https://github.com/katrinleinweber/r-novice-inflammation

Archive of Software Carpentry's R Novice Inflammation lesson

https://github.com/katrinleinweber/r-novice-inflammation

Repository

Archive of Software Carpentry's R Novice Inflammation lesson

https://github.com/katrinleinweber/r-novice-inflammation/blob/gh-pages/

r-novice-inflammation
=====================

Introduction to R for non-programmers using inflammation data.

Maintainers:

* [Daniel Chen](http://software-carpentry.org/team/#chen_daniel)
* [Harriet Dashnow](http://software-carpentry.org/team/#dashnow_harriet)

The goal of this lesson is to teach novice programmers to write modular code to
perform a data analysis. R is used to teach these skills because it is a
commonly used programming language in many scientific disciplines. However, the
emphasis is not on teaching every aspect of R, but instead on
language agnostic principles like automation with loops and encapsulation with
functions (see [Best Practices for Scientific Computing][best-practices] to
learn more). This lesson is a translation of the [Python version][py],
and is also available in [MATLAB][MATLAB].

The example used in this lesson analyzes a set of 12 data files with
inflammation data collected from a trial for a new treatment for arthritis (the
data was simulated). Learners are shown how it is better to create a function
and apply it to each of the 12 files using a loop instead of using copy-paste
to analyze the 12 files individually.

[best-practices]: http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001745
[py]: https://github.com/swcarpentry/python-novice-inflammation
[MATLAB]: https://github.com/swcarpentry/matlab-novice-inflammation

## Contributing

Please see the current list of [issues][] for ideas for contributing to this
repository. For making your contribution, we use the GitHub flow, which is
nicely explained in the chapter [Contributing to a Project][pro-git] in Pro Git
by Scott Chacon.

General instructions for making contributions are summarized in [CONTRIBUTING.md](https://github.com/swcarpentry/r-novice-inflammation/blob/gh-pages/CONTRIBUTING.md).
When editing topic pages for R lessons, you should change the source R Markdown
file (*.Rmd). Only changes to R markdown files and other supporting files (e.g. data files) should be committed to Git.

To view how the changes will look, when viewed in a web browser, you can render the html pages by running `make preview` from the base of the repository. Generating the html file(s) is required for viewing the [online version of the lessons][online] (you can learn more about the design of the build process [here][design]). Building the rendered page with the Makefile requires installing some dependencies first. In addition to the dependencies listed in the [lesson template documentation][dependencies], you also need to install the R package [knitr][].

Once you've made your edits and rendered the corresponding html files,
you need to add, commit, and push just the source R Markdown file(s)
and any supporting files (e.g. data files). Changes generated by the `make preview` command should not be committed or included in a pull request. These changes will be taken care of by the lesson maintainer when the PR is merged.

## Getting Help

Please see [https://github.com/swcarpentry/lesson-example](https://github.com/swcarpentry/lesson-example)
for instructions on formatting, building, and submitting lessons,
or run `make` in this directory for a list of helpful commands.

If you have questions or proposals, please send them to the [r-discuss][] mailing list.

[dependencies]: https://github.com/swcarpentry/lesson-example#dependencies
[design]: https://github.com/swcarpentry/lesson-example/blob/gh-pages/DESIGN.md
[issues]: https://github.com/swcarpentry/r-novice-inflammation/issues
[knitr]: http://cran.r-project.org/web/packages/knitr/index.html
[online]: http://swcarpentry.github.io/r-novice-inflammation/
[pro-git]: http://git-scm.com/book/en/v2/GitHub-Contributing-to-a-Project
[r-discuss]: http://lists.software-carpentry.org/mailman/listinfo/r-discuss_lists.software-carpentry.org

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