Deploying barnacle settlement plates

As the northeast slowly starts to shrug off the shackles of winter, the barnacles decide to start spawning their planktonic larvae that float around for a few days, looking for a place to settle. We use barnacles in experiments all the time, so we set out little granite tiles in the field in central Maine to give the barnacle cyprids (larvae) a place to settle and metamorphose. We can then return in a few weeks and bring the tiles back to the laboratory, where the barnacles continue to grow until we use them in an experiment. Unfortunately, doing all … Continue Reading

Extracting sea surface temperatures from NOAA’s OISSTv2

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, https://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.

Sea surface temperatures

NOAA’s Physical Sciences Division produces a global map of weekly averaged sea … Continue Reading

RStudio – another integrated development environment for R

RStudio for Windows, Linux, and Mac OS X

If you’re in the market for a very easy-to-setup integrated development environment for R, wander over to RStudio.org. They’ve just released a beta version of their freely-available front end for R that runs under Windows, Linux and Mac OS X (for R versions 2.11 and later).

If you’re not familiar with the idea of an integrated development environment, it’s simply an attempt to bring all of the tools needed for working with R into one uniform interface. Much like the basic … Continue Reading

Converting MATLAB and R date and time values

For some unknown reason, MATLAB codes its date/time values as the number of elapsed days starting from January 1 in the year 0000. R uses the equally arbitrary, but much more widespread POSIX/Unix epoch as a reference for time keeping, so that R’s POSIX time values are stored internally as the elapsed seconds since 00:00 January 1, 1970. Converting back and forth between the two values requires just a bit of doing.

Inside R, converting from the MATLAB ‘datenum‘ value into the R POSIXt standard is fairly straightforward: Subtract 719529 from your MATLAB datenum to get the … 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

Time lapse of fall 2010

The video above is a series of photos, taken around 8am daily between Oct 10, 2010 and Jan 1, 2011. The view is of the backyard of my current abode. Taken with a Canon 5D (try the HD version on youtube), 35/1.4, Av mode at f/8, ISO 200. My ocean view, such as it is, reappeared around Thanksgiving, and the first snow hits December 21st.

Additionally, below is a 1-day time lapse of the snow storm that hit Boston on January 12, 2011. The images were … Continue Reading

Book Review: 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
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