Closes #33 Create RECIST data

.gitignore

@@ -20,6 +20,9 @@
 # RStudio files
 .Rproj.user/
 
+# helper files for interchange data between scripts
+data-raw/tu_help_data.rds
+
 # produced vignettes
 vignettes/*.html
 vignettes/*.pdf

NEWS.md

@@ -4,4 +4,7 @@
 
  - Ophthalmology variants of `ex` and `qs` SDTM datasets added. (#15)
  - Migrate data and function `get_terms()` from `admiral.test`. (#1, #49)
+ - Oncology datasets `tu_onco_recist`, `tr_onco_recist`, and `rs_onco_recist`
+ using RECIST 1.1 response criteria. The datasets contain just a few patients.
+ They are intended for vignettes and examples of ADaM datasets creation.
 

R/data.R

@@ -128,6 +128,32 @@
 #' @author Gopi Vegesna
 "rs_onco"
 
+#' Tumor Results Dataset (RECIST 1.1)
+#'
+#' A SDTM TR dataset using RECIST 1.1. The dataset contains just a few patients.
+#' It is intended for vignettes and examples of ADaM dataset creation.
+#'
+#' @author Stefan Bundfuss
+"tr_onco_recist"
+
+#' Tumor Identification Dataset (RECIST 1.1)
+#'
+#' A SDTM TU dataset using RECIST 1.1. The dataset contains just a few patients.
+#' It is intended for vignettes and examples of ADaM dataset creation.
+#'
+#' @author Stefan Bundfuss
+"tu_onco_recist"
+
+#' Disease Response Dataset (RECIST 1.1)
+#'
+#' A SDTM RS dataset using RECIST 1.1. The dataset contains just a few patients.
+#' It is intended for vignettes and examples of ADaM dataset creation.
+#'
+#' @source The dataset is derived from \code{tr_onco_recist}.
+#'
+#' @author Stefan Bundfuss
+"rs_onco_recist"
+
 #' Supplemental Adverse Events Dataset
 #'
 #' A SDTM SUPPAE dataset from the CDISC pilot project

data-raw/rs_onco_recist.R

@@ -0,0 +1,98 @@
+# ATTENTION: tr_onco_recist.R and tu_onco_recist.R must be run before this script
+library(admiral)
+
+data("tu_onco_recist")
+data("tr_onco_recist")
+
+tu <- tu_onco_recist
+
+# add location to tr
+tr <- derive_vars_merged(
+  tr_onco_recist,
+  dataset_add = tu,
+  by_vars = exprs(USUBJID, TREVAL = TUEVAL, TREVALID = TUEVALID, TRLNKID = TULNKID),
+  new_vars = exprs(TRLOC = TULOC)
+)
+
+# select tr results to consider:
+tr <- tr %>%
+  filter(
+    TRTESTCD == "LDIAM" & TRLOC != "LYMPH NODE" |
+      TRTESTCD == "LPERP" & TRLOC == "LYMPH NODE" |
+      TRTESTCD == "TUMSTATE"
+  ) %>%
+  # flag complete response by tumor
+  mutate(
+    CRFL = if_else(
+      TRTESTCD == "LDIAM" & TRSTRESN == 0 |
+        TRTESTCD == "LPERP" & TRSTRESN < 10 |
+        TRTESTCD == "TUMSTATE" & TRSTRESC == "ABSENT",
+      TRUE,
+      FALSE
+    )
+  )
+
+# derive sums of diameters
+sums <- tr %>%
+  group_by(STUDYID, USUBJID, TREVAL, TREVALID, TRACPTFL, VISITNUM, VISIT, TRDTC) %>%
+  summarise(
+    TRSTRESN = sum(TRSTRESN),
+    CRFL = all(CRFL),
+    IDS = paste(sort(TRLNKID), collapse = ", "),
+    NTFL = all(substr(TRLNKID, 1, 1) == "N")
+  ) %>%
+  mutate(TRTESTCD = "SUMDIAM") %>%
+  ungroup()
+
+sums <- derive_vars_merged(
+  sums,
+  dataset_add = sums,
+  filter_add = VISIT == "SCREENING",
+  by_vars = exprs(USUBJID, TREVAL, TREVALID),
+  new_vars = exprs(BASE = TRSTRESN, BASEIDS = IDS)
+)
+sums <- derive_vars_joined(
+  sums,
+  dataset_add = sums,
+  by_vars = exprs(USUBJID),
+  order = exprs(TRSTRESN),
+  new_vars = exprs(NADIR = TRSTRESN),
+  join_vars = exprs(VISITNUM),
+  filter_add = BASEIDS == IDS,
+  filter_join = VISITNUM > VISITNUM.join,
+  mode = "first",
+  check_type = "none"
+)
+
+# derive responses
+rs_onco_recist <- sums %>%
+  mutate(
+    DOMAIN = "RS",
+    .before = STUDYID
+  ) %>%
+  mutate(
+    RSTESTCD = "OVRLRESP",
+    RSTEST = "Overall Response",
+    RSORRES = case_when(
+      CRFL & IDS == BASEIDS ~ "CR",
+      TRSTRESN - NADIR >= 5 & TRSTRESN / NADIR >= 1.2 ~ "PD",
+      TRSTRESN / BASE <= 0.7 & IDS == BASEIDS ~ "PR",
+      !is.na(TRSTRESN) & IDS == BASEIDS ~ "SD",
+      NTFL ~ "NON-CR/NON-PD",
+      TRUE ~ "NE"
+    ),
+    RSSTRESC = RSORRES,
+    RSEVAL = TREVAL,
+    RSEVALID = TREVALID,
+    RSACPTFL = TRACPTFL,
+    RSDTC = TRDTC
+  ) %>%
+  select(-starts_with("TR"), -BASE, -BASEIDS, -NADIR, -IDS, -CRFL, -NTFL) %>%
+  filter(VISIT != "SCREENING") %>%
+  derive_var_obs_number(
+    by_vars = exprs(USUBJID),
+    new_var = RSSEQ,
+    order = exprs(VISITNUM, RSEVAL, RSEVALID)
+  )
+
+usethis::use_data(rs_onco_recist, overwrite = TRUE)