rOpenSci
- rOpenSci wins runner up prize in PLoS + Mendeley’s Binary Battle!
- Write replies to interview questions with Mendeley.
- roxygenizing documentation for RMendeley – about half done
pdg-control
- Call with Jake scheduled for tomorrow
- Emails with Michael. I’ll implement delay intervals, he’ll add costs to adjustment.
- Need to fix/finish delay interval optimization calculation (exponent of matrix & beta)
Warning Signals
Meeting with Alan
- Regime shifts
- Emphasize the RO curve in uncertainty analysis
- See (Dulvy et. al. 2003) (relevant) & (more for fun) (Le Quesne & Jennings, 2012)
Seminars
Excellent discussion panel with Jonathan Eisen, Jon Wilbanks, and Mario Biagioli. Looks like the beginning of a successful collaboration between Davis Open Science and the Center for Science & Innovation Studies at UC Davis.
Evolution
- Evolution manuscript accepted, pending a few minor checks.
- Complete documentation and submit associated pmc package
Wrightscape debugging process
Into the C code, checking the equations & implementation of the likelihood calculation.
Day’s plots on the feed:
[flickr-gallery mode=“search” tags=“phylogenetics pdgcontrol” min_upload_date=“2011-11-30 7:00:37” max_upload_date=“2011-11-30 23:23:37”]
References
Dulvy N, Sadovy Y and Reynolds J (2003). “Extinction Vulnerability in Marine Populations.” Fish And Fisheries, 4. ISSN 1467-2960, https://dx.doi.org/10.1046/j.1467-2979.2003.00105.x.
Le Quesne W and Jennings S (2012). “Predicting Species Vulnerability With Minimal Data to Support Rapid Risk Assessment of Fishing Impacts on Biodiversity.” Journal of Applied Ecology, 49. https://dx.doi.org/10.1111/j.1365-2664.2011.02087.x.