error check create_clean_reported_cases and add unit tests to cover f…

…unction
epiforecasts · seabbs · Jan 9, 2024 · Dec 18, 2023 · Dec 18, 2023 · Dec 18, 2023
commit 3ee24d32be4a6349986a42c2ecc1f00b40d16759
diff --git a/R/create.R b/R/create.R
@@ -18,6 +18,8 @@
 #' @author Sam Abbott
 #' @author Lloyd Chapman
 #' @export
+#' @examples
+#' create_clean_reported_cases(example_confirmed, 7)
 create_clean_reported_cases <- function(reported_cases, horizon,
                                         filter_leading_zeros = TRUE,
                                         zero_threshold = Inf) {
@@ -38,7 +40,9 @@ create_clean_reported_cases <- function(reported_cases, horizon,
   reported_cases <- data.table::setorder(reported_cases, date)
   ## Filter out 0 reported cases from the beginning of the data
   if (filter_leading_zeros) {
-    reported_cases <- reported_cases[order(date)][min(date[confirm > 0])]
+    reported_cases <- reported_cases[order(date)][
+      date >= min(date[confirm[!is.na(confirm)] > 0])
+    ]
   }
 
   # Check case counts preceding zero case counts and set to 7 day average if

diff --git a/tests/testthat/test-create_clean_reported_cases.R b/tests/testthat/test-create_clean_reported_cases.R
@@ -0,0 +1,32 @@
+
+test_that("create_clean_reported_cases runs without errors", {
+  expect_no_error(create_clean_reported_cases(example_confirmed, 7))
+})
+
+test_that("create_clean_reported_cases returns a data table", {
+  result <- create_clean_reported_cases(example_confirmed, 7)
+  expect_s3_class(result, "data.table")
+})
+
+test_that("create_clean_reported_cases filters leading zeros correctly", {
+  # Modify example_confirmed to have leading zeros
+  modified_data <- example_confirmed
+  modified_data[1:3, "confirm"] <- 0
+
+  result <- create_clean_reported_cases(modified_data, 7)
+  # Check if the first row with non-zero cases is retained
+  expect_equal(result$date[1], min(modified_data$date[modified_data$confirm > 0]))
+})
+
+test_that("create_clean_reported_cases replaces zero cases correctly", {
+  # Modify example_confirmed to have zero cases that should be replaced
+  modified_data <- example_confirmed
+  modified_data$confirm[10:16] <- 0
+  threshold <- 10
+
+  result <- create_clean_reported_cases(
+    modified_data, 0, zero_threshold = threshold
+  )
+  # Check if zero cases within the threshold are replaced
+  expect_equal(sum(result$confirm == 0, na.rm = TRUE), 0)
+})