Blog Archives

Mason Earles on interfacing R with the Forest Vegetation Simulator

February 13, 2013
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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. FVS has recently gone open-source (its...

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Ryan Peek on using xts and ggplot for time-series data

February 6, 2013
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Ryan Peek on using xts and ggplot for time-series data

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 XTS is a very helpful package...

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Steve Culman on the `plyr` Package

January 17, 2013
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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. A lot of useful related...

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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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