Naomi model for subnational HIV estimates
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")
make test
or via R using devtools::test()
to ensure changes don't cause regressions to existing functionalitymake build
and make check
from command line or devtools::check()
from RTo check code coverage from R.
cov <- covr::package_coverage()
covr::report(cov)
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.
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.
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