From 9e988fddbbe698ea87b4b121e2188d04c2789caa Mon Sep 17 00:00:00 2001
From: Stefan Bundfuss <stefan.bundfuss@roche.com>
Date: Tue, 29 Aug 2023 12:13:07 +0000
Subject: [PATCH] #33 recist: fix variable names

---
 data-raw/rs_onco_recist.R |   6 +++---
 data-raw/tr_onco_recist.R |  14 +++++++-------
 data-raw/tu_onco_recist.R |   6 +++---
 data/tr_onco_recist.rda   | Bin 4734 -> 4737 bytes
 data/tu_onco_recist.rda   | Bin 917 -> 918 bytes
 man/tr_onco_recist.Rd     |   2 +-
 6 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/data-raw/rs_onco_recist.R b/data-raw/rs_onco_recist.R
index 144dc2d..1dc81ce 100644
--- a/data-raw/rs_onco_recist.R
+++ b/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()
diff --git a/data-raw/tr_onco_recist.R b/data-raw/tr_onco_recist.R
index c49bd34..2718fa5 100644
--- a/data-raw/tr_onco_recist.R
+++ b/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)
diff --git a/data-raw/tu_onco_recist.R b/data-raw/tu_onco_recist.R
index e4faf8a..e935bf3 100644
--- a/data-raw/tu_onco_recist.R
+++ b/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
diff --git a/data/tr_onco_recist.rda b/data/tr_onco_recist.rda
index 044f522f19d86cbb66ef5ace03c6e68728bcd0f7..e949b68704987d4d68fce8210526584c03d5eb23 100644
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diff --git a/data/tu_onco_recist.rda b/data/tu_onco_recist.rda
index 411642458a193bb8e7d1a03c470381e3380b6e77..93dada40eb85f616bac6a3e57b753e9b55b56426 100644
GIT binary patch
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diff --git a/man/tr_onco_recist.Rd b/man/tr_onco_recist.Rd
index d94618a..02ed140 100644
--- a/man/tr_onco_recist.Rd
+++ b/man/tr_onco_recist.Rd
@@ -5,7 +5,7 @@
 \alias{tr_onco_recist}
 \title{Tumor Results Dataset (RECIST 1.1)}
 \format{
-An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 444 rows and 18 columns.
+An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 444 rows and 19 columns.
 }
 \usage{
 tr_onco_recist