Monday / Tuesday

  • rfishbase updated to Duncan’s feedback
  • writing intro section on Prosecutor’s Fallacy.
  • wrightscape update project repository. Scripts mostly in demos, results in notebook. Notebook makes is easy to get the most recent writeup on the topic, from where I can start to track back the history, but doesn’t provide a good at-a-glance view of the analyses I’ve run side-by-side. Moving the R script demos/ into markdown knitted files in inst/examples/ and rerunning. See directory.
  • Files that require cluster computation won’t be able to upload graphs directly. Should separate these scripts from their respective plotting scripts.

Working examples

  • Have labrid_data, labrid_mc, focal_examples, simulated_release working. See directory. Running the direct model comparisons on the other traits.

Data management

  • Trying out the API for for storing data. Starting with the python tool, some difficulty getting this running. Detailed issue log
  • Also put in form to get www hosting through NERSC.
  • Meanwhile, am just tossing data into the webserver running on our local lab computers. This just provides a home for the data so I don’t have binary files on github – the metadata for these objects is handled by the README that lives with the code.
  • For large data files (which I’m not generating in these codes) the clear way forward is storage you can send the computation to, rather than downloading. For above solutions work for users of our cluster, or of NERSC, but for a more general audience AmazonS3 is the obvious choice (though involves monthly fees). Looks like there is already a good way to put this into my workflow using RAmazonS3

First install libraries for Ubuntu:

sudo apt-get install libmime-base64-urlsafe-perl libdigest-hmac-perl libdigest-sha1-perl

Then install

install.packages("RAmazonS3", repo="")

And then we’re ready to roll. See Duncan’s tutorial

Will consider a tutorial for this + maybe Segue for Duncan’s seminar. (Note that Duncan’s moved lots of onto github, which we’ll be using for all the class content.)



modify knitr hook for formatting inline code, e.g.

knit_hooks$set(inline = function(x) {
 prettyNum(round(x,2), big.mark=",")