Workflow for setting up ClinSight for a new study

[LDSamson]

Maybe useful as context: below is a template of a script I use to setup and renew clinsight data for practically all studies.

The function renew_study_data will download data again with an API connection if it is run interactively, or if data is not yet available, otherwise the already available data is used. This way, I can update the metadata or provide study-specific data, run the script and test clinsight directly with the updated metadata. A few study-specific scripts are defined in a file elsewhere (although this can also be added here directly if needed).

@Jeff-Thompson12 and @aclark02-arcus is your workflow similar?

### This file is to prepare and to download data for the study mentioned below. 

study_name <- "STUDY_NAME_HERE"

#remotes::install_github("openpharma/clinsight", ref = "v0.3.0", upgrade = "never")
#remotes::install_github("gcp-service/viedoc_import", ref = "v0.1.4", upgrade = "never")
library(clinsight)
library(viedocimport)

if (rlang::is_interactive()){
  cat(time_stamp(), ": Running script interactively\n", sep = "")
  data_folder <- file.path(Sys.getenv("DATA_FOLDER"), paste0(tolower(study_name), "_data"))
} else {
  data_folder <- Sys.getenv("DATA_FOLDER")
}

############ Load custom functions ############ 
source(file.path(data_folder, "fct_data_general.R"))
source(file.path(data_folder, paste0("fct_data_", tolower(study_name), ".R") ))

############ Renew study data ############ 
renew_study_data(study_name = study_name, data_folder = data_folder)
metadata <- readRDS(file.path(data_folder, "metadata.rds"))
raw_data_files <- readRDS(file.path(data_folder, "raw_data_files.rds"))

############ Apply study-specific changes ##############
study_data <- raw_data_files |>
  merge_imported_data() |> 
  merge_meta_with_data(metadata) |> 
  convert_birthyear_to_age(birthyear_label = "Age") |> 
  adjust_drugadmindata() |> 
  adjust_subject_status()

# ########### End of study-specific changes ################
saveRDS(study_data, file.path(data_folder, "study_data.rds"))
if(rlang::is_interactive()){
  source(file.path(data_folder, "fct_runtime.R"))
  withr::with_options(list(golem.app.prod = TRUE), test_clinsight(study_data, metadata))
}