From 28f700de616df2af409f4902ea7600c075c605c3 Mon Sep 17 00:00:00 2001
From: Rammprasad Ganapathy <ganapathy.rammprasad@gene.com>
Date: Tue, 16 Jan 2024 06:43:23 +0000
Subject: [PATCH] pipeline failures

---
 DESCRIPTION                            |  6 +++---
 inst/create_cm_template.R              |  4 ++--
 man/sdtm.oak-package.Rd                | 12 +++++++++---
 vignettes/articles/algorithms.Rmd      |  3 ++-
 vignettes/articles/study_sdtm_spec.Rmd | 14 +++-----------
 5 files changed, 19 insertions(+), 20 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 38c3b021..b146c351 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -32,9 +32,9 @@ Depends: R (>= 4.1)
 Imports: 
     admiraldev,
     dplyr (>= 1.0.0),
-    purrr (>= 1.0.0),
-    rlang (>= 1.0.0),
-    stringr,
+    purrr (>= 0.3.3),
+    rlang (>= 0.4.4),
+    stringr (>= 1.4.0),
     tibble
 Suggests:
     knitr,
diff --git a/inst/create_cm_template.R b/inst/create_cm_template.R
index dbd93549..6e6e3ab5 100644
--- a/inst/create_cm_template.R
+++ b/inst/create_cm_template.R
@@ -14,13 +14,13 @@ library(dplyr)
 
 # Read Specification
 
-# sdtm_spec <- read_sdtm_spec(filename = "~/study/study_sdtm_spec.csv")
+sdtm_spec <- read_sdtm_spec(filename = "~/study/study_sdtm_spec.csv")
 
 study_ct <- read_study_ct(filename = "~/study/study_sdtm_ct.csv")
 
 # Read in raw data
 
-MD1 <- read_raw_data_csv(filename = "~/study/MD1.csv") |>
+md1 <- read_raw_data_csv(filename = "~/study/MD1.csv") |>
   # Derive oak_id_vars
   derive_oak_id_vars()
 
diff --git a/man/sdtm.oak-package.Rd b/man/sdtm.oak-package.Rd
index fc04b354..20606fa4 100644
--- a/man/sdtm.oak-package.Rd
+++ b/man/sdtm.oak-package.Rd
@@ -6,7 +6,7 @@
 \alias{sdtm.oak-package}
 \title{sdtm.oak: SDTM Data Transformation Engine}
 \description{
-An EDC and Data Standard agnostic SDTM data transformation engine that automates the transformation of raw clinical data in ODM format to SDTM based on standard mapping algorithms.
+An EDC and Data Standard-agnostic SDTM data transformation engine 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 SDTM Implemetation guide as defined by CDISC \url{https://www.cdisc.org/standards/foundational/sdtmig}
 }
 \seealso{
 Useful links:
@@ -18,11 +18,17 @@ Useful links:
 
 }
 \author{
-\strong{Maintainer}: Omar Garcia \email{ogcalderon@cdisc.org}
+\strong{Maintainer}: Rammprasad Ganapathy \email{ganapathy.rammprasad@gene.com}
 
 Authors:
 \itemize{
-  \item Rammprasad Ganapathy
+  \item Adam Forys
+  \item Edgar Manukyan
+  \item Rosemary Li
+  \item Preetesh Parikh
+  \item Lisa Houterloot
+  \item Yogesh Gupta
+  \item Omar Garcia \email{ogcalderon@cdisc.org}
   \item Ramiro Magno \email{rmagno@pattern.institute} (\href{https://orcid.org/0000-0001-5226-3441}{ORCID})
 }
 
diff --git a/vignettes/articles/algorithms.Rmd b/vignettes/articles/algorithms.Rmd
index 48ed689b..c1e4cf51 100644
--- a/vignettes/articles/algorithms.Rmd
+++ b/vignettes/articles/algorithms.Rmd
@@ -186,7 +186,8 @@ algorithms <- data.frame(
     ),
     paste("AE = 'Adverse Events' on early phase SAE form"),
     paste("EC = 'Exposure as Collected'")
-  )
+  ),
+  stringsAsFactors = TRUE
 )
 knitr::kable(algorithms)
 ```
diff --git a/vignettes/articles/study_sdtm_spec.Rmd b/vignettes/articles/study_sdtm_spec.Rmd
index 98459bcc..9e60057f 100644
--- a/vignettes/articles/study_sdtm_spec.Rmd
+++ b/vignettes/articles/study_sdtm_spec.Rmd
@@ -351,16 +351,8 @@ definition <- data.frame(
     "GROUP_BY",
     "ASSIGN_NO_CT",
     "ASSIGN_NO_CT"
-  )
-)
-# We do not want URLs to be activated since they are part of the longer API calls
-# and direct use is faulty.
-definition$Example_Values <- ifelse(
-  grepl("http", definition$Example_Values),
-  yes = paste0("`", definition$Example_Values, "`"),
-  no = definition$Example_Values
+  ),
+  stringsAsFactors = TRUE
 )
-
-knitr::kable(definition, col.names = gsub("_", " ", names(definition)))
+knitr::kable(definition)
 ```
-</div>