From 3bad70e5390927d117e4a67832ccf4c172adc1cf Mon Sep 17 00:00:00 2001 From: Rammprasad Ganapathy Date: Tue, 16 Jan 2024 05:40:54 +0000 Subject: [PATCH] review comments & pipeline failures --- DESCRIPTION | 2 +- inst/create_cm_template.R | 7 +++++-- staged_dependencies.yaml | 1 - 3 files changed, 6 insertions(+), 4 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 0b65f266..4b2d72ac 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -18,7 +18,7 @@ Authors@R: c( person("Pfizer Inc", role = c("cph", "fnd")) ) Description: An EDC and Data Standard-agnostic SDTM data transformation engine -designed for SDTM programming in R. Powered by metadata {sdtm.oak} can automate +designed for SDTM programming in R. Powered by metadata `sdtm.oak` can automate the conversion of raw clinical data to SDTM through standardized mapping algorithms. SDTM is one of the required standards for data submission to FDA (U.S.) and PMDA (Japan). SDTM standards are implemented in accordance with the diff --git a/inst/create_cm_template.R b/inst/create_cm_template.R index d802b13c..dbd93549 100644 --- a/inst/create_cm_template.R +++ b/inst/create_cm_template.R @@ -220,9 +220,12 @@ cm <- MD1 |> derive_usubjid() |> derive_sequence(keys = c(USUBJID, CMTRT)) |> derive_visit_visitnum() |> - derive_study_day( + calculate_study_day( + dm_domain = dm, + study_day_var = "RFSTDTS", var_in = CMSTDTC, - target_var = CMSTDY + target_var = CMSTDY, + merge_key = "USUBJID" ) |> derive_study_day( var_in = CMENDTC, diff --git a/staged_dependencies.yaml b/staged_dependencies.yaml index 72a49b08..a1406e69 100644 --- a/staged_dependencies.yaml +++ b/staged_dependencies.yaml @@ -8,4 +8,3 @@ downstream_repos: current_repo: repo: pharmaverse/sdtm.oak host: https://github.com - \ No newline at end of file