test: update fimsfit snapshot with real fit output

tests/testthat/_snaps/fimsfit.md

@@ -1,14 +1,14 @@
 # print.fimsfit prints summary correctly
 
     Code
-      print.fimsfit(fit_obj)
+      print.fimsfit(fit_obj_fix_runtime)
     Message
-      i FIMS model version: "1.0"
-      i Total run time was 10 seconds
+      i FIMS model version: "Model Comparison Project example"
+      i Total run time was 0.607 seconds
       i Number of parameters: total=77, fixed_effects=77, and random_effects=0
-      i Maximum gradient= 1e-04
+      i Maximum gradient= 0.00248
       i Negative log likelihood (NLL):
-      * Marginal NLL= 1498.433
-      * Total NLL= 1498.33
-      i Terminal SB= 10000
+      * Marginal NLL= 1498.43281
+      * Total NLL= 1498.43281
+      i Terminal SB= 1514.67842
 

tests/testthat/helper-integration-tests-setup.R

@@ -43,11 +43,11 @@
 #'   estimation_mode = TRUE
 #' )
 setup_and_run_FIMS_without_wrappers <- function(iter_id,
-                               om_input_list,
-                               om_output_list,
-                               em_input_list,
-                               estimation_mode = TRUE,
-                               map = list()) {
+                                                om_input_list,
+                                                om_output_list,
+                                                em_input_list,
+                                                estimation_mode = TRUE,
+                                                map = list()) {
   # Load operating model data for the current iteration
   om_input <- om_input_list[[iter_id]]
   om_output <- om_output_list[[iter_id]]
@@ -208,7 +208,7 @@ setup_and_run_FIMS_without_wrappers <- function(iter_id,
   opt <- NULL
   if (estimation_mode == TRUE) {
     opt <- stats::nlminb(obj$par, obj$fn, obj$gr,
-                         control = list(eval.max = 800, iter.max = 800)
+      control = list(eval.max = 800, iter.max = 800)
     )
   }
   # Call report using MLE parameter values, or
@@ -277,11 +277,12 @@ setup_and_run_FIMS_without_wrappers <- function(iter_id,
 #'   estimation_mode = TRUE
 #' )
 setup_and_run_FIMS_with_wrappers <- function(iter_id,
-                                                om_input_list,
-                                                om_output_list,
-                                                em_input_list,
-                                                estimation_mode = TRUE,
-                                                map = list()) {
+                                             om_input_list,
+                                             om_output_list,
+                                             em_input_list,
+                                             estimation_mode = TRUE,
+                                             map = list(),
+                                             return_fit = FALSE) {
   # Load operating model data for the current iteration
   om_input <- om_input_list[[iter_id]]
   om_output <- om_output_list[[iter_id]]
@@ -435,17 +436,29 @@ setup_and_run_FIMS_with_wrappers <- function(iter_id,
   parameters <- list(p = get_fixed())
   input <- list()
   input$parameters <- parameters
-  input$version = "Model Comparison Project example"
+  input$version <- "Model Comparison Project example"
   fit <- fit_fims(input, do.fit = estimation_mode)
 
   clear()
   # Return the results as a list
-  return(list(
-    parameters = fit$input$parameters,
-    obj = fit$obj,
-    opt = fit$opt,
-    report = fit$rep,
-    sdr_report = fit$sd
-  ))
-}
+  if(return_fit){
+    return(list(
+      parameters = fit$input$parameters,
+      obj = fit$obj,
+      opt = fit$opt,
+      report = fit$rep,
+      sdr_report = fit$sd,
+      fit = fit
+    ))
+  } else {
+    return(list(
+      parameters = fit$input$parameters,
+      obj = fit$obj,
+      opt = fit$opt,
+      report = fit$rep,
+      sdr_report = fit$sd,
+      fit = fit
+    ))
+  }
 
+}

tests/testthat/test-fimsfit.R

@@ -1,6 +1,16 @@
+load(test_path("fixtures", "integration_test_data.RData"))
+iter_id <- 1
+result <- setup_and_run_FIMS_with_wrappers(
+  iter_id = iter_id,
+  om_input_list = om_input_list,
+  om_output_list = om_output_list,
+  em_input_list = em_input_list,
+  estimation_mode = TRUE,
+  return_fit = TRUE
+)
+fit_obj <- result$fit
+
 test_that("fimsfit creates an object of class 'fimsfit'", {
-  fit_obj <- list(version = "1.0", timing = list(time_total = 10), opt = list(num_pars = list(total = 10, fixed_effects = 5, random_effects = 5)), rep = list(ssb = 1), parList = list(), obj = NULL)
-  class(fit_obj) <- "list"
   result <- fimsfit(fit_obj)
 
   expect_s3_class(result, "fimsfit")
@@ -13,46 +23,31 @@ test_that("fimsfit returns a warning for non-list input", {
 })
 
 test_that("fimsfit stops for missing version", {
-  fit_obj <- list(timing = list(time_total = 10), opt = list(num_pars = list(total = 10, fixed_effects = 5, random_effects = 5)), rep = list(ssb = 1), parList = list(), obj = NULL)
-  class(fit_obj) <- "list"
-  expect_error(fimsfit(fit_obj), "No version found, something went wrong")
+  fit_obj_no_version <- fit_obj
+  fit_obj_no_version <- within(fit_obj_no_version, rm(version))
+  expect_error(fimsfit(fit_obj_no_version), "No version found, something went wrong")
 })
 
 test_that("is.fimsfit detects fimsfit objects correctly", {
-  fit_obj <- list(version = "1.0", timing = list(time_total = 10), opt = list(num_pars = list(total = 10, fixed_effects = 5, random_effects = 5)), rep = list(ssb = 1), parList = list(), obj = NULL)
-  class(fit_obj) <- c("fimsfit", "list")
 
   expect_true(is.fimsfit(fit_obj))
-  expect_false(is.fimsfit(list(version = "1.0")))
+  expect_false(is.fimsfit(list(version = "Model Comparison Project example")))
 })
 
 test_that("is.fimsfits detects lists of fimsfit objects correctly", {
-  fit_obj <- list(version = "1.0", timing = list(time_total = 10), opt = list(num_pars = list(total = 10, fixed_effects = 5, random_effects = 5)), rep = list(ssb = 1), parList = list(), obj = NULL)
-  class(fit_obj) <- c("fimsfit", "list")
 
   fit_list <- list(fit_obj, fit_obj)
   non_fit_list <- list(fit_obj, list(version = "1.0"))
 
   expect_true(is.fimsfits(fit_list))
   expect_false(is.fimsfits(non_fit_list))
-  expect_false(is.fimsfits("not_a_list"))
+  expect_warning(is.fimsfits("not_a_list"))
 })
 
 test_that("print.fimsfit prints summary correctly", {
-  fit_obj <- list(version = "1.0",
-                  timing = list(time_total = 10),
-                  opt = list(num_pars = list(total = 77,
-                                             fixed_effects = 77,
-                                             random_effects = 0),
-                             max_gradient = 0.0001,
-                             objective = 1498.433),
-                  rep = list(ssb = list(rep(10000, 5)),
-                             jnll = 1498.33),
-                  parList = list()
-                  )
-  class(fit_obj) <- c("fimsfit", "list")
-
+  fit_obj_fix_runtime <- fit_obj
+  fit_obj_fix_runtime$timing$time_total <- 0.607
   expect_snapshot(
-    print.fimsfit(fit_obj)
+    print.fimsfit(fit_obj_fix_runtime)
   )
 })