Sunday

Completed phylogenetic power manuscript updates based on Peter’s comments. Graham will read Monday.
Took a whack at updating the treebase package with a method for grabbing nexus character matrices. Seegithub issues log, querying Emmanuel on this one.
Local directory management / cleanup

Phylogenetics Power manuscript. Nearly there. (SICB presentation)
Warning signals manuscript resubmission. (Presenting at ESA)
Generalized comparative method/release of constraint – method done, time to write. (Presenting at Evolution.)
TreeBASE manuscript. (Presenting at iEvoBio.)

Public API done,
I’ve learned to create windows binaries, and it’s now being tested by some of the Mendeley team (W. Gunn).
Need an authentication example to do the user-specific API
Have some requests up on the Mendeley development list and the developer wiki for some modifications to API (i.e. search stats should return paper uuids)
Considering entering in the competition? Not to win but could be fun, and would get some free Amazon time.

API implementation is done for the phylogenies.
Example explorations up in notebook:
Issues list on github
Waiting for treeBASE developers to add Dryad IDs to pull dryad data out as well. Meanwhile, working on a work-around using the Dryad database
Presenting as a lightning talk at iEvoBio conference
Considering combining with Dryad and Mendeley and entering into the data integration challenge at iEvoBio conference. Thoughts?
Starting short manuscript, could try bioinformatics or BMC bioinformatics, could certainly go in

Basic data-pulling interface implemented.
Scott Chamberlain, Graduate Student at Rice. now helping with development of the package.
Scott has added the metadata search capacity.

gitR, etc. Need to update this to use native R functions instead of the command-line utilities for flickr, twitter, git.
I need to figure out explicit semantics we discussed, and then figure out how to save/log work. Will try and write this out carefully.

There are lots of reasons this uses flickR for images over an S3 repository (though maybe good reasons to do both).

Flickr API is already built and already familiar to a large userbase,
Flickr has a database structure, making it easy to tag, search, browse by date, etc
Flickr API is widely implemented – easy to get simulation results in real time on my phone, add results to wordpress realtime using plugin with search criteria, etc.
Flickr is a social web app, with notions of privacy, sharing, licensing, searching

From Friday

Edits to pmc package
begun package vignette in Sweave to illustrate how results are produced.
would be nice if sweave had syntax highlighting, see thestackoverflow on this. Can’t seem to get minted.sty working, won’t recognize my install of pygmatize.

ROC Curves.