Development

Setup clugenr development

Clone the package, cd into to the package’s folder and start R:

$ git clone https://github.com/clugen/clugenr.git
$ cd clugenr

Developing clugenr requires devtools, thus make sure it’s installed before continuing. Open an R prompt at the clugenr folder and install clugenr’s development dependencies:

devtools::install_dev_deps()

The package can be tested as follows:

devtools::test()

There are four levels of testing, by increasing thoroughness (and slowness): cran, ci, normal and full. The first two run by default on CRAN and CI environments, respectively. The third one, normal, is the default mode when running the tests locally, and may take some time (10-20 minutes). The last one, full is more thorough and can take a few hours. It’s possible to define the tests thoroughness by setting the CLUGENR_TEST_MODE environment variable. For example, to simulate how tests would run in CRAN as follows:

Sys.setenv(CLUGENR_TEST_MODE = "cran")
devtools::test()
Sys.unsetenv("CLUGENR_TEST_MODE")

The following instruction updates the documentation, then builds and checks the package locally:

devtools::check()

It’s also possible to define the environment in which to run the tests when performing the check:

Sys.setenv(CLUGENR_TEST_MODE = "ci")
devtools::check()
Sys.unsetenv("CLUGENR_TEST_MODE")

Create or update the generated documentation in man/, file collation and NAMESPACE:

devtools::document()

Build clugenr’s website (requires pkgdown, ggplot2, patchwork and rgl):

pkgdown::build_site()
# Can also be done with devtools::build_site()
# In either case add option `preview = F` to avoid opening the browser

Install the package locally with:

devtools::install()

Check that it works:

library(clugenr)
x <- clugen(2, 5, 800, c(-1, 1), 0.6, c(4, 6), 5, 0.4, 0.5)
plot(x$points, col = x$clusters, xlab = "x", ylab = "y", asp = 1)

Code style

To contribute to clugenr, follow the tidyverse style guide. Some highlights include, but are not limited to:

  • File encoding: UTF-8
  • Indentation: 2 spaces (no tabs)
  • Line size limit: 80 chars
  • Newlines: Unix style, i.e. LF or \n