Table 1:

File folder structure for organizing model and analysis files used in the proposed DARTH coding framework.

Folder name	Folder function
data-raw	This is where raw data is stored alongside “.R” scripts that read in raw data, process these data, and calls use_this::use_data(<processed data>) to save .rda formatted data files in the “data” folder. These data could include a “.csv” file with input parameters derived from the published literature, as well as internal R data files (with .RData, .rds, or .rda extensions) containing primary data from which model input values will be estimated through statistical models embedded into the analysis.
data	This is where input data is stored to be used in the different components of the CEA. These data could be generated from raw data stored in the “data-raw” folder. Essentially, this folder stores the cleaned or processed versions of raw data that has been gathered from elsewhere
R	This is where “.R” files that define functions to be used as part of the analysis are stored. These are functions that are specific to the analysis. The model will be one such function; however, other functions will likely be used, such as computing the fit of the model output to the specific calibration targets of the analysis. This folder also stores “.R” scripts that document the datasets in the “data” folder.
analysis	This is where interactive scripts of the analysis would be stored. These scripts control the overall flow of the analysis. This is also where many operations that ultimately become functions will be developed and debugged.
output	This is where output files of the analysis should be stored. These files may be internal R data files (“.RData”, “.rds”, “.rda”) or external data files (such as “.csv”). Examples of files stored here would be the output of the model calibration component or the PSA dataset generated in the uncertainty analysis component. These data files can then be loaded by other components without having to first rerun previous components (e.g. the calibrated model values can be loaded for a base case analysis without re-running the calibration).
figs	For analyses that will include figures, we generally create a separate figures folder. Though these could be stored in the output folder, it can be helpful to have a separate folder so that the images of the figure files can be easily previewed. This is particularly important for analyses that generate a large number of figures.
tables	This folder includes tables to be included in a publication or report, such as the table of intervention costs and effects and ICERs.
report	A report folder could be used to store R Markdown files to describe in detail the model-based CEA by using all the functions and data of the framework, run analyses and display figures. The R Markdown files can be compiled into .html, .doc or .pdf files to generate a report of the CEA. This report could be the document submitted to HTA agencies accompanying the R code of the model-based CEA.
vignettes	A vignettes folder could be used to describe the usage of the functions and data of each of some or all components of the framework through accompanying R Markdown files as documentation. The R Markdown file can use all the functions, outputs, and figures to integrate the R code into the Markdown text.
tests	A tests folder includes “.R” scripts that runs all the unit tests of the functions in the framework. A good practice is to have one file of tests for each complicated function or for each of the components of the framework.

PSA probabilistic sensitivity analysis; ICERs incremental cost-effectiveness ratios; CEA cost-effectiveness analysis; HTA health technology assessment.