Dynamic Modeling of Health Impact Assessment in R • hiaR

The goal of the hiaR R package is to provide a user-friendly interface to the DYNAMO-HIA software tool. It contains R functions to configure and run DYNAMO-HIA, and to visualize the results. The package also contains a Shiny app to interactively run DYNAMO-HIA.

DYNAMO-HIA (DYNamic MOdeling for Health Impact Assessment) is a generic software tool specially designed to aid the quantification step in health impact assessment. DYNAMO-HIA is generic in the sense that it allows arbitrary chronic diseases or risk-factors that fit the standard causal pathway of the health impact assessment framework to be modeled. The user can import and use his or her own data to add and analyze diseases or populations that are of interest to him or her.

Getting Started

Running the Shiny App

You can start the Shiny app with hiaR::launch_application:

hiaR::launch_application()

Running DYNAMO-HIA from R

You can run DYNAMO-HIA from R using the hiaR::run_dynamo_hia function. This function requires a specific folder structure, reference data, and simulation configuration file to be present. See the hiaR documentation for a detailed example.

Installation

You can install the hiaR package from GitHub via remotes:

remotes::install_github("Dynamo-HIA/hiaR")

User Documentation

The documentation of the hiaR package is available at https://dynamo-hia.github.io/hiaR/.

The documentation of DYNAMO-HIA including the user manual, examples, and reference datasets is available at https://dynamo-hia.github.io/.

Development Documentation

Make sure you have the right settings for line endings. If you open the project in RStudio, the settings are automatically set. Otherwise, you can set them manually:

RStudio

Open Tools $\rightarrow$ Project Options $\rightarrow$ Code Editing
Tick Ensure that source files end with newline
Set Line ending conversions to Windows (CR/LF)

Console

Run usethis::use_rstudio(line_ending = "windows")

On Windows, make sure that git config core.autocrlf is set to false.

Conventions

We follow the tidyverse style guide for R code. You can use the styler package to automatically format your code:

# Style single R file (has tidyverse style as default)
styler::style_file("R/myfile.R")

# Apply style to entire package
styler::style_pkg()

Naming of Modules

For R Shiny modules, use the following naming pattern:

The R file with the module should be named my_purpose_module.R
Inside my_purpose_module.R, define the functions my_purpose_ui for the user interface and my_purpose_server for the server
If possible, add automatic tests for the server functionality. The UI functionality is more complex to test and we decided to test this manually for now.

Imports

Any functions from shiny and shinyFiles can be used directly without the shiny:: prefix. For any other packages, be explicit and use mypackage::myfunction().

Before Making a Release

Before making a release, please change the default value for the release_tag argument in the download_github_release function to the tag of the latest release of DYNAMO-HIA if necessary.

Credits

The hiaR package is developed by the Netherlands eScience Center and the Rijksinstituut voor Volksgezondheid en Milieu (RIVM; National Institute for Public Health and the Environment).

Generative AI Statement

The code in this repository has been partly generated and/or refined using ChatGPT 4, Claude 3.5 Sonnet, and/or GitHub Copilot Individual. All AI-generated output has been verified for correctness, accuracy, and completeness, adapted where needed, and approved by the authors.