hiar

https://github.com/dynamo-hia/hiar

Repository

README.Rmd

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# Dynamic Modeling of Health Impact Assessment in R


[![R-CMD-check](https://github.com/Dynamo-HIA/hiaR/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/Dynamo-HIA/hiaR/actions/workflows/R-CMD-check.yaml)
[![Codecov test coverage](https://codecov.io/gh/Dynamo-HIA/hiaR/graph/badge.svg)](https://app.codecov.io/gh/Dynamo-HIA/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`:

```r
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](https://dynamo-hia.github.io/hiaR/docs/articles/example.html) for a detailed example.

## Installation

You can install the `hiaR` package from GitHub via `remotes`:

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

## User Documentation

The documentation of the `hiaR` package is available at [https://dynamo-hia.github.io/hiaR/](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/](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**

1. Open `Tools` $\rightarrow$ `Project Options` $\rightarrow$ `Code Editing`
2. Tick `Ensure that source files end with newline`
3. 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](https://style.tidyverse.org/) style guide for R code. You can use the `styler` package to automatically format your code:

```r
# 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](https://github.com/Dynamo-HIA/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.

Owner

Citation (CITATION.cff)

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: Dynamic Modeling of Health Impact Assessment in R
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: Hendriek
    family-names: Boshuizen
    email: hendriek.boshuizen@rivm.nl
    orcid: "https://orcid.org/0000-0002-3916-9095"
  - given-names: Malte
    family-names: Lüken
    email: m.luken@esciencecenter.nl
    orcid: "https://orcid.org/0000-0001-7095-203X"
  - given-names: Flavio
    family-names: Hafner
    email: f.hafner@esciencecenter.nl
    orcid: "https://orcid.org/0009-0000-5893-9000"
  - given-names: Laurens
    family-names: Bogaardt
    email: laurens.bogaardt@rivm.nl
    orcid: "https://orcid.org/0000-0002-7712-6627"
repository-code: 'https://github.com/Dynamo-HIA/hiaR'
url: 'https://dynamo-hia.github.io/hiaR/'
abstract: >-
  The hiaR package provides 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. Users
  can import and use their own data to add and analyze
  diseases or populations of interest.
license: GPL-3.0-or-later
version: 1.0.0

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