#256 admiral_updates: fix flagging of worst

pharmaverse · Dec 12, 2023 · e8b5b7f · e8b5b7f
1 parent a4c655e
commit e8b5b7f
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Showing 4 changed files with 53 additions and 5 deletions.
diff --git a/inst/templates/ad_adrs.R b/inst/templates/ad_adrs.R
@@ -77,12 +77,24 @@ adrs <- adrs %>%
 # parameter derivations - here only valid assessments and those occurring on or
 # after randomization date, if there is more than one assessment per date the
 # worst one is flagged
+worst_resp <- function(arg) {
+  case_when(
+    arg == "CR" ~ 1,
+    arg == "PR" ~ 2,
+    arg == "SD" ~ 3,
+    arg == "NON-CR/NON-PD" ~ 4,
+    arg == "NE" ~ 5,
+    arg == "PD" ~ 6,
+    TRUE ~ 0
+  )
+}
+
 adrs <- adrs %>%
   restrict_derivation(
     derivation = derive_var_extreme_flag,
     args = params(
       by_vars = exprs(STUDYID, USUBJID, ADT),
-      order = exprs(AVAL, RSSEQ),
+      order = exprs(worst_resp(AVALC), RSSEQ),
       new_var = ANL01FL,
       mode = "last"
     ),

diff --git a/inst/templates/ad_adrs_basic.R b/inst/templates/ad_adrs_basic.R
@@ -85,12 +85,24 @@ adrs <- adrs %>%
 # parameter derivations - here only valid assessments and those occurring on or
 # after randomization date, if there is more than one assessment per date the
 # worst one is flagged
+worst_resp <- function(arg) {
+  case_when(
+    arg == "CR" ~ 1,
+    arg == "PR" ~ 2,
+    arg == "SD" ~ 3,
+    arg == "NON-CR/NON-PD" ~ 4,
+    arg == "NE" ~ 5,
+    arg == "PD" ~ 6,
+    TRUE ~ 0
+  )
+}
+
 adrs <- adrs %>%
   restrict_derivation(
     derivation = derive_var_extreme_flag,
     args = params(
       by_vars = exprs(STUDYID, USUBJID, ADT),
-      order = exprs(AVAL, RSSEQ),
+      order = exprs(worst_resp(AVALC), RSSEQ),
       new_var = ANL01FL,
       mode = "last"
     ),

diff --git a/vignettes/adrs.Rmd b/vignettes/adrs.Rmd
@@ -230,12 +230,24 @@ those occurring on or after randomization date. If there is more than
 one assessment at a date, the worst one is flagged.
 
 ```{r}
+worst_resp <- function(arg) {
+  case_when(
+    arg == "CR" ~ 1,
+    arg == "PR" ~ 2,
+    arg == "SD" ~ 3,
+    arg == "NON-CR/NON-PD" ~ 4,
+    arg == "NE" ~ 5,
+    arg == "PD" ~ 6,
+    TRUE ~ 0
+  )
+}
+
 adrs <- adrs %>%
   restrict_derivation(
     derivation = derive_var_extreme_flag,
     args = params(
       by_vars = exprs(STUDYID, USUBJID, ADT),
-      order = exprs(AVAL, RSSEQ),
+      order = exprs(worst_resp(AVALC), RSSEQ),
       new_var = ANL01FL,
       mode = "last"
     ),
@@ -492,7 +504,7 @@ rsp_y
 adrs <- adrs %>%
   derive_extreme_event(
     by_vars = exprs(STUDYID, USUBJID),
-    order = exprs(ADT, event_nr),
+    order = exprs(event_nr, ADT),
     tmp_event_nr_var = event_nr,
     mode = "first",
     events = list(rsp_y, no_data_n),

diff --git a/vignettes/adrs_basic.Rmd b/vignettes/adrs_basic.Rmd
@@ -229,12 +229,24 @@ those occurring on or after randomization date. If there is more than
 one assessment at a date, the worst one is flagged.
 
 ```{r}
+worst_resp <- function(arg) {
+  case_when(
+    arg == "CR" ~ 1,
+    arg == "PR" ~ 2,
+    arg == "SD" ~ 3,
+    arg == "NON-CR/NON-PD" ~ 4,
+    arg == "NE" ~ 5,
+    arg == "PD" ~ 6,
+    TRUE ~ 0
+  )
+}
+
 adrs <- adrs %>%
   restrict_derivation(
     derivation = derive_var_extreme_flag,
     args = params(
       by_vars = exprs(STUDYID, USUBJID, ADT),
-      order = exprs(AVAL, RSSEQ),
+      order = exprs(worst_resp(AVALC), RSSEQ),
       new_var = ANL01FL,
       mode = "last"
     ),