test(consistent): add Rmd and test that checks if data produced by mo…

…del is consistent to previous runs (also renamed test files)
pythonhealthdatascience · Jan 15, 2025 · 59f82a7 · 59f82a7
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diff --git a/.gitignore b/.gitignore
@@ -3,3 +3,4 @@
 .RData
 .Ruserdata
 inst/doc
+inst/*html
diff --git a/inst/generate_exp_results.Rmd b/inst/generate_exp_results.Rmd
@@ -0,0 +1,72 @@
+---
+title: "Generate expected results"
+output: html_document
+---
+
+This notebook is used to run a specific version of the model and save each results dataframe as a csv. These are used in `test-backtest.R` to verify that the model produces consistent results.
+
+The `.Rmd` file is provided as it is possible that results may change due to alterations to the model structure and operations. Once it has been confirmed that changes are intentional and not any introduced errors, this script can be run to regenerate the `.csv` files used in the test.
+
+The run time is provided at the end of this notebook.
+
+## Set-up
+
+Load required packages.
+
+```{r setup}
+library(simmer)
+library(simulation)
+```
+
+Start timer.
+
+```{r start_timer}
+start_time <- Sys.time()
+```
+
+Define path to expected results.
+
+```{r path}
+tests <- "../tests/testthat/testdata/"
+```
+
+## Run model and save results
+
+```{r}
+# Define model parameters
+param <- defaults()
+param["patient_inter"] <- 4.0
+param["mean_n_consult_time"] <- 10.0
+param["number_of_nurses"] <- 5.0
+param["data_collection_period"] <- 80.0
+param["number_of_runs"] <- 10.0
+param["cores"] <- 1.0
+
+# Run the trial
+envs <- trial(param = param)
+```
+
+```{r}
+# Monitored data about arrivals
+result_arrivals <- do.call(rbind, lapply(envs, get_mon_arrivals))
+write.csv(result_arrivals, file.path(tests, "arrivals.csv"), row.names = FALSE)
+```
+
+```{r}
+# Monitored data about resources
+result_resources <- do.call(rbind, lapply(envs, get_mon_resources))
+write.csv(result_resources, file.path(tests, "resources.csv"), row.names = FALSE)
+```
+
+## Calculate run time
+
+```{r end_timer}
+# Get run time in seconds 
+end_time <- Sys.time()
+runtime <- as.numeric(end_time - start_time, units="secs")
+
+# Display converted to minutes and seconds
+minutes <- as.integer(runtime / 60)
+seconds <- as.integer(runtime %% 60)
+print(sprintf("Notebook run time: %dm %ds", minutes, seconds))
+```
diff --git a/tests/testthat/test-backtest.R b/tests/testthat/test-backtest.R
@@ -0,0 +1,32 @@
+# Back testing for the Discrete-Event Simulation (DES) Model.
+#
+# These check that the model code produces results consistent with prior code.
+
+test_that("results from a new run match those previously generated", {
+  # Choose a specific set of parameters (ensuring test remains on the same
+  # set, regardless of any changes to defaults())
+  param <- defaults()
+  param["patient_inter"] <- 4.0
+  param["mean_n_consult_time"] <- 10.0
+  param["number_of_nurses"] <- 5.0
+  param["data_collection_period"] <- 80.0
+  param["number_of_runs"] <- 10.0
+  param["cores"] <- 1.0
+
+  # Run the trial then get the monitored arrivals and resources
+  envs <- trial(param = param)
+  arrivals <- do.call(rbind, lapply(envs, simmer::get_mon_arrivals))
+  resources <- do.call(rbind, lapply(envs, simmer::get_mon_resources))
+
+  # Import the expected results
+  exp_arrivals <- read.csv(test_path("testdata", "arrivals.csv"))
+  exp_resources <- read.csv(test_path("testdata", "resources.csv"))
+
+  # Remove the na.action attribute before comparing
+  attr(arrivals, "na.action") <- NULL
+  attr(resources, "na.action") <- NULL
+
+  # Compare results
+  expect_equal(arrivals, exp_arrivals)
+  expect_equal(resources, exp_resources)
+})
diff --git a/tests/testthat/test-model.R → tests/testthat/test-unittest.R b/tests/testthat/test-model.R → tests/testthat/test-unittest.R
@@ -1,3 +1,8 @@
+# Unit testing for the Discrete-Event Simulation (DES) Model.
+#
+# These check specific parts of the simulation and code, ensuring they work
+# correctly and as expected.
+
 test_that("the same seed returns the same result", {
 
   # Run model twice using same run number (which will set the seed)

diff --git a/tests/testthat/testdata/arrivals.csv b/tests/testthat/testdata/arrivals.csv
@@ -0,0 +1,184 @@
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