Publications by Noam Ross
A Null Model for Age Effects in Disease with Multiple Infections
Here’s a little thought exercise I did that has caused me to go back and restart my Sudden Oak Death modeling in a new framework. Feedback welcome. I’m especially interested in relevant literature – I haven’t found many good examples of macroparasite/multiple infection models with age structure. Introduction Cobb et al. (2012) develop two...
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The null model for age effects with overdispersed infection
How does overdispersion of infections affect the behavior of the multiple-infection model? I redefine the model to account for overdispersion, assuming the same overdispersion occurs in both age classes. The parameter varies inversely with the degree of overdispersion. Again, the classes are demographically identical, and infection affects morta...
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Dave Harris on Maximum Likelihood Estimation
At our last Davis R Users’ Group meeting of the quarter, Dave Harris gave a talk on how to use the bbmle package to fit mechanistic models to ecological data. Here’s his script, which I ran throgh the spin function in knitr: # Load data library(emdbook) ## Loading required package: MASS Loading required package: lattice library(bbmle) ## L...
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Printing R help files in the console or in knitr documents
Yesterday, I was creating a knitr document based on a script, and was looking for a way to include content from an R help file. The script, which was a teaching document, had a help() command for when the author wanted to refer readers to R documentation. I wanted that text in my final document, though. There’s no standard way to do this in R, ...
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How to format plots for publication using ggplot2 (with some help from Inkscape)
The following is the code from a presentation made by Rosemary Hartman to the Davis R Users’ Group. I’ve run the code through the spin function in knitr to produce this post. Download the script to walk through here. First, make your plot. I am going to use the data already in R about sleep habits of different animals. It’s the same one Noa...
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Ryan Peek on Creating Shiny Apps
Yesterday at the Davis R User’s Group1, Ryan Peek gave a talk about using the shiny package to create interactive web apps with R. Here are his slides. Ryan includes a bunch of links to examples and tutorials, as well as his own thermohydrographs app: Thanks to Revolution Analytics for another year of sponsorship!↩ Related To leave a comme...
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Using Dates and Times in R
Today at the Davis R Users’ Group, Bonnie Dixon gave a tutorial on the various ways to handle dates and times in R. Bonnie provided this great script which walks through essential classes, functions, and packages. Here it is piped through knitr::spin. The original R script can be found as a gist here. Date/time classes Three date/time classes a...
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Vectorization in R: Why?
Here are my notes from a recent talk I gave on vectorization at a Davis R Users’ Group meeting. Thanks to Vince Buffalo, John Myles White, and Hadley Wickham for their input as I was preparing this. Feedback welcome! Beginning R users are often told to “vectorize” their code. Here, I try to explain why vectorization can be advantageous in R...
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What shall we talk about at ESA?
ESA is just around the corner, and many of us are gearing up and trying to figure out a schedule to cover all the talks and people we can pack in. ESA is a big conference and there’s far too much for any one person to see. In the end, everyone experiences a different part of the elephant. However, I thought it would be interesting to take a loo...
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ESA 2014: Don’t Know Much About History…
After my last post text-mining ESA Annual Meeting abstracts, Nash Turley was interested in the presence of the term “natural history” in ESA abstracts. I decided to collect a little more data by including programs back to 2010, giving a five-year data set. Thankfully the program back to 2010 remains in mostly the same format, so it’s easy t...
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