Notes

pdg-control Call

• Send Figure 3 and 4 with stock dynamics to Paul.

Detailed to do items coming out of talk filed as Github Issues for pdg-control (policycosts)

• Comparisons between assumed and true policy costs (Figure 5 style but as a Table)
• Snappier, more meaningful names for “L1”, “L2” etc
• Write real-world context/significance of L1, L2, fixed, etc.
• Add graph & discussion of stock dynamics for Fig 3 & 4
• Figure 5 interpretation
• Fix boundary issues in Figure 4
• Resolve confusion about apples-to-apples / definition of NPV0
• Resolve cost structure question
• On functional forms, drop ALL asymmetric cases for now.

Comment piece

Round 1 revisions sent to Lucy and Alan.

Workflow Workshop

At Simone’s invitation, I’m running a little session on workflow in git/Github, Rstudio, and knitr for the Mangel lab group. A quick brainstorm for an outline:

A first tutorial

1. Create a new repository on Github
2. launch an RStudio session, select create new project
3. Add the git@ url to the project, select a local directory, hit “create”
4. In Rstudio, create new R Markdown file.
   
5. Editing the file. Hit “Knit HTML” button.
   
6. add the files to git: git tab, check boxes.
7. commit the .Rmd and md files, and push files to Github.
   

8. Viewing files on github.

9. Navigating Github: Project directory, viewing .md files, raw mode, viewing history of a file, getting permanent links to specific versions.
   10: Github extras: using issues. (Referencing issues in commits)

10. Recovering a deleted file.

Git More Advanced

• Create a gh-pages branch and add the html generated from the Rstudio/knitr. (Covers branching & webpage hosting on github)
• Create a github homepage
• Merging changes, resolving conflicts.
• collaborating via github.
  
• why sha hashes are awesome
• private repositories
• Repo Readmes

Other topics

• Managing references. Sharing collections (Mendeley)
• References in markdown. Pandoc. (knitcitations?)
• Managing data. Figshare.
  
• Social media for science.