#107 move tempates to sep file

R/generate_code_tempates.R

@@ -0,0 +1,62 @@
+
+#' The template suffix for the cm code
+#'
+#' @noRd
+#' @keywords internal
+cm_template_prefix <- stringr::str_glue('
+library(sdtm.oak)
+library(dplyr)
+
+
+# Read CT Specification
+study_ct <- read.csv("./datasets/sdtm_ct.csv")
+
+# Read in raw data
+cm_raw_data <- read.csv("./datasets/cm_raw_data_cdash.csv")
+
+cm_raw_data <- admiral::convert_blanks_to_na(cm_raw_data)
+
+# derive oak_id_vars
+cm_raw_data <- cm_raw_data %>%
+  generate_oak_id_vars(
+    pat_var = "PATNUM",
+    raw_src = "cm_raw_data"
+  )
+
+# Read in DM domain to derive study day
+dm <- read.csv("./datasets/dm.csv")
+
+dm <- admiral::convert_blanks_to_na(dm)
+')
+
+#' The template suffix for the cm code
+#'
+#' @noRd
+#' @keywords internal
+cm_template_suffix <- stringr::str_glue('
+dplyr::mutate(
+  STUDYID = "test_study",
+  DOMAIN = "CM",
+  CMCAT = "GENERAL CONMED",
+  USUBJID = paste0("test_study", "-", cm_raw_data$PATNUM)
+) %>%
+derive_seq(tgt_var = "CMSEQ",
+           rec_vars= c("USUBJID", "CMTRT")) %>%
+derive_study_day(
+  sdtm_in = .,
+  dm_domain = dm,
+  tgdt = "CMENDTC",
+  refdt = "RFXSTDTC",
+  study_day_var = "CMENDY"
+) %>%
+derive_study_day(
+  sdtm_in = .,
+  dm_domain = dm,
+  tgdt = "CMSTDTC",
+  refdt = "RFXSTDTC",
+  study_day_var = "CMSTDY"
+) %>%
+dplyr::select("STUDYID", "DOMAIN", "USUBJID", "CMSEQ", "CMTRT", "CMCAT", "CMINDC",
+              "CMDOSE", "CMDOSTXT", "CMDOSU", "CMDOSFRM", "CMDOSFRQ", "CMROUTE",
+              "CMSTDTC", "CMENDTC","CMSTDY", "CMENDY", "CMENRTPT", "CMENTPT")
+')