tavareshugo / 2019-02-19-cambridge

Into to R - Data Carpentry course Cambridge 19-20 Feb 2019

workshop-template

This repository is Software Carpentry and Data Carpentry's template for creating websites for workshops.

1. Please do not fork this repository directly on GitHub. Instead, please use GitHub's importer following the instructions below to copy this workshop-template repository and customize it for your workshop.

2. Please do your work in your repository's gh-pages branch, since that is what is automatically published as a website by GitHub.

3. Once you are done, please also let us know the workshop URL. If this is a self-organised workshop, you should also fill in the self-organized workshop form (if you have not already done so), so we can keep track of all workshops. We build the list of workshops on our websites from the data included in your index.md page. We can only do that if you customize that page correctly and let us know the workshop URL.

If you run into problems, or have ideas about how to make this process simpler, please get in touch. The pages on customizing your website, the FAQ, and the design notes have more detail on what we do and why. And please note: if you are teaching Git, please create a separate repository for your learners to practice in.

Creating a Repository

1. Log in to GitHub. (If you do not have an account, you can quickly create one for free.) You must be logged in for the remaining steps to work.

2. Go to GitHub's importer.

3. Paste the url of this repo as the old repository to clone: https://github.com/swcarpentry/workshop-template.

4. Select the owner for your new repository. (This will probably be you, but may instead be an organization you belong to.)

5. Choose a name for your workshop website repository. This name should have the form YYYY-MM-DD-site, e.g., 2016-12-01-miskatonic, where YYYY-MM-DD is the start date of the workshop.

6. Make sure the repository is public.

7. At this point, you should have a page like this:

   

   You can now click "Begin Import". When the process is done, you will receive a message like "Importing complete! Your new repository gvwilson/2016-12-01-miskatonic is ready." and you can go to the new repository by clicking on the name.

Note: some people have had intermittent errors during the import process, possibly because of the network timing out. If you experience a problem, please re-try; if the problem persists, please get in touch.

Customizing Your Website

1. Go into your newly-created repository, which will be at https://github.com/your_username/YYYY-MM-DD-site. For example, if your username is gvwilson, the repository's URL will be https://github.com/gvwilson/2016-12-01-miskatonic.

2. Ensure you are on the gh-pages branch by clicking on the branch under the drop down in the menu bar (see the note below):

   

3. Edit the header of index.md to customize the list of instructors, workshop venue, etc. You can do this in the browser by clicking on it in the file view on GitHub and then selecting the pencil icon in the menu bar:

   

   Editing hints are embedded in index.md, and full instructions are in the customization instructions.

4. Edit _config.yml to customize certain site-wide variables, such as: carpentry (to tell us which carpentry workshop this is), title (overall title for all pages), repository (so that URLs resolve correctly both locally and on GitHub), workshop_repo (the URL of the workshop repository on GitHub) and workshop_site (the repository's GitHub Pages URL).

   Editing hints are embedded in _config.yml, and full instructions are in the customization instructions.

5. Edit the schedule.html file to edit the schedule for your upcoming workshop. This file is located in the _includes directory, make sure to choose the one from the appropriate dc (Data Carpentry workshop), lc (Library Carpentry), or sc (Software Carpentry) subdirectory.

6. Alternatively, if you are already familiar with Git, you can clone the repository to your desktop, edit index.md, _config.yml, and schedule.html there, and push your changes back to the repository.

   git clone -b gh-pages https://github.com/your_username/YYYY-MM-DD-site
   

   You should specify -b gh-pages to checkout the gh-pages branch because the imported repository doesn't have a master branch.

   In order to view your changes once you are done editing, you must push to your GitHub repository:

   git push origin gh-pages
   

7. When you are done editing, go to the GitHub Pages URL for your workshop and preview your changes. In the example above, this is https://gvwilson.github.io/2016-12-01-miskatonic. The finished page should look something like this.

8. Optional: you can now change the README.md file in your website's repository, which contains these instructions, so that it contains a short description of your workshop and a link to the workshop website.

Note: please do all of your work in your repository's gh-pages branch, since GitHub automatically publishes that as a website.

Note: this template includes some files and directories that most workshops do not need, but which provide a standard place to put extra content if desired. See the design notes for more information about these.

Further instructions are available in the customization instructions. This FAQ includes a few extra tips (additions are always welcome) and these notes on the background and design of this template may help as well.

Checking Your Changes

If you want to preview your changes on your own machine before publishing them on GitHub, you can do so as described below.

1. Install the software described below. This may require some work, so feel free to preview by pushing to the website.

2. Run the command

   make serve
   

   and go to http://0.0.0.0:4000 to preview your site. You can also run this command by typing make serve (assuming you have Make installed).

3. Run the command

   make workshop-check
   

   to check for a few common errors in your workshop's home page. (You must have Python 3 installed to do this.)

(Optional) Linking to Your Page

At the top of your repository on GitHub you'll see

No description or website provided. — Edit

Click 'Edit' and add:

1. A very brief description of your workshop in the "Description" box (e.g., "Miskatonic University workshop, Dec. 2016")

2. The URL for your workshop in the "Website" box (e.g., https://gvwilson.github.io/2016-12-01-miskatonic)

This will help people find your website if they come to your repository's home page.

Creating Extra Pages

In rare cases, you may want to add extra pages to your workshop website. You can do this by putting either Markdown or HTML pages in the website's root directory and styling them according to the instructions give in the lesson template. If you do this, you must also edit _config.yml to set these three values:

1. carpentry is either "dc" (for Data Carpentry), "swc" (for Software Carpentry), or "lc" (for Library Carpentry). This determines which logos are loaded.

2. title is the title of your workshop (typically the venue and date).

3. email is the contact email address for your workshop, e.g., [email protected].

Note: carpentry and email duplicate information that's in index.md, but there is no way to avoid this without requiring people to edit both files in the usual case where no extra pages are created.

Installing Software

If you want to set up Jekyll so that you can preview changes on your own machine before pushing them to GitHub, you must install the software described below. (Note: Julian Thilo has written instructions for installing Jekyll on Windows.)

1. Ruby. This is included with Linux and macOS; the simplest option on Windows is to use RubyInstaller. You can test your installation by running ruby --version. For more information, see the Ruby installation guidelines.

2. RubyGems (the package manager for Ruby). You can test your installation by running gem --version.

3. Jekyll. You can install this by running gem install jekyll.

Setting Up a Separate Repository for Learners

If you are teaching Git, you should create a separate repository for learners to use in that lesson. You should not have them use the workshop website repository because:

• your workshop website repository contains many files that most learners don't need to see during the lesson, and

• you probably don't want to accidentally merge a damaging pull request from a novice Git user into your workshop's website while you are using it to teach.

You can call this repository whatever you like, and add whatever content you need to it.

Getting and Giving Help

We are committed to offering a pleasant setup experience for our learners and organizers. If you find bugs in our instructions, or would like to suggest improvements, please file an issue or mail us.

2019-02-19-cambridge's Issues

Instructor notes

To make it easier for us, the exercises for the course have been compiled here.

Some notes on the things to cover:

• Create Rproj and a project folder with sub-folders "data", "data_output" and "scripts"
  • try to make students use a "tidy" directory structure
• Intro
  • Covers exercises 1.1 and 1.2
• data.frames
  • use read_csv() from the beginning to simplify things? (optional, but I find it useful to keep consistency across the course)
    • although not in the current materials, I think it's worth insisting on explicitly using option on how missing values are encoded
  • skip factors - I've found it more intuitive to cover them in plotting lesson (see below)
  • Main thing is to explain [rows, columns] for subset and $ to access column. For example I personally avoid showing the 4 different ways to access a column listed in the materials (usually it's quite confusing for beginners)
  • Covers exercise 1.3
• dplyr
  • Covers exercises 2.1, 2.2, 2.3, 2.4
    • Often do exercise 2.4 with students to save time
• ggplot2:
  • skip themes and customisation - usually we just demonstrate a couple of things and then refer to the materials showing other things that can be done
  • encourage learners to use web search when wanting to customise their ggplots. E.g. "how to change axis label orientation ggplot2".
  • extra: see note below to mention factors
  • exercises 3.1-4 (if time is short do some exercises together)
    • I've changed some of the exercises in relation to the materials, for example to include one where we use factors to improve visualisation.
  • There's "extra" exercises for more advanced/quick learners.

---

note: extra material for ggplot2 section

So that students intuitively understand factors, introduce them in the plotting
section.

The narrative goes something like this:

When doing this plot:

surveys_complete %>% 
  ggplot(aes(sex, hindfoot_length)) +
  geom_boxplot()

What if we want to change the order of the x-axis labels to be "M" first?

Then we need to learn about factors, which are a special way that R has to
encode categorical variables.

Let's look at factors using a simple example first. Then go through the example
of the course materials here, but only the very first section of it.

From there, jump back to the plotting problem and resolve it:

surveys_complete %>% 
  mutate(sex = factor(sex, levels = c("M", "F")))
  ggplot(aes(sex, hindfoot_length)) +
  geom_boxplot()

Exercise 3.4 applies this concept.

sticky note feedback

Day 1 - am

To improve

• (2x) bit too fast in R
• (6x) too slow
  • I think this might be related with the slow start with the spreadsheets lesson
• (3x) Less time on excel
  • one idea would be to actually do the Excel session as the very last thing in the course
• Subsetting syntax
• Having the vector that instructor is creating written somewhere, as sometimes hard to copy exactly what is being typed
• Some more detail on the operations we use
• Some Mac specific issues
• No new info for those that already attended other courses
  • This is an issue that should be solved in the future when there's less redundancy between courses
• Didn't go through solution of first exercise

Good

• (5x) General OK comments, good explanations
• (6x) Good pace
• (3x) Liked messy vs tidy data lesson
• Missing values
• Thorough
• (2x) Interactive
• (2x) manipulating vectors
• (2x) Like sticky note system
• (2x) Like exercise time
• (3x) Materials are available and detailed
• Good time for exercise
• Availability of instructors