1. fixed footnotes issue in pdf version.
  2. Externalize tables in word version.
    knit_hooks$set(chunk = function(x, options) {
      if (!options$split) return(x)
     cat(x, file = fig_path('.md', options))
  • Consider more intuitive function names rather than function arguments?


  • Needs additional functions replacing sapply queries and argument queries.
  • Table of functions
  • re-organize presentation

rOpenSci GSOC

GSoC applications were due at noon today. Provided final rounds of feedback to our three applicants. Proposals (secure):


Berkeley adaptive management / resource economics

Also looking at Mangel’s Decision-making and investment under uncertainty, particularly within a Bayesian framework, and ecological detection, with application to adaptive management.

  • “Ecology, Conservation and Public Policy: A Vision for the 21st Century”, Astor Lecture, University of Oxford, April 2007 slides
  • Ecosystem management perspective Pikitch, 2004, (Carpenter et. al. 2009), (Mangel & Levin, 2005)
  • Adaptive management NCEAS synthesis [cite]10.1002/(SICI)1520-6602(1998)1:1<16::AID-INBI3>3.0.CO;2-D[/cite]
  • nice treatment of stochastic transitions in (Mangel, 1994)

Other reading


  • Carpenter S, Armbrust E, Arzberger P, Chapin F, Elser J, Hackett E, Ives A, Kareiva P, Leibold M, Lundberg P, Mangel M, Merchant N, Murdoch W, Palmer M, Peters D, Pickett S, Smith K, Wall D and Zimmerman A (2009). “Accelerate Synthesis in Ecology And Environmental Sciences.” Bioscience, 59. ISSN 0006-3568,

  • Mangel M and Levin P (2005). “Regime, Phase And Paradigm Shifts: Making Community Ecology The Basic Science For Fisheries.” Philosophical Transactions of The Royal Society B: Biological Sciences, 360. ISSN 0962-8436,

  • Mangel M (1994). “Barrier Transitions Driven by Fluctuations, With Applications to Ecology And Evolution.” Theoretical Population Biology, 45. ISSN 00405809,

  • Ecology: Ecosystem-Based Fishery Management, E. K. Pikitch, (2004) Science, 305 10.1126/science.1098222