expose stan data

R/biokinetics.R

@@ -280,6 +280,11 @@ biokinetics <- R6::R6Class(
         package = "epikinetics"
       )
     },
+    #' @description View the data that is passed to the stan model, for debugging purposes.
+    #' @return A list of arguments that will be passed to the stan model.
+    get_stan_data = function() {
+      private$stan_input_data
+    },
     #' @description Fit the model and return CmdStanMCMC fitted model object.
     #' @return A CmdStanMCMC fitted model object: <https://mc-stan.org/cmdstanr/reference/CmdStanMCMC.html>
     #' @param ... Named arguments to the `sample()` method of CmdStan model.

tests/testthat/test-data.R

@@ -9,10 +9,10 @@ local_mocked_bindings(
 test_that("Can construct stan data", {
   dt <- data.table::fread(system.file("delta_full.rds", package = "epikinetics"))
   mod <- biokinetics$new(data = dt,
-                 priors = biokinetics_priors(),
-                 covariate_formula = ~0 + infection_history,
-                 preds_sd = 0.25,
-                 time_type = "relative")
+                         priors = biokinetics_priors(),
+                         covariate_formula = ~0 + infection_history,
+                         preds_sd = 0.25,
+                         time_type = "relative")
   # the fit function has been mocked above to return the stan inputs
   stan_dt <- mod$fit()
   expect_equal(stan_dt$N_events, 335)
@@ -21,11 +21,30 @@ test_that("Can construct stan data", {
 
 test_that("Can initialise file path data", {
   expect_true(inherits(biokinetics$new(file_path = system.file("delta_full.rds", package = "epikinetics"),
-                               priors = biokinetics_priors()), "biokinetics"))
+                                       priors = biokinetics_priors()), "biokinetics"))
 })
 
 test_that("Can provide data directly", {
   dat <- data.table::fread(system.file("delta_full.rds", package = "epikinetics"))
   expect_true(inherits(biokinetics$new(data = dat,
-                               priors = biokinetics_priors()), "biokinetics"))
+                                       priors = biokinetics_priors()), "biokinetics"))
+})
+
+test_that("Can get stan data", {
+  dat <- data.table::fread(system.file("delta_full.rds", package = "epikinetics"))
+  priors <- biokinetics_priors(mu_values = c(1, 2, 3, 4, 5, 6),
+                               sigma_values = c(0.1, 0.2, 0.3, 0.4, 0.5, 0.6))
+  mod <- biokinetics$new(data = dat, priors = priors)
+  stan_data <- mod$get_stan_data()
+  expect_true(is.list(stan_data))
+  expect_equal(names(stan_data), c("N", "N_events", "id", "value", "censored",
+                                   "titre_type", "preds_sd", "K", "N_uncens", "N_lo",
+                                   "N_me", "N_hi", "uncens_idx", "cens_lo_idx", "cens_me_idx",
+                                   "cens_hi_idx", "t", "X", "P", "mu_t0",
+                                   "mu_tp", "mu_ts", "mu_m1", "mu_m2", "mu_m3",
+                                   "sigma_t0", "sigma_tp", "sigma_ts", "sigma_m1", "sigma_m2",
+                                   "sigma_m3"))
+  expect_equal(stan_data$mu_t0, priors$mu_t0)
+  expect_equal(stan_data$sigma_t0, priors$sigma_t0)
+  expect_equal(stan_data$id, dat$pid)
 })