormal_uniform_lcdf,
+  formula = d | weights(n) + vreal(q) ~ 1,
+  family = primarycensored_lognormal_uniform_lpmf,
   data = data,
   stanvars = stanvars_all,
+  backend = "cmdstanr"
 )