Naomi

Naomi model for subnational HIV estimates

Installation

The package is not available from CRAN. 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 and add a news item describing the change
• Reviewer should check code and ensure the build passes on Buildkite before merging

Code coverage

To check code coverage from R.

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

Website

A pkgdown website 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.