#216 admiral_0_11_update: fix lintr and R-CMD check

pharmaverse · Jun 1, 2023 · 0cc661c · 0cc661c
1 parent 5579e71
commit 0cc661c
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Showing 5 changed files with 16 additions and 31 deletions.
diff --git a/R/derive_param_clinbenefit.R b/R/derive_param_clinbenefit.R
@@ -224,7 +224,11 @@ derive_param_clinbenefit <- function(dataset,
   assert_character_vector(clinben_vals)
 
   if (!missing(aval_fun)) {
-    deprecate_warn("0.4.0", "derive_param_clinbenefit(aval_fun = )", "derive_param_clinbenefit(set_values_to = )")
+    deprecate_warn(
+      "0.4.0",
+      "derive_param_clinbenefit(aval_fun = )",
+      "derive_param_clinbenefit(set_values_to = )"
+    )
     assert_function(aval_fun)
     set_values_to <- exprs(!!!set_values_to, AVAL = {{aval_fun}}(AVALC))
   }

diff --git a/R/derive_param_response.R b/R/derive_param_response.R
@@ -193,7 +193,11 @@ derive_param_response <- function(dataset,
   }
 
   if (!missing(aval_fun)) {
-    deprecate_warn("0.4.0", "derive_param_response(aval_fun = )", "derive_param_response(set_values_to = )")
+    deprecate_warn(
+      "0.4.0",
+      "derive_param_response(aval_fun = )",
+      "derive_param_response(set_values_to = )"
+    )
     set_values_to <- exprs(!!!set_values_to, AVAL = {{aval_fun}}(AVALC))
   }
 

diff --git a/inst/templates/ad_adrs.R b/inst/templates/ad_adrs.R
@@ -332,7 +332,7 @@ adslmdis <- adsl %>%
 
 adrs <- adrs %>%
   derive_param_exist_flag(
-    dataset_adsl = adslmdis,
+    dataset_ref = adslmdis,
     dataset_add = tu,
     condition = TUEVAL == "INVESTIGATOR" & TUSTRESC == "TARGET" & VISIT == "BASELINE",
     false_value = "N",

diff --git a/tests/testthat/test-derive_param_response.R b/tests/testthat/test-derive_param_response.R
@@ -67,7 +67,7 @@ test_that("derive_param_response Test 1: With source_pd", {
       source_pd = pd,
       source_datasets = list(adrs = adrs),
       set_values_to = exprs(
-        AVAL = yn_to_numeric(AVALC),
+        AVAL = admiral::yn_to_numeric(AVALC),
         PARAMCD = "RSP",
         PARAM = "Response by investigator"
       ),
@@ -109,7 +109,7 @@ test_that("derive_param_response Test 2: No source_pd", {
       source_pd = NULL,
       source_datasets = NULL,
       set_values_to = exprs(
-        AVAL = yn_to_numeric(AVALC),
+        AVAL = admiral::yn_to_numeric(AVALC),
         PARAMCD = "RSP",
         PARAM = "Response by investigator"
       ),
@@ -151,7 +151,7 @@ test_that("derive_param_response Test 3: deprecation warning for aval_fun", {
         filter_source = PARAMCD == "OVR" & AVALC %in% c("CR", "PR"),
         source_pd = NULL,
         source_datasets = NULL,
-        aval_fun = yn_to_numeric,
+        aval_fun = admiral::yn_to_numeric,
         set_values_to = exprs(
           PARAMCD = "RSP",
           PARAM = "Response by investigator"

diff --git a/vignettes/adrs.Rmd b/vignettes/adrs.Rmd
@@ -792,7 +792,7 @@ adslmdis <- adsl %>%
 
 adrs <- adrs %>%
   derive_param_exist_flag(
-    dataset_adsl = adslmdis,
+    dataset_ref = adslmdis,
     dataset_add = tu,
     condition = TUEVAL == "INVESTIGATOR" & TUSTRESC == "TARGET" & VISIT == "BASELINE",
     false_value = "N",
@@ -802,6 +802,7 @@ adrs <- adrs %>%
       PARAM = "Measurable Disease at Baseline by Investigator",
       PARCAT2 = "Investigator",
       PARCAT3 = "Recist 1.1",
+      AVAL = yn_to_numeric(AVALC),
       ANL01FL = "Y"
     )
   )
@@ -815,30 +816,6 @@ dataset_vignette(
 )
 ```
 
-## Derive `AVAL` for New Parameters {#aval}
-
-For cases where `AVALC` has been derived for new parameters above as `"Y"` or `"N"`,
-we need to set `AVAL` to numeric versions such as `1`/`0`.
-
-```{r eval=TRUE}
-adrs <- adrs %>%
-  mutate(
-    AVAL = case_when(
-      AVALC == "Y" ~ 1,
-      AVALC == "N" ~ 0,
-      TRUE ~ AVAL
-    )
-  )
-```
-
-```{r, eval=TRUE, echo=FALSE}
-dataset_vignette(
-  adrs,
-  display_vars = exprs(USUBJID, PARAMCD, AVALC, AVAL),
-  filter = USUBJID == "01-701-1015" & AVALC %in% c("Y", "N")
-)
-```
-
 ## Assign `ASEQ` {#aseq}
 
 The function `admiral::derive_var_obs_number()` can be used to derive