Blog Archives

Don’t R alone! A guide to tools for collaboration with R

January 7, 2013
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Don’t R alone! A guide to tools for collaboration with R

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 R code and collaborate with others. (Am I...

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Lauren Yamane on Matrix Population Models in R

November 30, 2012
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Lauren Yamane on Matrix Population Models in R

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 Marissa Baskett and Sebastian Schreiber in...

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A quick function for editing CSV files in R

November 19, 2012
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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. Unfortunately there doesn’t seem to be a good,...

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Simulating Sudden Oak Death Dynamics

November 16, 2012
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Simulating Sudden Oak Death Dynamics

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 al. (2012). The model in that paper simulates...

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Exploring GAMs with Rosemary Hartman

November 9, 2012
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Exploring GAMs with Rosemary Hartman

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 for this type of analysis, such as...

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Ryan Peek on Customizing Your R Setup

November 2, 2012
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Ryan Peek showed us how to use an .Rprofile file to customize your R setup. Here are his instructions and script: For Windows To change profile for R, go here: C:\Program Files\R\R-2.15.1\etc (or whatever version you are using) Edit the “Rprofile.site” file Restart R For Macs Create your Rprofile file. -use TextEdit or another editor to create a file called Rprofile.txt In a...

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Chris Hamm on using plot.new() for better combined plots

October 26, 2012
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Chris Hamm on using plot.new() for better combined plots

At DRUG today, Chris Hamm (email (cahamm at ucdavis dot edu)) showed us an easier way to combine multiple figures into one plot using plot.new, rather than par(mfrow=...) Here’s his script: A Report Generated by knitr # plot.new() [email protected] #I discovered this plotting method when trying to add an inset figure # to a plot # plot.new is part of the traditional graphics....

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Stella Copeland’s Intro to Mixed Models in R

October 19, 2012
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In D-RUG today, Stella Copeland gave a quick introduction to mixed models in R. Here’s the script that she presented: Get the data file for this script here Stella also recommends this paper by Ben Bolker as a quick introduction to the topic.

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A quick introduction to ggplot()

October 5, 2012
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A quick introduction to ggplot()

I gave a short talk today to the about ggplot. This what I presented. Additional resources at the bottom of this post ggplot is an R package for data exploration and producing plots. It produces fantastic-looking graphics and allows one to slice and dice one’s data in many different ways. Comparing with base...

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An R Users’ Group in Davis

September 24, 2012
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I’m excited to share that we’ve started a new R users’ group at UC Davis! Right now our main purpose is to run weekly 2-hour work/hack sessions where R users can get together to work through problems together. More info here

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