Blog Archives

Data mountains and streams – stacked area plots in R

December 9, 2013
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Data mountains and streams – stacked area plots in R

Below are two functions for producing stacked area plots. The first is the more typical approach where sequential series are stacked on top of another (function: plot.stacked), while the second approach is the more aesthetically-oriented version called...

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New version of image.scale function

December 5, 2013
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New version of image.scale function

Below is an updated version of the image.scale function. In the old version, one had to constantly use additional arguments to suppress axes and their labels. The new version contains the additional arguments axis.pos (1, 2, 3, or 4) for defining the s...

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Working with hdf files in R – Example: Pathfinder SST data

November 8, 2013
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Working with hdf files in R – Example: Pathfinder SST data

Following  a question that I posted on stackoverflow.com, I recieved the great advice to use the Bioconductor rhdf5 package to work with HDF5 files. The package is not located on CRAN, but can be sourced from the Bioconductor website: source("http://bioconductor.org/biocLite.R")biocLite("rhdf5") Created by Pretty...

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A first attempt at an individual-based model in R

October 29, 2013
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A first attempt at an individual-based model in R

I have been curious for a while as to how R might be used for the construction of an individually-based model (IBM), or agent-based model (ABM). In particular, what R objects lend themselves best to storing information on individuals, and allow for new...

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A plea for less word clouds

April 25, 2013
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A plea for less word clouds

Word cloud of DOMA hearing transcriptsI must admit, there is something appealing about the word cloud - that is, until you try to understand what it actually means...Word clouds are pervasive - even in the science world. I was somewhat spurred to wri...

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A plea for less word clouds

April 25, 2013
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A plea for less word clouds

Word cloud of DOMA hearing transcriptsI must admit, there is something appealing about the word cloud - that is, until you try to understand what it actually means...Word clouds are pervasive - even in the science world. I was somewhat spurred to write...

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My template for controlling publication quality figures

January 28, 2013
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My template for controlling publication quality figures

The following is a template that I usually start with when producing figures for publication. It allows me to control:The overall size of the figure (in inches) (WIDTH, HEIGHT)The layout of figure subplots (using the layout() function) (LO)The resoluti...

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My template for controlling publication quality figures

January 28, 2013
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My template for controlling publication quality figures

The following is a template that I usually start with when producing figures for publication. It allows me to control:The overall size of the figure (in inches) (WIDTH, HEIGHT)The layout of figure subplots (using the layout() function) (LO)The resolution of the figure (for a .png file) (RESO)I define the overall dimensions of...

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Choosing colors visually with ‘getcolors’

January 18, 2013
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Choosing colors visually with ‘getcolors’

When plotting, I am constantly defaulting to the "main" colors in R - In other words, the colors that one can quickly call by number (1="black", 2="red", 3="green", 4="blue", ... etc.) . In my opinion, these colors do not lend themselves well to compelling graphics. I imagine this is the reason for the inclusion...

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Lomb-Scargle periodogram for unevenly sampled time series

January 10, 2013
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Lomb-Scargle periodogram for unevenly sampled time series

In the natural sciences, it is common to have incomplete or unevenly sampled time series for a given variable. Determining cycles in such series is not directly possible with methods such as Fast Fourier Transform (FFT) and may require some degree o...

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