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

threeMC: Matt's Model for Male Circumcision
https://github.com/mrc-ide/threemc

Last synced: 25 days ago
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threeMC: Matt's Model for Male Circumcision

Host: GitHub
URL: https://github.com/mrc-ide/threemc
Owner: mrc-ide
License: other
Created: 2021-12-16T15:26:01.000Z (about 3 years ago)
Default Branch: master
Last Pushed: 2024-02-06T15:55:06.000Z (12 months ago)
Last Synced: 2024-11-06T02:31:30.235Z (2 months ago)
Language: R
Homepage:
Size: 70.5 MB
Stars: 0
Watchers: 4
Forks: 2
Open Issues: 2
Metadata Files:
- Readme: README.md
- License: LICENSE

Awesome Lists containing this project

README

# threemc

[![Project Status: Concept – Minimal or no implementation has been done yet, or the repository is only intended to be a limited example, demo, or proof-of-concept.](https://www.repostatus.org/badges/latest/concept.svg)](https://www.repostatus.org/#concept)
[![R build status](https://github.com/mrc-ide/threemc/workflows/R-CMD-check/badge.svg)](https://github.com/mrc-ide/threemc/actions)

## Installation

To install `threemc`:

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

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

## Development steps ##

(largely copied from [naomi](https://github.com/mrc-ide/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](https://semver.org/) 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](https://style.tidyverse.org) 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](https://tbaggery.com/2008/04/19/a-note-about-git-commit-messages.html)
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).

## License