Updates Across Various Projects

At home after birth of Edward since Jan 19th, leaving little time for research. Assembled notes from a few side projects I’ve moved forward in the wee hours. Covers the past several days.

XML and RDFa parsing

I have been using the lab notebook to explore technology for scientific communication, including making use of semantic and linked data concepts. To illustrate some of the potential these tools can offer I’ve started working on a short post with examples parsing and exploring the XML and RDFa data in the notebook. Still forthcoming. The any23 API provides a great tool for this (particularly RDFa to RDF XML, where we can then take full advantage of xpath tools on the semantics).

Other notebook updates

MathML: Can have Pandoc render source in MathML and MathJax will still perform the HTML rendering in all browsers. Unfortunately, certain commands seem not to parse in this mode that do parse in Pandoc mathjax mode (e.g. those with operatorname in 2012-11-01 post).

Updated timeout setting on twitter plugin. 0cb7a11

PDG Control Follow-up

Skype with Paul for follow-up on third working group meeting. Key steps forward on policy costs:

  • All comparisons should be with reference to total value/profit of the strategy, rather than induced cost. Then compare against induced values directly. (Issue #35)

  • Quadratic costs should appear in supplement only (Issue #45)

  • Real-world context framing worked out. (Issue #39)

These and further details are listed in issues tracker for the project.

Updates to knitcitations


  • Added a new display option, bibliography('markdown')
  • fixed BUG in the printing of the text-based name in bibliography for bibstyle-based calls


  • Semantic citations now enabled. bibliography can print with method ‘rdfa’ to provide RDFa enhanced HTML bibliography data, and citations can take cito arguments as an option. (Closes issues #16 and #17)
  • bibliography now takes more options to match the bibstyle and print.bibentry functions.
  • citet and citep take an optional argument for formating the citation, defaulting to authoryear format. Future versions may move this into an option.
  • newbib() function initializes and clears existing cache files.
  • README.md updated with semantic examples and more background text (generated by inst/examples/README.Rmd).
  • Some basic unit tests built in. Could use more, but meanwhile closes #8.
  • Test cases work with knit2html button in RStudio, closes #14


  • Switched to handling citation data using environment rather than an external bibfile. This does not refer to the handling of user-provided bibtex files as input data, which are supported as before, but changes only the backend management of that data. The external bibtex file method can be switched back on by setting options("bibtex_data" = TRUE).
  • There is no need to call print(bibliography, "html"), one can simply call bibliography() or bibliography("html"). Sort is still an option, other options that were for internal use (debug, remove_duplicates) are removed as they are no longer necessary.
  • Several new functions have been added to handle the new methods.


  • Fix vignette error that prevents knitr 1.0 submission
  • Fixed errors on installing package and lack of entries in bibliography
  • Semantic print option added but still in early testing


  1. O’Dwyer, J. P. & Green, J. L. 2010 Field theory for biogeography: a spatially explicit model for predicting patterns of biodiversity. Ecology letters 13, 87-95. (doi:10.1111/j.1461-0248.2009.01404.x)
  2. Stewart, E. C. A., Almes, G. T., Mccaulay, D. S. & Bradley, C. 2009 Cyberinfrastructure Software Sustainability and Reusability : Report from an NSF-funded workshop Report from an NSF-funded workshop held 27 and 28 March 2009.
  3. Ingram, T. & Mahler, D. L. 2013 SURFACE: detecting convergent evolution from comparative data by fitting Ornstein-Uhlenbeck models with stepwise AIC. Methods in Ecology and Evolution , 1-25. (doi:10.1111/2041-210X.12034)
  4. Shelton, A. & Munch, S. 2012 Maternal age, fecundity, egg quality, and recruitment: linking stock structure to recruitment using an age-structured Ricker model. Canadian Journal of … 1641, 1631-1641. (doi:10.1139/F2012-082)
  5. Regan, T. J., Chadès, I. & Possingham, H. P. 2011 Optimally managing under imperfect detection: a method for plant invasions. Journal of Applied Ecology 48, 76-85. (doi:10.1111/j.1365-2664.2010.01915.x)
  6. Gewin, V. 2013 Turning point: Carl Boettiger. Nature 493, 711-711. (doi:10.1038/nj7434-711a)
  7. Nicol, S. & Chadès, I. 2012 Which states matter? An application of an intelligent discretization method to solve a continuous POMDP in conservation biology. PloS one 7, e28993. (doi:10.1371/journal.pone.0028993)
  8. McDonald-Madden, E., Chadès, I., McCarthy, M. a, Linkie, M. & Possingham, H. P. 2011 Allocating conservation resources between areas where persistence of a species is uncertain. Ecological applications : a publication of the Ecological Society of America 21, 844-58.
  9. Krell 2011 The U.S. Department of Energy Computational Science Graduate Fellowship 1991-­‐2011: Recipient Outcomes and Programmatic Impacts.
  10. Dougherty, D. T., Hilborn, R., Punt, A. E. & Stewart, I. J. 2013 Modeling co-occurring species : a simulation study on the effects of spatial scale for setting management targets. 8, 1-8.
  11. Chadès, I., Martin, T. G., Nicol, S., Burgman, M. a, Possingham, H. P. & Buckley, Y. M. 2011 General rules for managing and surveying networks of pests, diseases, and endangered species. Proceedings of the National Academy of Sciences of the United States of America 108, 8323-8. (doi:10.1073/pnas.1016846108)
  12. Chad, I., Carwardine, J., Martin, T. G. & Nicol, S. In press. MOMDPs : A Solution for Modelling Adaptive Management Problems. , 267-273.
  13. Kapaun, U. & Quaas, M. 2012 Does the optimal size of a fish stock increase with environmental uncertainties?
  14. Mattmann, C. A. 2013 Computing: A vision for data science. Nature 493, 473-5. (doi:10.1038/493473a)
  15. Seekell, D. a., Cline, T. J. & Winchcombe, R. J. 2013 Can Management Reduce Harvest Inequality in Recreational Fisheries? North American Journal of Fisheries Management 33, 148-152. (doi:10.1080/02755947.2012.746246)