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packcircles version 0.2.0 released

Version 0.2.0 of the packcircles package has just been published on CRAN. This package provides functions to find non-overlapping arrangements of circles in bounded and unbounded areas. The package how has a new circleProgressiveLayout function. It uses an efficient deterministic algorithm to arrange circles by consecutively placing each one externally tangent to two previously placed circles while avoiding overlaps. It was adapted from a version written in C by Peter Menzel who lent his support to creating this R/Rcpp version. The underlying algorithm is described in the paper: Visualization of large hierarchical data by circle packing by Weixin Wang, Hui Wang, Guozhong Dai, and Hongan Wang. Published in Proceedings of the SIGCHI Conference on Human Factors in Computing Systems, 2006, pp. 517-520 (Available from ACM ). Here is a small example of the new function, taken from the package vignette: library(packcircles) library(ggplot2) t <- theme_bw() + theme(panel.grid =
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Graph-based circle packing

The previous two posts showed examples of a simple circle packing algorithm using the packcircles package (available from CRAN and GitHub ). The algorithm involved iterative pair-repulsion to jiggle the circles until (hopefully) a non-overlapping arrangement emerged. In this post we'll look an alternative approach. An algorithm to find an arrangement of circles satisfying a prior specification of circle sizes and tangencies was described by Collins and Stephenson in their 2003 paper in Computation Geometry Theory and Applications. A version of their algorithm was implemented in Python by David Eppstein as part of his PADS library (see CirclePack.py ). I've now ported David's version to R/Rcpp and included it in the packcircles package. In the figure below, the graph on the left represents the desired pattern of circle tangencies: e.g. circle 7 should touch all of, and only, circles 1, 2, 6 and 8. Circles 5, 7, 8 and 9 are internal , while the remaining circles are exter
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Static and moving circles

After the previous post on the packcircles package for R someone suggested it would be useful to be able to fix the position of selected circles. As a first attempt, I've added an optional weights argument to the circleLayout function. Weights can be in the range 0-1 inclusive, where a weight of 0 prevents a circle from moving, while a weight of 1 allows full movement. The updated code is at GitHub . Here's an example where the largest of a set of initially overlapping circles is fixed in place: And here is the code for the example: library(packcircles) library(ggplot2) library(gridExtra) # Generate some random overlapping circles ncircles <- 200 limits <- c(-50, 50) inset <- diff(limits) / 3 rmax <- 20 xyr <- data.frame( x = runif(ncircles, min(limits) + inset, max(limits) - inset), y = runif(ncircles, min(limits) + inset, max(limits) - inset), r = rbeta(ncircles, 1, 10) * rmax) # Index of the largest circle largest.id <- which(xyr$r ==
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Circle packing in R (again)

Back in 2010 I posted some R code for circle packing . Now, just five years later, I've ported the code to Rcpp and created a little package which you can find at GitHub . The main function is circleLayout which takes a set of overlapping circles and tries to find a non-overlapping arrangement for them. Here's an example: And here's the code: # Create some random circles, positioned within the central portion # of a bounding square, with smaller circles being more common than # larger ones. ncircles <- 200 limits <- c(-50, 50) inset <- diff(limits) / 3 rmax <- 20 xyr <- data.frame( x = runif(ncircles, min(limits) + inset, max(limits) - inset), y = runif(ncircles, min(limits) + inset, max(limits) - inset), r = rbeta(ncircles, 1, 10) * rmax) # Next, we use the `circleLayout` function to try to find a non-overlapping # arrangement, allowing the circles to occupy any part of the bounding square. # The returned value is a list with elements for
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Fitting an ellipse to point data

Some time ago I wrote an R function to fit an ellipse to point data, using an algorithm developed by Radim Halíř and Jan Flusser 1 in Matlab, and posted it to the r-help list . The implementation was a bit hacky, returning odd results for some data. A couple of days ago, an email arrived from John Minter asking for a pointer to the original code. I replied with a link and mentioned that I'd be interested to know if John made any improvements to the code. About ten minutes later, John emailed again with a much improved version ! Not only is it more reliable, but also more efficient. So with many thanks to John, here is the improved code: fit.ellipse <- function (x, y = NULL) { # from: # http://r.789695.n4.nabble.com/Fitting-a-half-ellipse-curve-tp2719037p2720560.html # # Least squares fitting of an ellipse to point data # using the algorithm described in: # Radim Halir & Jan Flusser. 1998. # Numerically stable direct least squares fitting of ellipses
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IDE errors with Maven projects after upgrading to NetBeans 7.2

A recent upgrade of NetBeans from version 7.1 to 7.2 seemed to cause problems with Maven multi-module projects. Normally, a newly created class in one Maven project module will be instantly visible to other modules open in the IDE, at least for editing purposes. But after the upgrade I started to see "cannot find symbol" errors in the IDE for such new classes. Despite this, a full build of the project would succeed. Googling for an answer drew a blank. The usual kludge fixes such as deleting the NetBeans cache (for NetBeans 7.2 on OSX this seems to have moved from ~/.netbeans to ~/Library/Application Support/Netbeans) and re-indexing my local repo didn't make any difference. Despair loomed. Happily, I stumbled across the cause of the problem after only a moderate amount of pulling of hair and gnashing of teeth. My Maven settings.xml file included this section... <profiles> <profile> <id>netbeans-ide</id> <
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Build an application plus a separate library uber-jar using Maven

I've been working on a small Java application with a colleague to simulate animal movements and look at the efficiency of different survey methods. It uses the GeoTools library to support map projections and shapefile output. GeoTools is great but comes at a cost in terms of size: the jar for our little application alone is less than 50kb but bundling it with GeoTools and its dependencies blows that out to 20Mb. The application code has been changing on a daily basis as we explore ideas, add features and fix bugs. Working with my colleague at a distance, over a fairly feeble internet connection, I wanted to package the static libraries and the volatile application into separate jars so that he only needed to download the former once (another option would have been for my colleague to set up a local Maven repository but for various reasons this was impractical). A slight complication with bundling GeoTools modules into a single jar (aka uber-jar) is that individual modules make ext
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