Merge branch 'gh-pages' into dataframe-as-numeric-updated

.github/ISSUE_TEMPLATE.md

@@ -0,0 +1,9 @@
+Please delete the text below before submitting your contribution. 
+
+---
+
+Thanks for contributing! If this contribution is for instructor training, please send an email to [email protected] with a link to this contribution so we can record your progress. You’ve completed your contribution step for instructor checkout just by submitting this contribution.  
+
+Please keep in mind that lesson maintainers are volunteers and it may be some time before they can respond to your contribution. Although not all contributions can be incorporated into the lesson materials, we appreciate your time and effort to improve the curriculum.  If you have any questions about the lesson maintenance process or would like to volunteer your time as a contribution reviewer, please contact Kate Hertweck ([email protected]).  
+
+---

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,9 @@
+Please delete the text below before submitting your contribution. 
+
+---
+
+Thanks for contributing! If this contribution is for instructor training, please send an email to [email protected] with a link to this contribution so we can record your progress. You’ve completed your contribution step for instructor checkout just by submitting this contribution.  
+
+Please keep in mind that lesson maintainers are volunteers and it may be some time before they can respond to your contribution. Although not all contributions can be incorporated into the lesson materials, we appreciate your time and effort to improve the curriculum.  If you have any questions about the lesson maintenance process or would like to volunteer your time as a contribution reviewer, please contact Kate Hertweck ([email protected]).  
+
+---

.mailmap

@@ -1,83 +1,44 @@
-Aron Ahmadia <[email protected]>
-Matthew Aiello-Lammens <matt.lammens@gmail.com>
-Joshua Ainsley <jainsley@gmail.com>
-James Allen <jamesallen0108@gmail.com>
+Abigail Cabunoc Mayes <[email protected]>
+Abigail Cabunoc Mayes <abigail.cabunoc@gmail.com> <[email protected]>
+Andy Boughton <[email protected]> <pchemist@gmail.com>
+Andy Teucher <[email protected]> <Andy.Teucher@gmail.com>
 Areej Alsheikh-Hussain <[email protected]>
-Paula Andrea <[email protected]>
-Jeffrey Arnold <[email protected]>
-Alex Bajcz <[email protected]>
-Piotr Banaszkiewicz <[email protected]>
+Beth Signal <[email protected]>
+Daniel Chen <[email protected]> <[email protected]>
+Daniel Turek <[email protected]>
 Diego Barneche <[email protected]>
-Greg Bass <[email protected]>
-Trevor Bekolay <[email protected]>
-Mik Black <[email protected]>
-John Blischak <[email protected]>
-Andy Boughton <[email protected]> <[email protected]>
-Karl Broman <[email protected]>
+Donna Henderson <[email protected]>
 Eric Bruger <[email protected]>
-Abigail Cabunoc Mayes <[email protected]> <[email protected]>
-Scott Chamberlain <[email protected]>
-Daniel Chen <[email protected]>
-Harriet Dashnow <[email protected]>
-Matt Dickenson <[email protected]>
-Alastair Droop <[email protected]>
-Jonah Duckles <[email protected]>
-Rémi Emonet <[email protected]> <[email protected]>
-Marianna Foos <[email protected]>
-Auriel Fournier <[email protected]>
-David Fredman <[email protected]>
-Javier García-Algarra <[email protected]>
-Noushin Ghaffari <[email protected]> <[email protected]>
-Heather Gibling <[email protected]>
-Jeremy Gray <[email protected]>
-Jessica Guo <[email protected]>
-Melissa Guzman <[email protected]>
-Denis Haine <[email protected]>
-Michael Hansen <[email protected]>
+Eric Milliman <[email protected]>
+Evan P. Williamson <[email protected]>
 Fabian Held <[email protected]>
-Donna Henderson <[email protected]>
-James Hiebert <[email protected]>
-Jeff Hollister <[email protected]>
-Mike Jackson <[email protected]>
-Elsie Jacobson <[email protected]>
-W. Trevor King <[email protected]>
-Michael Levy <[email protected]>
-Mark Mandel <[email protected]>
-Carlos Martinez <[email protected]>
-Ben Marwick <[email protected]>
+Félix-Antoine Fortin <[email protected]> <[email protected]>
 François Michonneau <[email protected]>
-James Mickley <[email protected]>
-Eric Milliman <[email protected]>
-Bill Mills <[email protected]>
+François Michonneau <[email protected]> <[email protected]>
+Ge Baolai <[email protected]>
+Greg Bass <[email protected]>
+Greg Wilson <[email protected]> <[email protected]>
+James Allen <[email protected]> <[email protected]>
+Javier García-Algarra <[email protected]>
+Jeffrey Arnold <[email protected]>
 Joaquin Moris <[email protected]>
-Hani Nakhoul <[email protected]>
-Matthias Nilsson <[email protected]>
-Aaron O'Leary <[email protected]>
-Frank Pennekamp <[email protected]>
-Raissa Philibert <[email protected]>
-Jon Pipitone <[email protected]>
-Timothée Poisot <[email protected]>
-Louis Ranjard <[email protected]>
-Joey Reid <[email protected]>
-Scott Ritchie <[email protected]>
-Natalie Robinson <[email protected]>
-Michael Sachs <[email protected]>
-Pat Schloss <[email protected]>
-Peter Schmiedeskamp <[email protected]>
-Beth Signal <[email protected]>
-Raniere Silva <[email protected]> <[email protected]> <[email protected]>
-Gavin Simpson <[email protected]>
-Karthik Srinivasan <[email protected]>
 Joseph Stachelek <[email protected]>
-Valentina Staneva <[email protected]>
-Sarah Stevens <[email protected]>
+Kara Woo <[email protected]>
+Karthik Srinivasan <[email protected]>
+Kate Hertweck <[email protected]>
+Louis Ranjard <[email protected]>
+Melissa Guzman <[email protected]>
 Michael Sumner <[email protected]>
+Mik Black <[email protected]>
+Mike Jackson <[email protected]> <[email protected]>
+Natalie Robinson <[email protected]>
+Noushin Ghaffari <[email protected]>
+Noushin Ghaffari <[email protected]> <[email protected]>
+Raniere Silva <[email protected]> <[email protected]>
+Raniere Silva <[email protected]> <[email protected]>
+Rémi Emonet <[email protected]> <[email protected]>
+Rémi Emonet <[email protected]> <[email protected]>
 Sarah Supp <[email protected]>
-Andy Teucher <[email protected]>
-Daniel Turek <[email protected]>
-Stephen Turner <[email protected]>
-Lukas Weber <[email protected]>
-Greg Wilson <[email protected]> <[email protected]>
-Kara Woo <[email protected]>
-Tom Wright <[email protected]>
-Naupaka Zimmerman <[email protected]>
+Scott Chamberlain <[email protected]>
+Timothée Poisot <[email protected]> <[email protected]>
+Valentina Staneva <[email protected]>

AUTHORS

@@ -7,6 +7,7 @@ Paula Andrea
 Jeffrey Arnold
 Alex Bajcz
 Piotr Banaszkiewicz
+Ge Baolai
 Diego Barneche
 Greg Bass
 Trevor Bekolay
@@ -19,11 +20,13 @@ Abigail Cabunoc Mayes
 Scott Chamberlain
 Daniel Chen
 Harriet Dashnow
+Gabriel A. Devenyi
 Matt Dickenson
 Alastair Droop
 Jonah Duckles
 Rémi Emonet
 Marianna Foos
+Félix-Antoine Fortin
 Auriel Fournier
 David Fredman
 Javier García-Algarra
@@ -36,10 +39,13 @@ Denis Haine
 Michael Hansen
 Fabian Held
 Donna Henderson
+Kate Hertweck
 James Hiebert
 Jeff Hollister
 Mike Jackson
 Elsie Jacobson
+Zbigniew Jędrzejewski-Szmek
+Jonathan Keane
 W. Trevor King
 Michael Levy
 Mark Mandel
@@ -77,6 +83,7 @@ Andy Teucher
 Daniel Turek
 Stephen Turner
 Lukas Weber
+Evan P. Williamson
 Greg Wilson
 Kara Woo
 Tom Wright

CONDUCT.md

@@ -32,13 +32,14 @@ or other unprofessional conduct.
 
 Project maintainers have the right and responsibility to remove, edit, or reject
 comments, commits, code, wiki edits, issues, and other contributions
-that are not aligned to this Code of Conduct.
+that are not aligned to our [Code of Conduct][coc].
 Project maintainers who do not follow the Code of Conduct may be removed from the project team.
 
 Instances of abusive, harassing, or otherwise unacceptable behavior
-may be reported by opening an issue or contacting one or more of the project maintainers.
+may be reported by following our [reporting guidelines][coc-reporting].
 
-This Code of Conduct is adapted from
-the [Contributor Covenant][contrib-covenant] Version 1.0.0.
 
-[contrib-covenant]: http://contributor-covenant.org/
+- [Software and Data Carpentry Code of Conduct][coc]
+- [Code of Conduct Reporting Guide][coc-reporting]
+
+{% include links.md %}

CONTRIBUTING.md

@@ -46,8 +46,8 @@ and to meet some of our community members.
 ## Where to Contribute
 
 1.  If you wish to change this lesson,
-    please work in <https://github.com/swcarpentry/r-novice-inflammation>,
-    which can be viewed at <https://swcarpentry.github.io/r-novice-inflammation>.
+    please work in <https://github.com/swcarpentry/FIXME>,
+    which can be viewed at <https://swcarpentry.github.io/FIXME>.
 
 2.  If you wish to change the example lesson,
     please work in <https://github.com/swcarpentry/lesson-example>,
@@ -140,13 +140,12 @@ You can also [reach us by email][contact].
 [dc-lessons]: http://datacarpentry.org/lessons/
 [dc-site]: http://datacarpentry.org/
 [discuss-list]: http://lists.software-carpentry.org/listinfo/discuss
-[example-site]: https://swcarpentry.github.io/lesson-example/
 [github]: http://github.com
 [github-flow]: https://guides.github.com/introduction/flow/
 [github-join]: https://github.com/join
 [how-contribute]: https://egghead.io/series/how-to-contribute-to-an-open-source-project-on-github
-[issues]: https://github.com/swcarpentry/r-novice-inflammation/issues/
-[repo]: https://github.com/swcarpentry/r-novice-inflammation/
+[issues]: https://github.com/swcarpentry/FIXME/issues/
+[repo]: https://github.com/swcarpentry/FIXME/
 [swc-issues]: https://github.com/issues?q=user%3Aswcarpentry
 [swc-lessons]: http://software-carpentry.org/lessons/
 [swc-site]: http://software-carpentry.org/

LICENSE.md

@@ -73,7 +73,7 @@ WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 
 ## Trademark
 
-"Software Carpentry" an "Data Carpentry" and their respective logos
+"Software Carpentry" and "Data Carpentry" and their respective logos
 are registered trademarks of [NumFOCUS][numfocus].
 
 [cc-by-human]: https://creativecommons.org/licenses/by/4.0/

Makefile

@@ -9,18 +9,19 @@ DST=_site
 
 # Controls
 .PHONY : commands clean files
+.NOTPARALLEL:
 all : commands
 
 ## commands         : show all commands.
 commands :
 	@grep -h -E '^##' ${MAKEFILES} | sed -e 's/## //g'
 
 ## serve            : run a local server.
-serve : lesson-rmd
+serve : lesson-md
 	${JEKYLL} serve
 
 ## site             : build files but do not run a server.
-site : lesson-rmd
+site : lesson-md
 	${JEKYLL} build
 
 # repo-check        : check repository settings.
@@ -53,7 +54,7 @@ workshop-check :
 ## ----------------------------------------
 ## Commands specific to lesson websites.
 
-.PHONY : lesson-check lesson-rmd lesson-files lesson-fixme
+.PHONY : lesson-check lesson-md lesson-files lesson-fixme
 
 # RMarkdown files
 RMD_SRC = $(wildcard _episodes_rmd/??-*.Rmd)
@@ -79,13 +80,16 @@ HTML_DST = \
   $(patsubst _extras/%.md,${DST}/%/index.html,$(wildcard _extras/*.md)) \
   ${DST}/license/index.html
 
-## lesson-rmd       : convert Rmarkdown files to markdown
-lesson-rmd: $(RMD_SRC)
-	@bin/knit_lessons.sh $(RMD_SRC)
+## lesson-md        : convert Rmarkdown files to markdown
+lesson-md : ${RMD_DST}
+
+# Use of .NOTPARALLEL makes rule execute only once
+${RMD_DST} : ${RMD_SRC}
+	@bin/knit_lessons.sh ${RMD_SRC}
 
 ## lesson-check     : validate lesson Markdown.
 lesson-check :
-	@bin/lesson_check.py -s . -p ${PARSER}
+	@bin/lesson_check.py -s . -p ${PARSER} -r _includes/links.md
 
 ## lesson-check-all : validate lesson Markdown, checking line lengths and trailing whitespace.
 lesson-check-all :

README.md

@@ -11,13 +11,13 @@ Maintainers:
 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 the focus is on
+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). In fact, this lesson is a translation of the [Python version][py],
-and the lesson is also available in [MATLAB][].
+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 is analyzing a set of 12 data files with
+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
@@ -42,7 +42,7 @@ To view how the changes will look, when viewed in a web browser, you can render
 
 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 off by the lesson maintainer when the PR is merged.
+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