ggplot2 has just hit 0.9.2, and with the change comes a new theme system. Previous versions of ggplot2 offered a theme_blank(), which was a stripped-down, essentially blank plotting canvas, but it is now deprecated. github user jrnold has produced a s... [Read more...]

Sometimes, as with cross-validation, one needs to generate k partitions, each with an equal number of observations. There are probably an infinite number of ways this could be done in R, but the Gist below illustrates one way to do it in four lines, w... [Read more...]

If you’ve ever written code that generates a whole whack of files, you may have came across the following problem when processing them. Using a naming convention wherein files are numbered will  gum up any ordering which is based on string sorting (ls, for example). What you end up ... [Read more...]

In our previous post, we used a quick-and-dirty method for ordering the axes on our heatmap. It has been pointed out to me that There is a Package for That (which is my nominee for a new slogan for R — not that it needs a slogan). seriation offe... [Read more...]

Dispersal is a key process in many domains, and particularly in ecology. Individuals move in space, and this movement can be modelled as a random process following some kernel. The dispersal kernel is simply a probability distribution describing the distance travelled in a given time frame. Since space is continuous, ... [Read more...]

Featuring the lovely “spectral” palette from Colorbrewer. This really just serves as a reminder of how to do four things I frequently want to do: Make a heatmap of some kind of matrix, often a square correlation matrix Reorder a factor vari... [Read more...]

A tweet from @coneee yesterday about merging two datasets using columns of data that don’t quite match got me wondering about a possible R recipe for handling partial matching. The data in question related to country names in a datafile that needed fusing with country names in a listing ... [Read more...]

This is something I have had the occasion to do, and never remember how, so this is legitimately a reminder to my future self of how to do things with off-diagonal elements of a matrix. Select rows and columns are easy: mat[1:10, ] or mat[, -c(5)], for... [Read more...]

As a follow-up to yesterday’s post on producing visually-weighted regression plots, here is some code which illustrates the production of similar plots, but using Zelig’s convenient modeling and simulation functions. This code was produced... [Read more...]

There has recently been a lot of discussion of so-called “visually-weighted regression” plots. Folk hero Hadley Wickham suggests that such plots would be easy to implement with ggplot2, and so I have attempted to prove him right. The approa... [Read more...]

As you advance in your R use past “canned” functions and packages made by others, you may want to take information from one R object for use in another. For example, you may want to estimate a linear model, then use the results of that esti... [Read more...]

We’ve already briefly covered making a reproducible example, but I thought I’d go a little more in-depth on the very helpful function dput(). Whenever I am having trouble applying an operation to some R object, and need help, but want to av... [Read more...]

Today, we will go further on the inference of copula functions. Some codes (and references) can be found on a previous post, on nonparametric estimators of copula densities (among other related things).  Consider (as before) the loss-ALAE data... [Read more...]

As mentioned in the course last week Venter (2003) suggested nice functions to illustrate tail dependence (see also some slides used in Berlin a few years ago). Joe (1990)'s lambda Joe (1990) suggested a (strong) tail dependence index. For lower t... [Read more...]

At last weekend’s Hack Ta Ville event here in Montreal, I joined up with some talented urban planners and web devs to realize Vélobstacles. The idea of the project is to crowd source information on cycling conditions around the city. As with any crowd sourcing project, we were ... [Read more...]

This image comes from the cover of Preliminary Papers of the Second International Workshop on Artificial Intelligence and Statistics (1989). Someone abandoned it in the lobby of my building at school. Whatever for, I’ll never know. I just love the idea of machine learning/AI/Statistics evoking a robot hand ... [Read more...]

Rather belatedly, I got around to posting a series of posts summarising the Formula One season to date: F1 2012 Mid-Season Review – Grid/Classification Analysis: for example, how do the drivers’ grid and final classifications compare? F1 2012 Mid-Season Review – Pit Stops: for example, how does pit stop performance across the teams ... [Read more...]

As an invasion biologist, the process of spatial spread is at the heart of what I do. When I came across this dataset of Walmart store openings since 1962 I couldn’t help but see it as an invasion front which looks a lot like a biological invasion or (albeit slow) ... [Read more...]

One of the possible barriers to widespread adoption of open notebook science is knowing where to start. Video reports of lab experiments hosted on Youtube can be easily embedded in a hosted WordPress blog; a MediaWiki wiki can be used to provide one page per experiment, with change tracking/history ... [Read more...]

A while ago I wrote this post with some R code to visualize the updating of a beta distribution as the outcome of Bernoulli trials are observed. The code provided a single plot of this process, with all the curves overlayed on top of one another. Then John Myles White (... [Read more...]