Blog Archives

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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A Null Model for Age Effects in Disease with Multiple Infections

June 11, 2013
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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 models of forest stand demography...

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Robert Hijmans on Spatial Data Analysis

May 23, 2013
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Last week at the Davis R Users’ Group Robert Hijmans gave a talk about spatial data analysis in R. Robert is a professor of biogeography at UC Davis and the author of the raster (analysis of gridded data), dismo (species distribution modeling), and geosphere (spherical trigonometry), packages. Robert’s presentation spanned topics including basic...

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Improved R Profiling Summaries

May 2, 2013
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In my last post I mentioned that I had improved on R’s summaryRprof() function with a custom function called proftable(). I’ve updated proftable() to take advantage of R 3.0.0’s ability to record line numbers while profiling. I’ve put it on github – you can get it there or below. proftable reads in a file generated by...

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FasteR! HigheR! StrongeR! – A Guide to Speeding Up R Code for Busy People

April 25, 2013
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FasteR! HigheR! StrongeR! – A Guide to Speeding Up R Code for Busy People

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,...

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Debugging Tools in R with Michael Hannon

April 18, 2013
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Debugging Tools in R with Michael Hannon

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...

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Demographic analysis using the `popbio` library and some other fun stuff

April 4, 2013
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Demographic analysis using the `popbio` library and some other fun stuff

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...

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Model Selection and Multi-Model Inference

February 20, 2013
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Model Selection and Multi-Model Inference

At D-RUG this week Rosemary Hartman presented a really useful case study in model selection, based on her work on frog habitat. Here is her code run through ‘knitr’. Original code and data are posted here. (yes, I am just doing this for the flying monkey) Editor’s note: we’re giving away flying monkey dolls from our...

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