#2510 enhance_derive_param_computed: add note if no records were adde…

…d due to NAs

R/derive_param_computed.R

@@ -122,6 +122,9 @@
 #'   If the argument is set to a list of variables, observations are added even
 #'   if some of specified variables are `NA` (see Example 1c).
 #'
+#'   *Permitted Values:* `TRUE`, `FALSE`, or a list of variables created by
+#'   `exprs()` e.g. `exprs(ADTF, ATMF)`
+#'
 #' @details For each group (with respect to the variables specified for the
 #'   `by_vars` parameter) an observation is added to the output dataset if the
 #'   filtered input dataset (`dataset`) or the additional dataset
@@ -390,13 +393,26 @@ derive_param_computed <- function(dataset = NULL,
     } else {
       na_vars <- analysis_vars_chr
     }
+    nobs_before <- nrow(hori_data)
     hori_data <- filter(
       hori_data,
       !!!parse_exprs(map_chr(
         na_vars,
         ~ str_c("!is.na(", .x, ")")
       ))
     )
+    if (nobs_before > 0 && nrow(hori_data) == 0) {
+      cli_inform(c(
+        paste(
+          "No computed records were added because for all potential computed",
+          "records at least one of the contributing values was {.val {NA}}."
+        ),
+        paste(
+          "If this is not expected, please check the input data and the value of",
+          "the {.arg keep_nas} argument."
+        )
+      ))
+    }
   }
 
   # add computed variables like AVAL and constant variables like PARAMCD

tests/testthat/_snaps/derive_param_computed.md

@@ -9,15 +9,38 @@
       Error in `derive_param_computed()`:
       ! Argument `keep_nas` must be either TRUE, FALSE, or a list of <symbol>, but is a number.
 
-# assert_parameters_argument Test 12: error if argument is of wrong type
+# derive_param_computed Test 12: inform if no new records due to NAs
+
+    Code
+      derive_param_computed(advs, by_vars = exprs(USUBJID, AVISIT), parameters = c(
+        "SYSBP", "DIABP"), set_values_to = exprs(AVAL = (AVAL.SYSBP + 2 *
+      AVAL.DIABP) / 3, PARAMCD = "MAP", PARAM = "Mean Arterial Pressure (mmHg)", ADT = ADT.SYSBP,
+      ADTF = ADTF.SYSBP))
+    Message
+      No computed records were added because for all potential computed records at least one of the contributing values was NA.
+      If this is not expected, please check the input data and the value of the `keep_nas` argument.
+    Output
+      # A tibble: 8 x 7
+        USUBJID     PARAMCD PARAM                         AVAL AVISIT ADT        ADTF 
+        <chr>       <chr>   <chr>                        <dbl> <chr>  <date>     <chr>
+      1 01-701-1015 DIABP   Diastolic Blood Pressure (m~    51 BASEL~ 2024-01-10 <NA> 
+      2 01-701-1015 DIABP   Diastolic Blood Pressure (m~    50 WEEK 2 2024-01-24 <NA> 
+      3 01-701-1015 SYSBP   Systolic Blood Pressure (mm~   121 BASEL~ 2024-01-10 <NA> 
+      4 01-701-1015 SYSBP   Systolic Blood Pressure (mm~   121 WEEK 2 2024-01-24 <NA> 
+      5 01-701-1028 DIABP   Diastolic Blood Pressure (m~    79 BASEL~ 2024-01-10 <NA> 
+      6 01-701-1028 DIABP   Diastolic Blood Pressure (m~    80 WEEK 2 2024-01-24 <NA> 
+      7 01-701-1028 SYSBP   Systolic Blood Pressure (mm~   130 BASEL~ 2024-01-10 <NA> 
+      8 01-701-1028 SYSBP   Systolic Blood Pressure (mm~    NA WEEK 2 2024-01-24 <NA> 
+
+# assert_parameters_argument Test 13: error if argument is of wrong type
 
     Code
       assert_parameters_argument(myparameters <- c(1, 2, 3))
     Condition
       Error in `assert_parameters_argument()`:
       ! `myparameters <- c(1, 2, 3)` must be a character vector or a list of expressions but it is a double vector.
 
-# get_hori_data Test 13: error if variables with more than one dot
+# get_hori_data Test 14: error if variables with more than one dot
 
     Code
       get_hori_data(input, parameters = exprs(SYSBP, DIABP), by_vars = exprs(USUBJID,

tests/testthat/test-derive_param_computed.R

@@ -490,18 +490,53 @@ test_that("derive_param_computed Test 11: error if keep_nas is invalid", {
   )
 })
 
+## Test 12: inform if no new records due to NAs ----
+test_that("derive_param_computed Test 12: inform if no new records due to NAs", {
+  advs <- tibble::tribble(
+    ~USUBJID,      ~PARAMCD, ~PARAM,                            ~AVAL, ~AVISIT,
+    "01-701-1015", "DIABP",  "Diastolic Blood Pressure (mmHg)",    51, "BASELINE",
+    "01-701-1015", "DIABP",  "Diastolic Blood Pressure (mmHg)",    50, "WEEK 2",
+    "01-701-1015", "SYSBP",  "Systolic Blood Pressure (mmHg)",    121, "BASELINE",
+    "01-701-1015", "SYSBP",  "Systolic Blood Pressure (mmHg)",    121, "WEEK 2",
+    "01-701-1028", "DIABP",  "Diastolic Blood Pressure (mmHg)",    79, "BASELINE",
+    "01-701-1028", "DIABP",  "Diastolic Blood Pressure (mmHg)",    80, "WEEK 2",
+    "01-701-1028", "SYSBP",  "Systolic Blood Pressure (mmHg)",    130, "BASELINE",
+    "01-701-1028", "SYSBP",  "Systolic Blood Pressure (mmHg)",     NA, "WEEK 2"
+  ) %>%
+    mutate(
+      ADT = case_when(
+        AVISIT == "BASELINE" ~ as.Date("2024-01-10"),
+        AVISIT == "WEEK 2" ~ as.Date("2024-01-24")
+      ),
+      ADTF = NA_character_
+    )
+
+  expect_snapshot(derive_param_computed(
+    advs,
+    by_vars = exprs(USUBJID, AVISIT),
+    parameters = c("SYSBP", "DIABP"),
+    set_values_to = exprs(
+      AVAL = (AVAL.SYSBP + 2 * AVAL.DIABP) / 3,
+      PARAMCD = "MAP",
+      PARAM = "Mean Arterial Pressure (mmHg)",
+      ADT = ADT.SYSBP,
+      ADTF = ADTF.SYSBP
+    )
+  ))
+})
+
 # assert_parameters_argument ----
-## Test 12: error if argument is of wrong type ----
-test_that("assert_parameters_argument Test 12: error if argument is of wrong type", {
+## Test 13: error if argument is of wrong type ----
+test_that("assert_parameters_argument Test 13: error if argument is of wrong type", {
   expect_snapshot(
     assert_parameters_argument(myparameters <- c(1, 2, 3)),
     error = TRUE
   )
 })
 
 # get_hori_data ----
-## Test 13: error if variables with more than one dot ----
-test_that("get_hori_data Test 13: error if variables with more than one dot", {
+## Test 14: error if variables with more than one dot ----
+test_that("get_hori_data Test 14: error if variables with more than one dot", {
   input <- tibble::tribble(
     ~USUBJID, ~PARAMCD, ~PARAM, ~AVAL, ~AVALU, ~VISIT,
     "01-701-1015", "DIABP", "Diastolic Blood Pressure (mmHg)", 51, "mmHg", "BASELINE",