Updated site files

FAQ.md

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+# Can we use the SAS university edition for workshops? #
+
+We are looking into that.  But probably!
+
+# I have a Mac, can I use SAS? #
+
+With the SAS University Edition you can.  We personally have not tried
+it, but it does say it can work for Mac's.
+
+# How do I install SAS on a laptop without a CD drive? #
+
+If you bought the SAS CD, it comes with a License key that you can use
+to download SAS using the SAS Download Manager.
+
+# Message `sh.exe: nano: command not found`. Help? #
+
+> I was just practicing what we’ve done last Tuesday and I am getting
+> this message for nano command: sh.exe”: nano: command not found. It
+> worked well in class, but is not working now. Would you happen to know
+> the solution?  I did specify at the beginning git config --global
+> core.editor "notepad"
+
+Thanks for your question. Looks like your git was configured to use
+Notepad as the text editor, not Nano. Try replacing "nano" with
+"notepad" in your code and see if that works.
+
+# What is a repository? #
+
+> What exactly a repository is? Is it that folder we created named
+> “practice”?
+
+A repository is a history of all your commits. Everytime you do `git
+commit`, it saves the files you are committing into the
+repository. The physical repository is the `.git` folder, but it
+tracks everything in that folder (the "practice" folder).
+
+# Why do we need to check the repo's status so often? #
+
+Checking often is important to make sure you are aware of what is
+going on in your repository.
+
+# What exactly the "untracked" means? #
+
+"Untracked" means that the file is seen by git, but is not
+followed. So any changes to the file will not be recognized by git
+*until* you follow it (track it).  (Like following people on Facebook
+or twitter.  They exist when you aren't following them, but you don't
+keep updated on their status or what they are doing.).
+
+# What happens with the saved files but not committed? #
+
+Saved files (`git add` you mean?) are put into the staging area so
+that they can be committed into the history (the git repository). If
+you don't commit them, they stay there, but they do *not* go into the
+history. Modified files (when you *don't* `git add` them, continue to
+stay modified as you edit them, but they do not get saved until you do
+`git add` and `git commit`.
+
+# 'No new line at the end of file' after running `git diff` #
+
+This can easily be fixed by pressing Enter at the bottom of the file.
+This occurs because (more or less) Git follows the Unix convention.
+If you want a more detailed answer, see
+[this answer on the why](http://stackoverflow.com/a/5813359/2632184)
+and
+[this answer on the history of why](http://stackoverflow.com/questions/729692/why-should-files-end-with-a-newline).
+
+# My terminal is stuck and I can't get back to the prompt (`$` or `>`) #
+
+If you ever get stuck in the terminal, hit `Control-c` to 'c'ancel the
+command and get back to the prompt (the `$` or `>` characters).
+
+

README.md

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+Code As Manuscript Workshops
+============================
+
+This series of *hands-on* workshops aims to introduce students to the
+concept of research reproducibility and to get the students practicing
+with using version control systems and with using modern techniques in
+R (or SAS) that make analyses less error prone and reproducible, and
+that make you more efficient, productive, and in control.  Techniques
+for using version control systems to faciliate greater collaboration
+among peers are also taught.  The ultimate goal of the workshop is to
+show how to reduce the number of steps needed to go from the initial
+data analysis to the final written manuscript or thesis (hence the
+name *Code As Manuscript*).
+
+The `workshops` repository is where the material is developed and
+sent to the website (which is on the `gh-pages` branch).
+
+To contribute, fork the repository and submit a pull request!
+
+# Resources for developing the lessons: #
+
+For images, put them in the `/lessons/images` folder and reference
+them within the lesson using `../images/`.
+
+For developing lesson plans, using the pull request feature.  For
+maintaining the site and the repository, use direct pushing.

about.md

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+---
+layout: page
+title: About
+sidebar: true
+permalink: /
+---
+
+<p class="message">
+
+  <b>Code As Manuscript</b> is a group that teaches a series of workshops on
+  rethinking how code and analyses are structured, and how to
+  implement it.  Our mission is to provide training to researchers and
+  scientists on how to make their analyses more reproducible and to
+  change how researchers view their code.
+
+</p>
+
+We get much inspiration for our workshops from
+[Software Carpentry (SWC)](http://software-carpentry.org/), of which
+we are also SWC instructors.
+
+Currently, we teach these workshops to graduate students in our home
+department and are in the process of expanding to the
+[Graduate Professional Skills program](http://www.sgs.utoronto.ca/currentstudents/Pages/Professional-Development.aspx)
+at the University of Toronto.  Our material is in general split into
+two parts:
+
+* [Lesson content](lessons/)
+* [GPS content](gps/), which also encompasses the lesson content
+
+## Misc facts about this website ##
+
+* Uses the [Hyde](http://hyde.getpoole.com/)
+  [Jekyll](http://jekyllrb.com) theme
+* Developed on GitHub and hosted for free on [GitHub Pages](https://pages.github.com)
+* The content on our site is [licensed](LICENSE/) under CC-BY, while
+  the website design is under MIT.  Check out our
+  [license page](LICENSE/) for more info.
+
+Have questions or suggestions? Feel free to
+[open an issue on GitHub](https://github.com/codeasmanuscript/development/issues/new)
+or email the *Code As Manuscript* instructors (<[email protected]>) for
+more information
+
+# Site listing and content: #
+
+{% for cat in site.category-list %}
+
+## {{ cat }} ##
+
+<ul>
+  {% for page in site.pages %}
+      {% for pc in page.categories %}
+        {% if pc == cat %}
+          <li><a href="{{ site.github.url }}{{ page.url }}">{{ page.title }}</a></li>
+        {% endif %}   <!-- cat-match-p -->
+      {% endfor %}  <!-- page-category -->
+  {% endfor %}  <!-- page -->
+</ul>
+{% endfor %}

gps/about.md

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+---
+layout: page
+sidebar: true
+title: GPS
+permalink: gps/
+---
+
+GPS, or
+[Graduate Professional Skills program](http://www.sgs.utoronto.ca/currentstudents/Pages/Professional-Development.aspx),
+is offered by the
+[School of Graduate Studies](http://www.sgs.utoronto.ca/Pages/default.aspx)
+at the University of Toronto.  The goal of the program is to provide
+workshops that teach students skills that may be useful in careers
+after they graduate.  Completing the GPS program is recorded on the
+students' transcript.  Our GPS-approved *Code As Manuscript* series of
+workshops provide credits to completion of the GPS program.  Our links
+for the workshop series are:
+
+* [Syllabus](sas-syllabus/) for our SAS workshops.
+* [Syllabus](r-syllabus/) for our R workshops.

gps/r-syllabus.md

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+---
+title: "Code as Manuscript: Data wrangling, visualization, and reproducibility in R"
+author:
+    - Luke W. Johnston
+    - Sarah Meister
+date: 2015-10-17
+layout: page
+sidebar: false
+tag:
+    - GPS
+    - R
+    - Syllabus
+categories:
+    - GPS
+    - R
+    - Syllabus
+---
+
+## Course description: ##
+
+This series of *hands-on* workshops aims to introduce students to the
+concept of research reproducibility and to get the students practicing
+with using version control systems and with using modern techniques in
+R that make analyses less error prone and reproducible, and that make
+you more efficient, productive, and in control.  Techniques for using
+version control systems to faciliate greater collaboration among peers
+will also be presented.  The ultimate goal of the workshop is to show
+how to reduce the number of steps needed to go from the initial data
+analysis to the final written manuscript or thesis (hence the name
+*Code As Manuscript*).  Given the applied nature of the concepts in
+these workshops, hands-on activities and
+[live coding](http://en.wikipedia.org/wiki/Live_coding) will be
+integrated into each workshop.
+
+## Goal: ##
+
+The expected goal of the workshops is that you will be able to:
+
+* Put your research under version control using Git.
+* Push and pull your git research repository to either
+  [GitHub](https://github.com/) or
+  [BitBucket](https://bitbucket.org/).
+* Learn the basics of R and functions within R
+* Produce publication quality plots
+* Quickly wrangle your data into an analyzable format
+* Reproducibly incorporate R code into your manuscript or thesis to
+  instantly add results and plots (no more copy and paste)
+
+Attaining these goals will be the first steps in making an efficient
+and highly productive workflow, that is also scientifically rigorous
+and transparent, and which you can take with you for the rest of your
+career (since R is free!).
+
+## Schedule ##
+
+Lesson content can be found [here]({{ site.github.url }}/lessons/).  The workshop will
+follow the following sequence of topics on **Mondays from 3:00-6:00pm** at **65
+St. George St., room 201**:
+
+1. Git & GitHub -- Oct. 26th
+2. Basics of R -- Nov. 2nd
+3. Visualization -- Nov. 9th
+4. Data wrangling -- Nov. 16th
+5. Dynamic report generation -- Nov. 23rd
+
+## Intended audience: ##
+
+Graduate students or post-docs whose research involves a fair amount
+of data analysis.  No experience necessary for these workshops.
+
+## Pre-requisites: ##
+
+* Fully charged laptop (though we do have outlets)
+* Install the appropriate software (see our
+  [instructions page, under the R section]({{ site.github.url }}/lessons/instructions/))
+* Bring a positive, not-afraid-of-making-mistakes-or-feeling-unsure
+  attitude!!  Learning any language (either human or computer) is
+  hard work and *not* easy, but can be done!
+
+## Assignments: ##
+
+Because this is a hands-on workshop, at the end of each workshop, we
+have an activity for you to try out.  And since this is a GPS-approved
+course, if you want to get a GPS credit, you will need to:
+
+1. Come to all the workshops (though we are flexible)
+2. Complete each workshop assignment and push to the shared repository
+   on GitHub (so we can track and view it).
+
+Don't worry if this doesn't make sense yet.  We will go over all these
+details over the workshop series.
+
+# Instructors #
+
+Luke Johnston, MSc, PhD (c)  
+[email protected]
+
+Sarah Meister, MSc (c)  
+[email protected]
+
+You can contact the workshop email at: [email protected]
+

gps/sas-syllabus.md

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+---
+title: "Code as Manuscript: Practices for Reproducibility and Efficiency in SAS"
+author:
+    - Luke Johnston
+    - Daiva Nielsen
+date: 2015-06-15
+geometry: margin=1in
+fontsize: 12pt
+papersize: letterpaper
+layout: page
+sidebar: false
+tag:
+    - GPS
+    - SAS
+    - Syllabus
+categories:
+    - GPS
+    - SAS
+    - Syllabus
+---
+
+## Course description: ##
+
+This series of workshops aims to introduce students to the concept of
+research reproducibility and to get the students practicing with using
+version control systems and with using techniques in SAS that make the
+analysis more efficient, less error prone, and less stressful.
+Techniques for using version control systems to faciliate greater
+collaboration among peers will also be presented.  The ultimate goal
+of the workshops is to demonstrate how to reduce the total number of
+steps required to produce a manuscript from the data analysis stage
+(hence the name *Code As Manuscript*).  Given the applied nature of
+the concepts in these workshops, hands-on activities and
+[live coding](http://en.wikipedia.org/wiki/Live_coding) will be
+integrated into each workshop.
+
+## Goal: ##
+
+The expected goal of the workshops is that you will be able to:
+
+* Put your research under version control using Git.
+* Push and pull your git research repository to either
+  [GitHub](https://github.com/) or
+  [BitBucket](https://bitbucket.org/).
+* Simplify your SAS code by using macros and ODS facilities in a way
+  that allows code to output results into a file that can be easily
+  incorporated into a manuscript or report.
+* To put the macros into either a macro file or as a SAS autocall
+  library so that the macros are useable in all your SAS files.
+
+Attaining these goals will the first steps in making an efficient and
+highly productive workflow, that is also scientifically rigorous and
+transparent, which you can take with you for the rest of your career.
+
+## Schedule ##
+
+Lesson content can be found [here]({{ site.github.url }}/lessons/).  The workshop will
+follow the following sequence of topics:
+
+1. Git: June 16th, 3:00-5:00pm
+2. GitHub: June 23rd, 3:00-5:00pm
+3. Macros: June 30th, 3:00-5:00pm
+4. ODS: July 7th, 3:00-5:00pm
+
+## Intended audience: ##
+
+Graduate students or post-docs whose research involves a fair amount
+of data analysis using SAS.
+
+## Pre-requisites: ##
+
+* Bring a fully charged laptop
+* Install the appropriate software (see our
+  [instructions page]({{ site.github.url }}/lessons/instructions/))
+* Fairly competent in coding SAS commands.  *We are not here to teach
+  an introduction to SAS*, we assume you are fairly competent with
+  using SAS.  If you are a novice, recognize that you may not
+  understand everything that is going on... *However*, you will still
+  likely learn a lot!!
+* Some familiarity with the command-line or with computing is
+  desirable, but not necessary.
+
+## Assignment: ##
+
+Because of the hands-on nature of the workshops, in order to obtain a
+GPS credit for the workshops you need to:
+
+1. Come to all the workshops
+2. Complete each workshop assignment
+
+To hand in the assignment, you will need to:
+
+1. Fork our shared workshop repository
+2. Clone it to your computer
+3. Create a new folder with your name
+4. Put the assignments for each workshop in your new folder
+5. Commit and push the assignments to your fork
+6. Submit a pull request to the main shared repository
+
+Don't worry if this doesn't make sense yet.  We will go over all these
+details over the workshop series.
+
+# Instructors #
+
+Luke Johnston, MSc, PhD (c)  
+[email protected]
+
+Daiva Nielsen, PhD  
+[email protected]