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https://github.com/mrc-ide/naomi

Naomi model for subnational HIV estimation
https://github.com/mrc-ide/naomi

Last synced: about 2 months ago
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Naomi model for subnational HIV estimation

Host: GitHub
URL: https://github.com/mrc-ide/naomi
Owner: mrc-ide
License: other
Created: 2019-08-28T15:32:00.000Z (over 5 years ago)
Default Branch: master
Last Pushed: 2024-10-29T11:41:54.000Z (about 2 months ago)
Last Synced: 2024-10-29T12:43:40.351Z (about 2 months ago)
Language: R
Homepage: https://mrc-ide.github.io/naomi
Size: 57 MB
Stars: 9
Watchers: 6
Forks: 9
Open Issues: 43
Metadata Files:
- Readme: README.md
- Changelog: NEWS.md
- License: LICENSE

Awesome Lists containing this project

README

## Naomi

[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
[![R-CMD-check](https://github.com/mrc-ide/naomi/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/mrc-ide/naomi/actions/workflows/R-CMD-check.yaml)
[![Codecov test coverage](https://codecov.io/gh/mrc-ide/naomi/branch/master/graph/badge.svg)](https://codecov.io/gh/mrc-ide/naomi?branch=master)

Naomi model for subnational HIV estimates

### Installation

The package is not available from [CRAN](https://cran.r-project.org/).
Instead, install the compiled version from the mrc-ide universe.

```
install.packages("naomi", repos = "https://mrc-ide.r-universe.dev")
```

Install from GitHub to install from source.
```
# install.packages("devtools") # Uncomment this line if devtools is not yet installed
devtools::install_github("mrc-ide/naomi")
```

### Development steps

* Make changes in a new branch
* Run tests from the command line using `make test` or via R using `devtools::test()` to ensure changes don't cause regressions to existing functionality
* Run build and check before pushing to remote using `make build` and `make check` from command line or `devtools::check()` from R
* When branch is ready for merging create a PR and add a reviewer
* Ensure that the version number has been updated according to [semantic versioning](https://semver.org/) and add a news item describing the change
* Reviewer should check code and ensure the build passes on [Buildkite](https://buildkite.com/mrc-ide/naomi) before merging

### Code coverage

To check code coverage from R.

```
cov <- covr::package_coverage()
covr::report(cov)
```

### Website

A [pkgdown website](https://mrc-ide.github.io/naomi) is available for the package. To update the website using most recent docs and vignettes type `make website` on the command line from the root directory. Note that to see the effects in place immediately you may need to refresh the browser cache by opening developer console and right click refresh button -> Empty Cache and Hard Reload.

### Generating test data

Run `./scripts/build_test_data` to run the model and output the fit data. This will speed up some tests and stop the model fitting and uncertainty calculations being done every time. This data is not on Github as it is quite large ~ 220MB for Malawi.