Articles by Marc in the box

R package “fishdynr”

February 1, 2015 | Marc in the box

The fishdynr package allows for the construction of some basic population dynamics models commonly used in fisheries science. Included are models of a single cohort, cohortSim, and a more complex iterative model that incorporates a stock-recruitment re... [Read more...]

Data point locator function

December 5, 2014 | Marc in the box

Here's a little function to select data points in an open graphical device (ptlocator()). The function does a scaling of the x and y axes in order to give them equal weighting and remove the influence of differing units or ranges. The function then cal... [Read more...]

Maximal Information Coefficient (Part II)

September 17, 2014 | Marc in the box

A while back, I wrote a post simply announcing a recent paper that described a new statistic called the "Maximal Information Coefficient" (MIC), which is able to describe the correlation between paired variables regardless of linear or nonlinear relationship. This turned out to be quite a popular post, and included ... [Read more...]

Rotated axis labels in R plots

August 5, 2014 | Marc in the box

It's somehow amazing to me that the option for slanted or rotated axes labels is not an option within the basic plot() or axis() functions in R.  The advantage is mainly in saving plot area space when long labels are needed (rather than as a means... [Read more...]

Importing bathymetry and coastline data in R

January 25, 2014 | Marc in the box

After noticing some frustrating inaccuracies with the high-resolution world coastlines and national boundaries database found in worldHires from the package mapdata (based on CIA World Data Bank II data), I decided to look into other options. Although listed as "depreciated", the data found in NOAAs online "Coastline Extractor" is a ... [Read more...]

GMT standard color palettes

January 25, 2014 | Marc in the box

GMT (Generic Mapping Tools) ( is a great mapping tool. I'm hoping to use it more in the future, but for the meantime I wanted to recreate some of the it's standard color palettes in R. Unfortunately, I couldn't find documen... [Read more...]

New version of image.scale function

December 5, 2013 | Marc in the box

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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A plea for less word clouds

April 25, 2013 | Marc in the box

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... [Read more...]

Choosing colors visually with ‘getcolors’

January 18, 2013 | Marc in the box

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 ... [Read more...]
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