Fix pipeline failures

R/dataset_oak_vignette.R

@@ -28,7 +28,6 @@
 #' @keywords internal
 #'
 dataset_oak_vignette <- function(dataset, display_vars = NULL, filter = NULL) {
-
   filter <- admiraldev::assert_filter_cond(rlang::enexpr(filter), optional = TRUE)
 
   out <- dataset |>

_pkgdown.yml

@@ -8,7 +8,7 @@ navbar:
   title: "sdtm.oak"
 
 reference:
-- title: SDTM Mapping Algorithms/function
+- title: SDTM Mapping Algorithms/functions
   desc: Set of functions to perform SDTM Mappings
   contents:
   - assign

tests/testthat/test-derive_study_day.R

@@ -54,7 +54,6 @@ test_that("`derive_study_day()` works as expected for invalid input", {
     RFSTDTC = c(123L, 456L, 789L),
     stringsAsFactors = FALSE
   )
-
 })
 
 test_that("`calculate_study_day()` works as expected for valid input", {

vignettes/articles/events_domain.Rmd

@@ -308,7 +308,8 @@ In this mapping, the `condition_add` function filters the cm domain created in t
 
 ```{r eval=TRUE}
 cm <- cm %>%
-  # Map qualifier CMDOSFRQ  Annotation text is If CMTRT is not null then map the collected value in raw dataset cm_raw and raw variable MDFRQ to CMDOSFRQ
+  # Map qualifier CMDOSFRQ  Annotation text is If CMTRT is not null then map
+  # the collected value in raw dataset cm_raw and raw variable MDFRQ to CMDOSFRQ
   {
     assign_ct(
       raw_dat = cm_raw,
@@ -358,7 +359,9 @@ The mapping logic for `CMMODIFY` is `If collected value in MODIFY in cm_raw is d
 
 ```{r eval=TRUE}
 cm <- cm %>%
-  # Map CMMODIFY  Annotation text  If collected value in MODIFY in cm_raw is different to CM.CMTRT then assign the collected value to CMMODIFY in CM domain (CM.CMMODIFY)
+  # Map CMMODIFY  Annotation text  If collected value in MODIFY in cm_raw is
+  # different to CM.CMTRT then assign the collected value to CMMODIFY in
+  # CM domain (CM.CMMODIFY)
   {
     assign_no_ct(
       raw_dat = cm_raw,
@@ -515,7 +518,10 @@ cm <- cm %>%
 sdtm.oak:::dataset_oak_vignette(
   cm,
   display_vars = exprs(
-    oak_id, raw_source, patient_number, CMTRT, CMGRPID, CMDOSU, CMSTDTC, CMSTRTPT, CMSTTPT, CMDOSFRQ, CMMODIFY, CMINDC, CMENDTC, CMENRTPT, CMENTPT, CMDOS, CMDOSTXT, CMDOSU, CMDOSFRM, CMROUTE, CMPROPH, CMDRG, CMDRGCD, CMDECOD, CMPNCD
+    oak_id, raw_source, patient_number, CMTRT, CMGRPID, CMDOSU, CMSTDTC,
+    CMSTRTPT, CMSTTPT, CMDOSFRQ, CMMODIFY, CMINDC, CMENDTC, CMENRTPT, CMENTPT,
+    CMDOS, CMDOSTXT, CMDOSU, CMDOSFRM, CMROUTE, CMPROPH, CMDRG, CMDRGCD,
+    CMDECOD, CMPNCD
   )
 )
 ```
@@ -563,7 +569,10 @@ cm <- cm %>%
 sdtm.oak:::dataset_oak_vignette(
   cm,
   display_vars = exprs(
-    oak_id, raw_source, patient_number, STUDYID, DOMAIN, USUBJID, CMGRPID, CMTRT, CMDOSU, CMSTDTC, CMSTRTPT, CMSTTPT, CMDOSFRQ, CMMODIFY, CMINDC, CMENDTC, CMENRTPT, CMENTPT, CMDOS, CMDOSTXT, CMDOSU, CMDOSFRM, CMROUTE, CMPROPH, CMDRG, CMDRGCD, CMDECOD, CMPNCD, CMSTDY, CMENDY
+    oak_id, raw_source, patient_number, STUDYID, DOMAIN, USUBJID, CMGRPID,
+    CMTRT, CMDOSU, CMSTDTC, CMSTRTPT, CMSTTPT, CMDOSFRQ, CMMODIFY, CMINDC,
+    CMENDTC, CMENRTPT, CMENTPT, CMDOS, CMDOSTXT, CMDOSU, CMDOSFRM, CMROUTE,
+    CMPROPH, CMDRG, CMDRGCD, CMDECOD, CMPNCD, CMSTDY, CMENDY
   )
 )
 ```

vignettes/articles/findings_domain.Rmd

@@ -435,7 +435,7 @@ vs_oxysat <-
 # Map topic variable VSALL from raw variable ASMNTDN with the logic if ASMNTDN  == 1 then VSTESTCD = VSALL
 vs_vsall <-
   hardcode_ct(
-    raw_dat = condition_add(vs_raw, ASMNTDN == 1),
+    raw_dat = condition_add(vs_raw, ASMNTDN == 1L),
     raw_var = "ASMNTDN",
     tgt_var = "VSTESTCD",
     tgt_val = "VSALL",