Brym 2016 Report

USU Employed

Jan

• Expand site documentation
  • The documentation for the course was previously located on the About page. This documentation was reorganized and expanded in docs/ to include course/, site/, and template/ materials. The goal was to provide ample resources for the navigation and customization of the course by collaborating instructors.
• Revise home page
  • The home page and sidebar were reorganized for clarity to distinguish important links for students and instructors.
• Restructure lecture materials
  • Lecture materials for the course were decentralized and stored in many places. This project moved all of the materials into materials/ and organized the course relevant materials into lectures/. The lectures/ pages are integrated into the automated schedule using the yaml tag title:.
• Add Good Style problem
  • Link to exercise
• Revise NEON Database problem
  • The exercise was revised to include import of the data and a JOIN problem.

Feb

• Update site configuration
  • Jekyll and GitHub pages required an update to _config.yml. markdown: was updated from rdiscount to kramdown. highlighter: was updated from pigments to rouge.
• Customize 'Page not found' response
  • The 404 page opens when a url entered within the site is not valid. This page was customized to include useful information to troubleshoot the invalid link/url, to try and navigate to the desired page, or to seek help.
• Combine Intro to R weeks
  • The first three weeks of introductory R material were combined into two weeks. The first week covers expressions, variables, and data structures. The second week focuses on data frame manipulation with dplyr.

UF Employed

Mar

• Restructure schedule page build and organization
  • The schedule page build organizes assignments/, readings/, and lectures/ by title:. The restructure replaced a clunky subtitle: tag with element: that refined automation. This move coincided with a reorganization of title: to replace a numbering scheme with descriptive names.
• Add missing links to home page
• Update Figshare and Data Carpentry links

Apr

• Update file names
  • The element pages retained file names with numbering that was updated to match the descriptive title:.
• Update site index pages
  • The index page for materials/, lectures/ and exercises/ needed to be updated to match the new site structure.
• Update site formatting for kramdown
  • Headings, code blocks, and table sections needed to be revised to match the kramdown site rendering.
• Update README to match new site structure and documentation

May

• Revise site navigation
  • Site navigation was revised to a hierarchical set of navigation pages to limit the number of top-level navigation links on the sidebar. The second level of link pages are organized in nav/. The links are complemented by icons.
• Revise exercise file structure
  • The file names and yaml were updated for all of the files in exercises/. File names were revised to the form: Topic-title-language.md. Numbered titles were replaced with descriptive names. Solutions and follow-up links were also revised to maintain parallel structure.

Jun

• Explore the use of Jekyll collections for site organization
  • The site requires special capitalization in the exercises/, readings/ and lectures/ for proper site build. Jekyll collections were tested to fix this build difficulty unsuccessfully.
• Develop course website template branch
  • In developing the site documentation for customization, it was determined that a site template might be a good starting point for new instructors. A branch was developed that stripped the course content from the site and left a template of the site structure. This strategy was abandoned as difficult to maintain, but identified areas to improve the site documentation.
• Lectures review and reformatting
  • The lecture notes were reviewed for content clarity and completeness from the perspective of a new instructor unfamiliar with the course. Each lecture note was reformatted to include action items set in block quotes, exercise links embedded in the lecture delivery, and various other minor revisions such as bullet pointing to improve the material.
• Add output links to individual exercise pages
• Add back-to-top links to exercises page
• Add language check for schedule build

Jul

• Update iPython notebooks
  • iPython notebooks are the lecture notes for Python material. They were moved into the appropriate materials/ folder and updated for relative link paths to data used in the lesson.
• Add tidyr lesson to "R-SQL" assignment
  • The table restructuring problems "Redundancy" and "Split Cells" were removed from the sql-joins assignment and the concepts were rewritten as the "Tree Biomass" exercise for the "R-SQL" assignment. The move was to make two improvements to the lesson: 1) kept students from completing a task by hand that they could automate, and 2) taught the tidyr package so students could automate the changes. A lecture notes for tidyr was also prepared.
• Draft "Fork the course" blog post
  • The blog post was drafted to introduce the features of the course that could be useful to new instructors. Further commentary was included to encourage new instructors to customize the course and contribute material back to the project.
• Remove lecture notes from exercise list in assignments
  • The assignments page build was revised to remove lecture notes from the exercises list that were appearing because of a matching title: to an exercise.
• Add individual exercise page link to exercise title in assignments page.
• Develop visualization-novice lesson design and assessment solution
  • The visualization-novice lesson was a collaborative effort with Greg Wilson and Software Carpentry to develop a lesson for teaching novice programmers how to choose the best graphic to address their research question and how to generate a publication quality figure using ggplot2. Greg uses the reverse instructional design method, which writes new lesson material from a lesson design and a final assessment goal that organize the lesson development.

Aug

• Add "Working with Spatial Data" assignment
  • The "Working with Spatial Data" assignment was added to include lecture material about working with spatial (or GIS) data and was a direct result of collaborative work with NEON. Tutorials from the NEON spatial data hackathon were used as a starting point for the assignment, which expanded on the raster and vector components of the NEON material.
• Replace _ in file names with -
  • File names were standardized across all of the site files to have - as a separator instead of _. The links were also updated throughout the site to match the new file names.
• Review "R for Data Science" by Hadley Wickham
  • The new ebook "R for Data Science" was compared to the existing reading materials for dplyr, ggplot2, and tidyr. The reading materials were revised for the best combination of content and clarity.
• Prepare course schedule for Fall 2016
  • The schedule was revised for course content intended for the Fall 2016 semester. The schedule build was revised to accommodate new content that lacked some of the reading-lecture-assignment elements.
• Revise SQL assignment content
  • Exercises and solutions were revised to improve content and clarity. The exercises were also renamed from numbers to something descriptive.
• Add in-class feedback page and links
• Draft episode content for visualization-novice
  • The lesson design and final assessment were approved by Greg Wilson. The next step was to merge the final assessment with the lesson design and draft episodes in preparation for a broader review.

Sep

• Clean and update materials/
  • Files were reorganized previously into materials/ but were not individually reviewed. Each file was updated (or removed) to ensure proper yaml front matter and links to the materials/index.
• Revise sql-intro assignment
  • The GROUP BY exercise was removed and the content was added to COUNT
• Revise dplyr assignment
  • The concepts of local and external tables were further described in the lecture notes and more clearly identified in the "Link to Databases" exercise using collect(). Multiple exercises were split in the dplyr assignment.
• Remove numbers from R exercise titles
  • Some numbering of sequential exercises remained in the R exercise titles and was removed in place of descriptive names.
• Merge "Built-in Functions"
  • There were two lessons that introduced built-in functions (one for math functions and one for string functions) that were merged.
• Add solutions to "Sexual Dimorphism" exercises
  • Two new exercises were added to the "Data Visualization" assignment which required solutions before class.

Oct

• Update dplyr solutions and lecture notes to new release (0.5.0)
• Revise "R-SQL" assignment to "Working with Databases"
  • The "Working with Databases" assignment was developed as a revision of the "R-SQL" assignment to focus on the database management features of dplyr instead of RSQLite. The lecture material was also revised.
• Consider R notebook implementation
  • R notebooks are a new feature of RStudio that integrates text, code, and output. The use of R notebooks for the course site was explored as an option to make lessons interactive and provide code chunks directly to students for exercises. The implementation was determined to be prohibitive.

Nov

• Add lecture notes link to assignment page
• Update documentation for previous lectures reformatting
• Revise knitr lecture content
  • The knitr lecture was presented independently of an assignment. It was developed using .md, .Rmd, and .Rpres. These files were merged into a single .md and revised as per class feedback.
• De-emphasize Python and Access materials
  • The order of materials was revised to move Python and Access materials to the bottom and clearly state that those materials are no longer being actively maintained.
• Revise ggplot lecture notes to use acacia data
  • The ggplot lecture was revised to use new data from 'Ecological Archives' because the portal data required dplyr data management and was overused.
• Troubleshoot and list customized courses
  • The "Fork our course" blog post was successful in identifying instructors that were interested in customizing the course for their own use. Some folks required help to get started and that feedback was incorporated into the site documentation. Each of the live sites that were customized were listed on the site.
• Add basic loops exercises
  • Students were having trouble with loops. Two new lessons that address basic loops with indexes and loops with vectors were added to the "Programming Fundamentals 2" assignment.

Dec

• Revise SQL Practice exercise
  • The SQL Practice exercise is used to give students a look back at basic SQL a few weeks after the assignment. The exercise tasks and solutions were revised to be sure the desired query and results were clear.
• Restructure SQL assignments
  • The sequence of SQL assignments previously organized the materials as basic queries and joins. The assignments were restructured to first focus on tidy data structure and data import followed by all queries.
• Move and revise version control assignment
  • The Version Control assignment was moved earlier in the semester to week 6 following the intro sequence to R (Intro R, Data, Data Vis). The lecture was revised to parallel the assignment with the houseelf data, so students could follow along in class. The lecture and assignment were further revised to start from a remote repository on GitHub instead of creating an new repository on the local machine. The assignment was also integrated with the class project structure and proposal material.
• Fix broken links for "Programming for Biologists"

Year in Stats

• Issues: 61
• Pull Requests: 142
• Commits: 326
• Line edits: 421,290 ++ / 405,228 --

Memorable Comments

• "This looks awesome! Great work."
• "May I just say that nicely delineated PRs and clear commit/PR messages make it really easy to move through reviews quickly. It's really nice tradecraft."
• "I really like the shift to element to generalize the structure."
• "I don't like the use of bolding inside of sentences. I tend to think that if one needs that sort of thing it's a sign that the text should be more concise instead."
• "Really nice job @brymz and a ton of work."
  • "That was fun! I had a great place to start."
• "I really like this. What's the argument for waiting until the end of the semester?"
  • After making a poor argument for waiting: "I'll go ahead and merge".