Some of the R code I have previously posted here for working with NOAA’s optimal interpolated sea surface temperature (OISST) datasets made its way into a recent piece in a Nature news and commentary piece on open-source map-making tools by Jeffrey Perkel. The article details the expansion of open-source ... [Read more...]

Processing R markdown (Rmd) documents with Eclipse/StatET external tools requires a different setup than processing ‘regular’ knitr documents (Rnw). I was having problems getting the whole rmarkdown -__ pandoc workflow working on Eclipse, but the following fix seems to have resolved it, and I can generate Word or HTML ... [Read more...]

Getting certain special symbols into R plots, combined with values that are currently stored in variables, has been an ongoing headache of mine. In particular, plotmath symbols such as the plus-minus sign (±), for which the plotmath command is %+-%, had always caused problems due to my inability to parse the ... [Read more...]

Joe Thorley at Poisson Consulting has released a new R package, rtide, (on which I am listed as a co-author) that provides the ability to predict future (and past) tide heights for 637 different tide stations in the United States and associated territories. The underlying data, consisting of tide harmonic constituents, ... [Read more...]

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 ... [Read more...]

To get the length of a text string (i.e. the number of characters in the string): Using length() would just give you the length of the vector containing the string, which will be 1 if the string is just a single string. To get the position of a regular expression ... [Read more...]

  Here’s a mostly useless visualization of the collection of journal articles that sits in my reference database in Endnote. I deal mostly in marine biology, physiology, biomechanics, and climate change papers, with a few molecular/genetics papers thrown in here and there. The database has 3325 entries, 2 of which have ... [Read more...]

I’ve written previously about some example R scripts I created to extract sea surface temperature data from NOAA’s Optimum Interpolated Sea Surface Temperature products. If you want daily global sea surface temperatures on a 0.25×0.25° grid, they gather those into 1-year files available at http://www.esrl.noaa.gov/... [Read more...]

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 a 0.25 x 0.25 degree grid, and provide an interpolated estimate of the sea surface temperature for each day of the year, based on a ... [Read more...]

Having just returned from the SICB 2014 meetings, the appearance of many people’s Powerpoint figures is fresh on my mind. The sheer number of tiny figure labels (tick marks, axis titles, legend text etc) is disappointing. If we want to point fingers, MATLAB users are clearly the worst offenders because ... [Read more...]

In the previous post, I outlined some tips for increasing the size of figure labels for figures that are meant to be displayed on a projector. The previous post used the base R plot() function, but the procedure when plotting with ggplot2 is different and usually quite a bit simpler ... [Read more...]

In the previous post I outlined how to query the XTide software with R and parse the results into a handy-dandy data frame. The biggest hurdle with that method is getting XTide up and running on your computer. The code outlined here works entirely within R, so you don’t ... [Read more...]

XTide is an open-source program that predicts tide heights and current speeds for hundreds of tide and current stations around the United States. It can be used to produce tide predictions in the past and future for a site at your chosen interval (down... [Read more...]

The first edition of The R Book by Michael J. Crawley was an ambitious work, but managed to be slightly rubbish due to the atrocious typographical layout of the original book. The good news is that the new 2nd edition, released in 2013, has a substanti... [Read more...]

Every so often I want to plot some data with pretty upper and lower error bounds, such as temperature data through time, perhaps with the maximum and minimum temperature range or standard error bounds for averaged data. The polygon( ) function can make those sorts of pretty plots. However, I’ll ... [Read more...]

Quite a while back I wrote some tutorials on getting the StatET plugin for Eclipse running, so that you can write R code and run it within the Eclipse development environment. The developers of all of these pieces of software have kept marching on with... [Read more...]

I was fooling around with including a p-value and R2 value on a plot I was putting together, and found myself quickly descending into the world of R graphics esoterica. I wanted to be able to include the values on the fly using values extracted from a ... [Read more...]

Previously I’ve detailed R scripts that automate the launching and downloading Maxim iButton thermochron data loggers. I’m typically doing the launching and downloading at separate times in my workflow, since I have duplicate iButtons to swap out, so separate scripts work for me. Ryan Knowles recently contributed a ... [Read more...]

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 ... [Read more...]

Maxim's iButton Thermochron temperature dataloggers are little silver doo-dads the size of a large watch battery that can record up to 2048 time-stamped temperature values. The internal battery is usually good for a few years of use. Maxim supplies a J... [Read more...]