threemc

Installation

To install threemc:

remotes::install_github("mrc-ide/threemc", upgrade = FALSE)

To see how threemc works for a simple example, please see the relevant vignette.

(largely copied from naomi)

Make changes in a new branch,
Run checks (requires goodpractice package). Also documents functions with devtools::check(). These checks can be run directly from the script scripts/goodpractice.R or from the command line with make goodpractice (use make goodpractice_vignette if making changes to vignettes, which are very slow to build),
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, and
Reviewer should check code and ensure the build passes on Buildkite before merging.

Additionally:

Wherever possible, add arguments for optional new functionality, with old functionality as default,
If changing threemc_aggregate or threemc_ppc (the slowest "purely R" functions in this package), a before vs after profiling would be useful, using e.g. profvis,
Follow the tidverse styleguide as much as possible, but at least have your commits pass the call to lintr from goodpractice,
Ensure that git commits (and R comments) are in the imperative case (see here for Tim Pope's rational behind this),
To avoid notes from devtools::check() when using non-standard evaluation (NSE),
- in dplyr, refer to all columns with rlang::`.data`, e.g. .data$col,
- in data.table, assign columns referenced in NSE to the value NULL at the beginning of a function (see threemc_ppc for an example).