Musings, Explorations, and Announcements

This is an overview of tools for speeding up your R code that I wrote for the Davis R Users’ Group. First, Ask “Why?” It’s customary to quote Donald Knuth at this point, but instead I’ll quote my twitter buddy Ted Hart to illustrate a point: I’m just going to say it.I like for loops in #Rstats, makes my code readable.All you [a-z]*ply snobs can shove it! — Ted Hart (@DistribEcology) March 12, 2013 Code optimization is a matter is a matter of personal taste and priorities.

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I recently wrote about my first peer-reviewed publication and lamented that it’s behind a $1500 paywall. I am not allowed to post the file to my website, but I am able to distribute the paper by e-mail, so I’ve set up a system to automate requests for the paper. Michael McCarthy wrote a similar post this fall for people using Outlook e-mail. My method is similar but is meant for Gmail.

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My first peer-reviewed publication is an encyclopedia article written with colleagues in economics in UC Davis: Economics and Ecology of Open-Access Fisheries K. Fuller, D. Kling, K. Kroetz, N. Ross and J.N. Sanchirico (2013) In: Shogren, J.F., (ed.) Encyclopedia of Energy, Natural Resource, and Environmental Economics, Vol. 2 Encyclopedia of Energy, Natural Resource, and Environmental Economics p.39-49. Amsterdam: Elsevier. http://dx.doi.org/10.1016/B978-0-12-375067-9.00114-5 Abstract In open-access fisheries, participation and harvest by fishermen are unregulated.

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Today at Davis R Users’ Group, Michael Hannon gave a great talk on how to use R’s native debugging functions. Here are his notes and code. Introduction This is a discussion of debugging techniques in R. It is based on a paper by Roger Peng, now at Johns Hopkins University (http://www.biostat.jhsph.edu/~rpeng/docs/R-debug-tools.pdf) Focus on five functions: traceback debug browser trace recover Severity level R mainly uses two ways of reporting a problem:

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This week at the Davis R Users’ Group we had a great presentation by Kara Moore O’Leary on using the popbio package to examine rare plant demographics. The following is her script run through knitr. You can download the original script and associated data here. Find out more about Kara and her work at her website here Demographic analysis using the popbio library and some other fun stuff A population viability type analysis for a rare herbacious perennial plant, Penstemon albomarginatus, for its only remaining California population

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