Schedule

  1. 8:30 - 9:30 am

    Github finish: Git lecture, II [15 min, NT] Assign env-info groups [5 min] Doodle preferred office hours for BB by 5pm today
    Git Assignment (Group), to create Github organization and respository [30 min, per group] Rmarkdown lecture & demo [BB, 30 min]

  2. 9:30 - 10:30 am

    Break [10 min] RMarkdown Assignment (Individually) to add student listing [30 min, individually] Programming concepts lecture Programming Lecture [20 min, NT]

  3. 10:30 - 11:30 am

    Programming exercise I [20 min, individually] More on Programming [20 min, NT] Programming exercise II [20 min, individually]

Github Demo II [NT]

# list git log in reverse order
git log --reverse

# go back in time
git reset #commit#

# go back and delete all subsequent commits!
git revert #commit# --hard

Assignment

Due: Jan 21, Thursday 5pm

Git Assignment (Group)

  1. Assign yourself to an env-info group

  2. The first person listed in the group should Create a new Github organization (eg <organization> is whaleroute) and Add organization members to the owner team (eg owner bbest adds username naomitague).

  3. The first person listed in the group should also Create a repository with Owner set to your organization (eg whaleroute, not your default username) and name it after your Github <organization>.github.io (eg whaleroute.github.io). Tick the box to initialize this repository with a README.

    This repository will store your organization’s website files, so the repository of files at http://github.com/<organization>/<organization>.github.io (eg http://github.com/whaleroute/whaleroute.github.io) will eventually be viewable at http://<organization>.github.io (eg http://whaleroute.github.io), but only after you add an index.html, per pages.github.com. That will come later, after you learn RMarkdown. For now you’ll use this repository to work on your Git and Github skills.

  4. Now every member of the group should obtain this repository onto your local machine for editing, ie git clone. You can do this via RStudio menu File, New Project…, Version Control, Git. Substitute with your own <organization> like below (not whaleroute):

  5. Finally, time to play with Git/Github in RStudio to make changes for your group’s data analysis.

    • Write a short Rscript to read or generate some data, manipulate it and plot it
    • Commit your file to the local repository and Push to the Github respository;
    • Have everyone in the group make some changes to the script. Commit them locally and then Push to Github.
    • Make a new branch, make some changes; commit them (locally)
    • Merge your fork to the main branch
    • Make an error, commit it
    • Go back!
    • Commit and push to Github

RMarkdown Assignment (Individually)

Add yourself to the students listing with a json 1 file, and a dedicated Rmarkdown document.

  1. Fork the ucsb-bren/env-info repository into your Github user space, and clone the repository <username>/env-info to your laptop to work on files, similar to how you previously cloned <organization>/<organization>.github.io (via RStudio menu File, New Project…, Version Control, Git). All paths below refer to wherever you cloned the env-info repo onto your local machine.

  2. Add yourself the students listing by adding a file per your Github <username>.json into the _data/ directory. Here’s an example for Github username bbest, so the file is at _data/bbest.json:

     {
 	"program": "lecturer",
 	"interests": "marine ecology, species distribution modeling",
 	"project": "route ships around marine mammal hotspots",
 	"organization": "whaleroute"
 }

    Using the format above, replace with your own program (eg "MS" or "PhD"), interests and project idea. Leave organization blank for now; you’ll update that once you’ve identified your group below.

    Commit and push your changes and make a new pull request. Once your new pull request gets accepted by @bbest / @naomitague, you should see the updated students listing with your organization linked to your <organization>.github.io.

  3. The students listing generated from the *.json files (using jekyll 2 ) links your user information to a details page at students/<username>.html. Create this using an Rmarkdown document (in RStudio, File > New File > R Markdown… Document in HTML format), so save it initially as <username> under the students folder and it will default to save as <username>.Rmd (ie students/<username>.Rmd). Click the “Knit HTML” as you go to render the students/<username>.html.

    • Add the following headings to your Rmd and replace the text below with your own content based on overlap with the course and your interests:

        ## Content
        
  What burning environmental question(s) would you like to address? Feel free to provide group project, dissertation, and/or personal interest. What's the study area?
        
  ## Techniques
        
  What techniques from the course do you think will be most applicable?
        
  ## Data
        
  What data have you already identified? Feel free to provide a link and/or details on the variables of interest.

    • For details on Rmarkdown syntax, see:

    • For instance, you could add an image into students/images/cool_idea.png using Mac Finder or Windows Explorer, and incorporate this into your students/<username>.Rmd by adding a line like:

        ![](images/cool_idea.png)

    • For this to work on the http://ucsb-bren.github.io/env-info site, you’ll need to commit and push the knitted <username>.html and images/cool_idea.png files. Play with formatting to add at least one italic, bold, list, link, and image.

    • Next, add a table of contents by replacing the front matter line (in YAML 3):

      output: html_document

      with

      output:
  html_document:
    toc: true
    toc_depth: 2

    • Next, add a chunk of R code to read a csv 4 data file and output a summary, like:

      ```{r}
# read csv
d = read.csv('bbest_ports.csv')
      
# output summary
summary(d)
```

      Try to use data relevant to your question of interest, and be sure to copy the csv data file into the students/data folder, preferably with a file name like <username>_<dataname>.csv. If you have trouble finding data, explore the links in Data.

    • Be sure to run the “Knit HTML” on your students/<username>.Rmd to generate the final desired students/<username>.html

  4. Commit, push and pull request your changes, per Github Workflow. This is how you’ll turn in this assignment.

    Review. We can provide line-by-line feedback directly within the pull request as part of a code review. You could even follow up with submitting corrections by pushing fixes up to your fork, which will be reflected in the pull request. When we’re finished giving feedback, we’ll close the pull request and leave a :+1: in the final comment.

Resources

Fixing rpostback-askpass error

If you get this rpostback-askpass error on a Mac when pushing in RStudio, see rpostback-askpass error on Mac doing Git Push from RStudio to Github · Issue #2 · ucsb-bren/env-info:

error: unable to read askpass response from 'rpostback-askpass'
fatal: could not read Username for 'https://github.com': Device not configured

Git, Github and RStudio

Rmarkdown

Footnotes

json

JavaScript Object Notation (json) is a lightweight data format, which is both human and machine readable with complex hierarchies like XML, but more compact (and less explicit with tags).

jekyll

Jekyll is a static site generator used by Github Pages (the website hosting capacity of Github, since default view of HTML is as code not rendered form) using the liquid templating language which has limited data file support for JSON in the _data folder for iterating through JSON file objects like in students/index.md and wrapping the template in layouts/default.html which uses the _includes to provide a common navigational bar for the site to yield the final students/index.html.

yaml

YAML is a human readable format for storing variables of various types (single values, lists, arrays) in a language agnostic manner. It’s commonly used in configuration files, and any modern language would have a library for reading and writing this format (eg yaml for R).

csv

CSV, Comma-separated_value, files store data in a human and machine readable format in which rows of data are seperated by a newline, and columns by a comma. This format is probably the most widespread for sharing tabular data, and is read by most database and spreadsheet programs, including Excel. CSV files are also nicely rendered in Github with column formatting, searching and even line-by-line linking. An emerging standard for tabular data stores data in CSV form and the metadata (ie variable description, variable type, dataset source, citation, etc) as JSON.