Fix basic_burden_sanity() crashing on failed checks

.Rbuildignore

@@ -9,6 +9,7 @@
 ^\.pre-commit-config\.yaml$
 ^_pkgdown\.yml$
 ^codecov\.yml$
+^CONTRIBUTING\.md$
 ^doc$
 ^docs$
 ^pkgdown$

CONTRIBUTING.md

@@ -0,0 +1,7 @@
+# Contributing
+
+## Versioning
+
+For bug fixes, increment the patch component of the package version in
+`DESCRIPTION` (for example, from `0.0.5` to `0.0.6`) and record the fix in
+`NEWS.md`.

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: vimcheck
 Title: Diagnostics for Vaccine Impact Modelling Consortium Burden and
     Impact Estimates
-Version: 0.0.5
+Version: 0.0.6
 Authors@R: c(
     person("Pratik", "Gupte", , "p.gupte24@imperial.ac.uk", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-5294-7819")),

NEWS.md

@@ -1,3 +1,8 @@
+# vimcheck (0.0.6)
+
+- Fixed `basic_burden_sanity()` to return failed-check messages instead of
+  erroring on R >= 4.2 or incorrectly appending `PASS.` on older R versions.
+
 # vimcheck 0.0.5
 
 - Added functions to plot impact and FVPs and coverage.

R/fn_burden_diagnostics.R

@@ -381,7 +381,7 @@ basic_burden_sanity <- function(burden) {
     mes <- c(mes, mes_not_numeric)
   }
 
-  if (mes == mes_start) {
+  if (identical(mes, mes_start)) {
     mes <- c(mes, "PASS.")
   }
 

tests/testthat/test-burden_diagnostics.R

@@ -259,3 +259,48 @@ test_that("`check_demography_alignment()` works", {
     permutation.of = expected_names
   )
 })
+
+test_that("`basic_burden_sanity()` passes clean numeric estimates", {
+  expected <- c("Basic sanity check for burden estimates:", "PASS.")
+
+  for (value in list(c(0, 1, 2), c(0L, 1L, 2L), numeric(0))) {
+    expect_no_condition(
+      output <- basic_burden_sanity(data.frame(value = value))
+    )
+    expect_identical(output, expected)
+  }
+})
+
+test_that("`basic_burden_sanity()` returns failed-check messages", {
+  header <- "Basic sanity check for burden estimates:"
+  missing_message <- paste0(
+    "Warning: Burden estimates should not have missing values, but some ",
+    "values are missing. Fix missing values by converting to zeros!"
+  )
+  negative_message <- paste0(
+    "Warning: Burden estimates should all be positive or zero, but found ",
+    "some negative estimates!"
+  )
+  non_numeric_message <- paste0(
+    "Warning: Burden estimates should be of type `numeric`, but are not. ",
+    "Convert burden estimates to `numeric`."
+  )
+
+  cases <- list(
+    list(value = c(1, NA_real_), messages = missing_message),
+    list(value = c(1, NaN), messages = missing_message),
+    list(value = c(0, -1), messages = negative_message),
+    list(value = c("0", "1"), messages = non_numeric_message),
+    list(value = c(NA_real_, -1), messages = c(
+      missing_message,
+      negative_message
+    ))
+  )
+
+  for (case in cases) {
+    expect_no_condition(
+      output <- basic_burden_sanity(data.frame(value = case$value))
+    )
+    expect_identical(output, c(header, case$messages))
+  }
+})