#33 recist: fix variable names

data-raw/rs_onco_recist.R

@@ -10,7 +10,7 @@ tu <- tu_onco_recist
 tr <- derive_vars_merged(
   tr_onco_recist,
   dataset_add = tu,
-  by_vars = exprs(USUBJID, TREVAL = TUEVAL, TREVALID = TUEVALID, TRLINKID = TULINKID),
+  by_vars = exprs(USUBJID, TREVAL = TUEVAL, TREVALID = TUEVALID, TRLNKID = TULNKID),
   new_vars = exprs(TRLOC = TULOC)
 )
 
@@ -38,8 +38,8 @@ sums <- tr %>%
   summarise(
     TRSTRESN = sum(TRSTRESN),
     CRFL = all(CRFL),
-    IDS = paste(sort(TRLINKID), collapse = ", "),
-    NTFL = all(substr(TRLINKID, 1, 1) == "N")
+    IDS = paste(sort(TRLNKID), collapse = ", "),
+    NTFL = all(substr(TRLNKID, 1, 1) == "N")
   ) %>%
   mutate(TRTESTCD = "SUMDIAM") %>%
   ungroup()

data-raw/tr_onco_recist.R

@@ -6,7 +6,7 @@ library(admiral)
 
 # create tumor results to be used for RS
 tr <- tribble(
-  ~SUBJNR,  ~TRLINKID, ~TRTESTCD,  ~TRORRES,  ~VISITNUM,
+  ~SUBJNR,  ~TRLNKID,  ~TRTESTCD,  ~TRORRES,  ~VISITNUM,
   # BOR = CR, CBOR = SD
   "1",      "T01",     "LDIAM",    "21",              1,
   "1",      "T02",     "LPERP",    "32",              1,
@@ -120,7 +120,7 @@ tr <- tribble(
 suppress_warning(
   tr_compl <- tr %>%
     mutate(
-      diff_percent = (as.numeric(SUBJNR) + as.numeric(substr(TRLINKID, 3, 3)) + VISITNUM) %% 11,
+      diff_percent = (as.numeric(SUBJNR) + as.numeric(substr(TRLNKID, 3, 3)) + VISITNUM) %% 11,
       TRORRES = case_match(
         TRTESTCD,
         "LDIAM" ~ as.character(as.numeric(TRORRES) * (1 - diff_percent / 100)),
@@ -144,7 +144,7 @@ tr <- bind_rows(tr, tr_compl)
 suppress_warning(
   tr_radio1 <- tr %>%
     mutate(
-      diff_percent = (as.numeric(SUBJNR) + as.numeric(substr(TRLINKID, 3, 3)) + VISITNUM) %% 7 - 3,
+      diff_percent = (as.numeric(SUBJNR) + as.numeric(substr(TRLNKID, 3, 3)) + VISITNUM) %% 7 - 3,
       TRORRES = if_else(
         TRTESTCD %in% c("LDIAM", "LPERP"),
         as.character(as.numeric(TRORRES) * (1 + diff_percent / 100)),
@@ -159,7 +159,7 @@ suppress_warning(
 suppress_warning(
   tr_radio2 <- tr %>%
     mutate(
-      diff_percent = (as.numeric(SUBJNR) + as.numeric(substr(TRLINKID, 3, 3)) + VISITNUM + 3) %% 7 - 3,
+      diff_percent = (as.numeric(SUBJNR) + as.numeric(substr(TRLNKID, 3, 3)) + VISITNUM + 3) %% 7 - 3,
       TRORRES = if_else(
         TRTESTCD %in% c("LDIAM", "LPERP"),
         as.character(as.numeric(TRORRES) * (1 + diff_percent / 100)),
@@ -174,11 +174,11 @@ tr <- bind_rows(tr, tr_radio1, tr_radio2) %>%
   select(-diff_percent) %>%
   mutate(
     TRGRPID = if_else(
-      substr(TRLINKID, 1, 1) == "T",
+      substr(TRLNKID, 1, 1) == "T",
       "TARGET",
       "NON-TARGET"
     ),
-    .before = TRLINKID
+    .before = TRLNKID
   ) %>%
   mutate(
     TREVAL = if_else(is.na(TREVALID), "INVESTIGATOR", "INDEPENDENT ASSESSOR"),
@@ -273,7 +273,7 @@ tr <- derive_var_obs_number(
 
 tr_screen <- tr %>%
   filter(VISITNUM == 1 & basicfl == "Y") %>%
-  select(STUDYID, USUBJID, SUBJNR, TRLINKID, TRTESTCD, VISIT, VISITNUM, TREVAL, TREVALID, TRACPTFL)
+  select(STUDYID, USUBJID, SUBJNR, TRLNKID, TRTESTCD, VISIT, VISITNUM, TREVAL, TREVALID, TRACPTFL)
 saveRDS(tr_screen, file = "data-raw/tu_help_data.rds")
 
 tr_onco_recist <- select(tr, -SUBJNR, -basicfl, -RFSTDT)

data-raw/tu_onco_recist.R

@@ -21,7 +21,7 @@ tu <- tr_screen %>%
     TULOC = if_else(
       TRTESTCD == "LPERP",
       "LYMPH NODE",
-      locations[as.numeric(SUBJNR) + as.numeric(substr(TRLINKID, str_length(TRLINKID), str_length(TRLINKID)))]
+      locations[as.numeric(SUBJNR) + as.numeric(substr(TRLNKID, str_length(TRLNKID), str_length(TRLNKID)))]
     ),
     TUTESTCD = "TUMIDENT",
     TUTEST = "Tumore Identification"
@@ -33,10 +33,10 @@ tu_onco_recist <- tu %>%
     .before = STUDYID
   ) %>%
   mutate(
-    TUORRES = if_else(substr(TRLINKID, 1, 1) == "T", "TARGET", "NON-TARGET"),
+    TUORRES = if_else(substr(TRLNKID, 1, 1) == "T", "TARGET", "NON-TARGET"),
     TUSTRESC = TUORRES,
     TUMETHOD = "CT SCAN",
-    TULINKID = TRLINKID,
+    TULNKID = TRLNKID,
     TUEVAL = TREVAL,
     TUEVALID = TREVALID,
     TUACPTFL = TRACPTFL