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 ... [Read more...]

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 ... [Read more...]

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 ... [Read more...]

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:

<span># Load data</span>
<span>library</span>(emdbook)

## Loading required package: MASS Loading required package: lattice

<span>library</span>(bbmle)

## Loading required package: stats4

<span>data</span>(ReedfrogFuncresp)
<span>plot</span>(ReedfrogFuncresp, <span>xlim =</span> <span>c</span>(<span>0</span>, <span>100</span>), <span>xaxs =</span> <span>"i"</span>)

Statistical models ... [Read more...]

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 ... [Read more...]

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. ... [Read more...]

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 ... [Read more...]

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 ... [Read more...]

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 ... [Read more...]

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 ... [Read more...]

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 ... [Read more...]

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’... [Read more...]

Mason Earles gave a great presentation this week at Davis R Users’ Group about linking R with the Forest Vegetation Simulator (FVS). FVS is a model developed by the US Forest Service to simulate forest growth over time. It’s written in FORTRAN and has been around since the 1970s. ... [Read more...]

At Davis R Users’ Group today, Ryan Peek gave a presentation on how he takes data from his field instruments and visualizes it in R. Here are his notes. The original *.Rmd file and data can be found here SHORT HOW-TO ON USING XTS AND GGPLOT FOR TIME SERIES DATA ... [Read more...]

At Davis R Users’ Group yesteray, Steve Culman gave us an introduction to the plyr package and how to use it to manipulate data. Here’s his presentation, and the accompanying demonstration script: Steve’s talk is based on this paper by Hadley Wickham in the Journal of Statistical Software. ... [Read more...]

This a brief guide to using R in collaborative, social ways. R is a powerful open-source programming language for data analysis, statistics, and visualization, but much of its power derives from a large, engaged community of users. This is an introduction to tools for engaging the community to improve your ... [Read more...]

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 ... [Read more...]

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. ... [Read more...]

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 ... [Read more...]

Today at Davis R Users’ Group, Rosemary Hartman took us through her work in progress fitting general additive models to organism presence/absence data. Below is her presentation and script. You can get the original script and data here Also, check the comments below for some discussion of other options ... [Read more...]