Blog Archives

More ESA 2014 Program Text-Mining: Topics as Communities

August 22, 2014
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More ESA 2014 Program Text-Mining: Topics as Communities

In my first pass at text analysis of the ESA program, I looked at how the frequency of words used in the ESA program differed from last year to this year. There are much more sophisticated ways at looking at word use in text, though, and I began to dive into the text-mining literature to find...

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ESA 2014: Don’t Know Much About History…

August 5, 2014
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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...

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What shall we talk about at ESA?

July 24, 2014
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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...

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Vectorization in R: Why?

April 16, 2014
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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...

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Using Dates and Times in R

February 10, 2014
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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...

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Ryan Peek on Creating Shiny Apps

January 28, 2014
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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...

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How to format plots for publication using ggplot2 (with some help from Inkscape)

November 20, 2013
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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...

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Printing R help files in the console or in knitr documents

June 18, 2013
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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...

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Dave Harris on Maximum Likelihood Estimation

June 17, 2013
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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) ## Loading required package:...

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The null model for age effects with overdispersed infection

June 12, 2013
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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 mortality but not growth: \[\begin{aligned} \frac{dJ}{dt}...

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