Musings, Explorations, and Announcements

My qualifying exams are on March 5, 2013. 78 days away! I’ll be trying to blog my reading as well as the development of my proposal here and in a github repository. Today - my topics and reading list. Forest Landscape Pathology Landscape-level disease management Sudden Oak Death Model Construction and Theory Approaches to building and using models SIR epidemiological models Population structure in disease dynamics Plant-specific applications Confronting Models with Data Fitting time-series data with iterative filtering Model Comparison Natural Resource Economics Forest rotation models Age-structured harvest models Insect control References Forest Landscape Pathology Examiner: David Rizzo

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Last week in Davis R Users’ Group, Lauren Yamane showed us how she created and analyzed a stochastic age-structured population in R. Her examples are below. Her original scripts can be found as *.Rmd files here A note to UC Davis students: This topic and others will be covered by Marissa Baskett and Sebastian Schreiber in their course this winter, Computational methods in population biology (ECL298) A discrete time, age-structured model of a salmon population (semelparous) that can live to age 5, with fishing and environmental stochasticity Parameter values

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This is a description of the model I’ve implemented in the SODDr package, which I prepared for a presentation for the Hastings lab meeting on November 29, 2012. Background Sudden Oak Death (SOD) is a disease that threatens tanoak populations in California. It’s cause is an introduced pathogen, Phytophthora ramorum. Phytophthora is a water mold that spreads by wind-blown rain and fog as well as through human transport (e.g., transportation of plants).

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I’ve been hunting for a lightweight CSV editor for OSX so I could to make fixes to data files and not need to fire up Excel. While you can edit a CSV file in any text editor, it’s a pain to navigate the files without a spreadsheet-like interface. Unfortunately there doesn’t seem to be a good, free option out there. Today I remembered R has a native XCode editor for editing data frames, and I realized I could write a function that would load the CSV as a data frame, let me edit it, then close and save it in CSV format again.

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I am working on a project with the Rizzo Lab examining the dynamics of Sudden Oak Death (SOD). I really have to write more about this, but today I’m just going to post the results of an initial exercise. Here I attempt to replicate model results from Cobb et al. (2012). The model in that paper simulates the spread of disease and resulting tree mortality and stand dynamics in a mixed system of tanoak, bay laurel, and redwood.

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