## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----setup, warning=FALSE-----------------------------------------------------
library(siera)

## ----example files------------------------------------------------------------
# To see a list of example files:
ARS_example()

# A temporary path to a specific file:
ARS_example("exampleARS_1.json")

## ----Excel ARS metadata example, message=FALSE--------------------------------

# Path to the Excel ARS metadata file: 
ARS_path <- ARS_example("Common_Safety_Displays_cards.xlsx")

# Path to a folder which will contain the Output meta-programmed R scripts (recommended to update
# to a more suitable local path)
output_folder <- tempdir()

# Path to the folder containing ADaM datasets in csv format (we will use temporary 
# directory tempdir() to make the code run in this vignette, but it's recommended to 
# 1. download the ADaMs required (csv ADSL and ADAE available using e.g. ARS_example("ADSL.csv"))
# 2. store it in a folder (the directly downloaded location can be found using dirname(ARS_example("ADSL.csv")), for example.  Use this location, or manually store the ADaM somewhere else)
# 3. use the folder path instead of tempdir() below.
ADaM_folder <- tempdir()

# run the readARS function with these 3 parameters.  This creates R scripts 
# (1 for each Output in output_folder)
readARS(ARS_path, output_folder, ADaM_folder)

## ----run ARD_xxx, message=FALSE, warning=FALSE, eval=TRUE---------------------

# Step 1: open ARD_xxx.R file
# Step 2: Confirm the location of ADaM dataset(s) is correct in the code section "Load ADaM".  
# For the sake of simplicity, the only update made to the ARD_Out14-1-1.R script was to point to the ADaM folder to ARS_example("ADSL.csv")
# Step 3: Run the code and enjoy automated analysis results generation. 
# Note: the ARD is contained in the object "ARD" (which contains the appended) mini-ARDs from all individual Analyses ARDs.

example_ARD_script = ARD_script_example("ARD_Out14-1-1.R")
source(example_ARD_script)
head(ARD)