* You are viewing Posts Tagged ‘R’

Using knitr and R to make instructor/student handout versions

I teach some of my lab sections using R, and so I need to create lab handouts that include nicely formatted R commands and R output as an example for the students. These handouts will also include exercises where the students will be writing their own R code, or interpreting the results, or generating figures. For these exercises, it is useful to also have an instructor version of the handout so that I can recall what I was hoping to have the students do, and so that other instructors in the course have some clue as to what I might … Continue Reading

NOAA OISST v2 High Resolution daily sea surface temperatures with R

Update, 2015-11-30 It appears that NOAA has gone through and upgraded all of the OISST files to the newer version of the NetCDF file format. As a result, the functions outlined in this post don’t work any longer. Instead, see the updated functions in my newer post, http://lukemiller.org/index.php/2014/11/extracting-noaa-sea-surface-temperatures-with-ncdf4/. The concepts are the same as described here, but the newer functions use the ncdf4 package to access the newer NetCDF file format.

The National Ocean and Atmospheric Administration generates freely-available world-wide estimates of mean daily sea surface temperature, and has been doing so back to 1981. The data are on … Continue Reading

R scripts for downloading iButton Thermochron dataloggers

Last time, I posted some R code to help quickly launch many iButton Thermochron temperature dataloggers with the same mission parameters. The R code makes use of a publicly-available command line utility released by the iButton’s manufacturer, Maxim.  Of course, Maxim also has a command line utility for downloading the data from those iButtons that you launched already. The code below will make use of that program to download an iButton, give the file a unique name of your choosing, parse the data out into a simple comma-separated-value file (for easy opening in R or Excel), and then … Continue Reading

Accessing NOAA tide data with R

Boston Harbor tides for December 2010, retrieved from NOAA CO-OPS server.

The National Oceanic and Atmospheric Administration makes the data from their many tide monitoring stations around the continent available for download. One way to access these data is through NOAA’s Center for Operational Oceanographic Products and Services (CO-OPS) website, which provides several access methods including an OPeNDAP server. The OPeNDAP server allows you to construct a fairly simple URL query to submit in a web browser, and it will return the requested data as ascii … Continue Reading

A lightweight object browser for R

The following post is based on information originally found here: http://r.789695.n4.nabble.com/Object-Browser-td2594912.html
If you use the basic R GUI and you can manage to remember what sorts of objects you have in the workspace more than 5 seconds after you enter them, you’ve got a better short term memory than I do. But if you constantly lose track of what variables, data frames, model objects and so forth you have in your R session, a separate “object browser” window can be a godsend.

Diehard R command line users just use the ls() command to list the objects in memory, and get a … Continue Reading

Book Review: Mixed Effects Models and Extensions in Ecology with R


Mixed Effects Models and Extensions in Ecology with R
Zuur, A.F., Ieno, E.N., Walker, N., Saveliev, A.A., Smith, G.M.
Springer, 2009

Somewhere along the line you probably realized that your undergraduate statistics classes didn’t quite cover the breadth of topics you’d end up needing for dealing with your data. The time constraints of a typical quarter or semester-long biostats class often leave you only scratching the surface of all of the issues you need to consider when analyzing a typical ecological data set. That’s … Continue Reading

Book Review: A Beginner’s Guide to R

A Beginner's Guide to R

A Beginner’s Guide to R

Alain F. Zuur, Elena N. Ieno, Erik H.W.G. Meesters
Springer, 2009

So you’ve decided to start learning R. Probably because someone in your institution, typically a gentleman with an unkempt beard who likes to rail on about open source software, has convinced you to abandon the comfortable GUI-driven statistics program you learned in undergrad. But it quickly becomes apparent that leaving the familiar point-and-click interface of JMP or Minitab or (horrors) Excel for the text-driven world of R isn’t as simple as downloading … Continue Reading

Book Review: R in a Nutshell

R in a Nutshell
R in a Nutshell
Joseph Adler
O’Reilly Media, 2010

If you’re looking for an introduction to the R computing language and statistical platform, R in a Nutshell, by Joseph Adler, may be worth a look. This book is a member of O’Reilly Media’s “In a Nutshell” series that may be familiar to you if you dabble in programming. The goal of the book is to introduce the reader to many aspects of the R language, from the basic architecture and syntax of R to some of the many available … Continue Reading

R 2.12.0 and Eclipse with StatET installation


A while back I outlined the setup process for running R under the Eclipse integrated development environment with the help of WalWare.de’s StatET plugin for Eclipse, in Windows 7. This post is an update on that procedure for the newer versions of each of the programs now available.

Specifically, this information pertains to an installation of Eclipse 3.6 (Helios), StatET version 0.9.1.b201011060900E36sw, and R 2.12.0, under Windows 7 64-bit (circa December 2010). The process for making R work within Eclipse has become a bit more … Continue Reading

Sorting out Sweave in Eclipse/StatET

Using Sweave to produce pretty-looking documentation for R is awfully handy. It takes a little tweaking to get set up in Eclipse and StatET though. I followed the information in Jeromy Anglim’s webpage to originally get Sweave set up. The following is my experience getting it working with Eclipse 3.5, StatET 0.9.1.b201011060900E35sw, Sweave Add-on for StatET 0.9.0.b201011060900E35sw, MiKTeK 2.9, and R 2.12.0 i386 on Windows 7 x64 circa November 2010.

I initially wrote a .Rnw file to be run through Sweave and converted to a pdf. I then set up Eclipse to process the .Rnw file using Sweave. I … Continue Reading

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