Lab Notes

This section includes links to various notes I've put together as part of my work. They are organized by date, and include a short description. Feel free to contact me with any questions or comments you have about them, or to reuse or redistribute the material in ways that are helpful.

3 June 2021: Very simple code for measuring light intensity with an Arduino, adapted from James Carlson. <link>

8 April 2021: An example showing when random effects that overlap perfectly with a categorical variable can lead to biased estimates (at least for lme4, the result is that the fixed effect is correctly estimated, but the random effect is set to zero). <link>

23 March 2021: A short discussion on how to measure the rates of an exponential process, either in terms of averages or half-lifes (and why half-lives are better). <link>

7 March 2021: A basic SIR model with re-infection. <link>

13 February 2021: A very simple power analysis comparing results from the recent study on AstraZeneca vaccine efficacy against the B.1.351 "South African" COVID variant. <link>

3 February 2021: An extended example for power analysis, showing how to deal with multivariate predictors. <link>

28 July 2020: Transforming Lotka-Volterra parameters from the linearized to the classic formulation - shows a short example with two species. <link>

11 May 2020: Weird things that R does - A compilation of notes related to R's many irrationalities that can stymie people who are just starting out with it, and some of my solutions for these problems. <link>

19 April 2020: A comparison of fitting methods for projecting a logistic growth curve, inspired by this post. Interestingly, the simple rate based fitting method performs much worse than a state-based method, which I would not have thought. <link>

21 March 2020: A more polished version of the SIR model, for making short-term forecasts in a few countries. Please see disclaimers in the file. <link>

10 March 2020: Update, testing per-capita growth rate of COVID-19 vs. number of cases. Requires data from the CSSEGISandData 'COVID-19' GitHub, available at https://github.com/CSSEGISandData/COVID-19. <link>

24 February 2020: A basic SIR model, based on rough current data about COVID-19. Note that this model assumes no changes in behavior or uncertainty in rate estimates, and is therefore highly unrealistic (i.e. don't take the forecast too seriously). <link>

9 January 2020: Some basic notes on applying power analyses with binary and continuous data. <link>

14 November 2019: Some example code and data for analyzing human population growth, and the competition/predation data from Gause 1934. For use as part of the Fall 2019 ecology course at Halle. <zip>

17 September 2019: Some notes on coexistence and stability that I've assembled as part of literature reviews for a few projects that I am working on. <pdf>

2 September 2019: Somewhat trivial simulation showing expected uptake of light by individual species in a multi-species mixed canopy. <R>

15 July 2019: Example analysis in response to a recent paper on potential logit regression, tweeted by Forian Hartig (thread available here). <R>