test: add multiple test datasets for integration tests

* use test fixtures to properly generate multiple combinations of available data
* add integration tests to validate handling of missing vlaues in the datasets

data-raw/data1.R

@@ -9,6 +9,10 @@
 #' * Timing:
 #'   * Fishery is assumed to operate over the entire year
 #'   * Survey occurs instantaneously at the start of the year
+#' * Note: If you encounter warning messages such as `cannot open 
+#'    the connection: warning messages from top-level task callback 'vsc.workspace'` 
+#'    while running the code in VS Code, try calling 
+#'    `removeTaskCallback("vsc.workspace")` before executing the code. 
 #'
 #' @author Kathryn L. Doering and Kelli F. Johnson
 #'
@@ -385,6 +389,11 @@ length_comp_data <- data.frame(
   )
 )
 
+# Save individual dataframes to a single file for {testthat} integration tests
+save(landings_data, index_data, age_data, weightatage_data, length_comp_data, length_age_data, 
+  file = testthat::test_path("fixtures", "integration_test_data_components.RData")
+)
+
 # Add the conversion matrix and length composition data to dataframe
 data1 <- rbind(data1, length_comp_data, length_age_data)
 

tests/testthat/fixtures/generate_test_datasets.R

@@ -0,0 +1,47 @@
+# This R script generates multiple test datasets for use in tests located in tests/testthat.
+# For example, it creates datasets containing only age composition, only length composition data,
+# or data with missing values.
+# Note: Run this script only after ensuring that the file tests/testthat/fixtures/integration_test_data_components.RData exists.
+# The integration_test_data_components.RData is generated after running the script R/data1.R.
+
+# Load required integration test data components
+load(test_path("fixtures", "integration_test_data_components.RData"))
+
+# Generate dataset with only age composition data
+# TODO: Check if we need to create a new "length" column with NAs
+data_age_comp_raw <- rbind(landings_data, index_data, age_data, weightatage_data)
+data_age_comp <- FIMS::FIMSFrame(data_age_comp_raw)
+saveRDS(data_age_comp, file = testthat::test_path("fixtures", "data_age_comp.RDS"))
+
+# Generate dataset with only length composition data
+data_length_comp_raw <- rbind(landings_data, index_data, weightatage_data) |>
+  dplyr::mutate(
+    length = NA,
+    .after = "age"
+  ) |>
+  rbind(length_comp_data, length_age_data)
+data_length_comp <- FIMS::FIMSFrame(data_length_comp_raw)
+saveRDS(data_length_comp, file = testthat::test_path("fixtures", "data_length_comp.RDS"))
+
+# Generate dataset with missing values in age composition for fleet1
+na_index <- as.Date("2-01-01")
+data_age_comp_na <- data_age_comp_raw |>
+  dplyr::filter(!(name == "fleet1" & type == "age" & datestart == na_index)) |>
+  FIMS::FIMSFrame()
+saveRDS(data_age_comp_na, file = testthat::test_path("fixtures", "data_age_comp_na.RDS"))
+
+# Generate dataset with missing values in length composition, age-to-length-conversion, and index for survey1
+data_length_comp_na <- data_length_comp_raw |>
+  dplyr::filter(!(name == "survey1" & type %in% c("index", "length", "age-to-length-conversion") & datestart == na_index)) |>
+  FIMS::FIMSFrame()
+saveRDS(data_length_comp_na, file = testthat::test_path("fixtures", "data_length_comp_na.RDS"))
+
+# Generate dataset with missing values in age composition, length composition for fleets
+age_na_index <- as.Date("2-01-01")
+length_na_index <- as.Date("12-01-01")
+data_age_length_comp_raw <- rbind(landings_data, index_data, age_data, weightatage_data)
+data_age_length_comp_na <- data_age_length_comp_raw |>
+  dplyr::filter(!(name == "survey1" & type %in% c("age") & datestart == age_na_index)) |>
+  dplyr::filter(!(name == "fleet1" & type %in% c("length", "age-to-length-conversion") & datestart == length_na_index)) |>
+  FIMS::FIMSFrame()
+saveRDS(data_age_length_comp_na, file = testthat::test_path("fixtures", "data_age_length_comp_na.RDS"))

tests/testthat/test-create_default_parameters.R

@@ -1,5 +1,4 @@
-data("data1")
-data <- FIMSFrame(data1)
+data <- FIMS::FIMSFrame(data1)
 
 fleet1 <- survey1 <- list(
   selectivity = list(form = "LogisticSelectivity"),

tests/testthat/test-fimsframe.R

@@ -1,6 +1,5 @@
 # tests for input objects
-data("data1", package = "FIMS")
-fims_frame <- FIMSFrame(data1)
+fims_frame <- FIMS::FIMSFrame(data1)
 
 test_that("Can create the S4 FIMSFrame classes", {
   expect_s4_class(fims_frame, "FIMSFrame")

tests/testthat/test-initialize_modules.R

@@ -1,5 +1,4 @@
-data("data1")
-data <- FIMSFrame(data1)
+data <- FIMS::FIMSFrame(data1)
 
 fleet1 <- survey1 <- list(
   selectivity = list(form = "LogisticSelectivity"),