Articles by Noam Ross

Ryan Peek on Creating Shiny Apps

January 28, 2014 | Noam Ross

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...]

Dave Harris on Maximum Likelihood Estimation

June 17, 2013 | Noam Ross

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>
## Loading required package: MASS Loading required package: lattice
## Loading required package: stats4
<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...]

The null model for age effects with overdispersed infection

June 12, 2013 | Noam Ross

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...]

Robert Hijmans on Spatial Data Analysis

May 23, 2013 | Noam Ross

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...]

Improved R Profiling Summaries

May 2, 2013 | Noam Ross

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...]

Debugging Tools in R with Michael Hannon

April 18, 2013 | Noam Ross

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...]

Model Selection and Multi-Model Inference

February 20, 2013 | Noam Ross

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...]

Steve Culman on the `plyr` Package

January 17, 2013 | Noam Ross

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...]

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

January 7, 2013 | Noam Ross

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...]

Lauren Yamane on Matrix Population Models in R

November 30, 2012 | Noam Ross

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...]

A quick function for editing CSV files in R

November 19, 2012 | Noam Ross

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...]

Simulating Sudden Oak Death Dynamics

November 16, 2012 | Noam Ross

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...]

Exploring GAMs with Rosemary Hartman

November 9, 2012 | Noam Ross

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...]
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