Articles by Luke Miller

Brief mention in Map-making on a budget

June 5, 2018 | Luke Miller

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 Rmarkdown documents with Eclipse and StatET

October 2, 2017 | Luke Miller

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...]

R plotmath functions combined with variable values

May 4, 2017 | Luke Miller

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...]

Basic text string functions in R

May 18, 2015 | Luke Miller

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...]

A plot of co-authorships in my little corner of science

April 22, 2015 | Luke Miller

  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...]

Extracting NOAA sea surface temperatures with ncdf4

November 25, 2014 | Luke Miller

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 [Read more...]

More tide prediction with R

May 19, 2013 | Luke Miller

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...]

Interfacing XTide and R

May 17, 2013 | Luke Miller

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...]

Another R + iButton script

October 8, 2012 | Luke Miller

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...]

R scripts for downloading iButton Thermochron dataloggers

July 11, 2012 | Luke Miller

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...]
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