I recently posted the slides from a guest lecture that I gave on Bayesian methods for biologists/ecologist. In an effort to promote active learning, the class was not a straight forward lecture, but rather a combination of informational input from me and opportunities for students to engage with the ... [Read more...]

I really enjoy using the DW-NOMINATE data for examples, as I do here. Sometimes it’s useful to indicate regions in the background of a plot — perhaps two-dimensional regions of interest, perhaps one-dimensional periods in time. It’s... [Read more...]

This is a talk I gave this week in Advanced Biostatistics at McGill. The goal was to provide an gentle introduction to Bayesian methodology and to demonstrate how it is used for inference and prediction. There is a link to an accompanying R script in the slides [Read more...]

Sometimes, people want to plot things in three dimensions. Others have spoken more eloquently than I could on the potential problems with plotting multiple two-dimensional relationships in a two-dimensional medium with an artificial three-dimensional ... [Read more...]

This Gist has a couple of things going on, I’ll just list them: It downloads the entire history of U.S. House DW-NOMINATE scores from voteview.com It evaluates aggregate statistics, with members grouped by party and congress, with easy weighted ... [Read more...]

(Click for a bigger version) I’m not sure when plotting raster images in an R scatter plot will end up being useful. It’s not something I expect to need to do in my day-to-day research, and I think in general probably adds more complexity ... [Read more...]

In honor of today’s announcement of the Nobel Prize for Roth and Shapley, I found an illustration of the deferred acceptance algorithm from 1962 in R. Credit for the code goes to the blogger at Letters from London, and I’ve included a Gi... [Read more...]

As often happens, I have learned of a technique just as it is being called into question. In this case, the technique is changing the aspect ratio of a line plot such that the typical slope of each segment is 45° (see), a rule of thumb which has bee... [Read more...]

The three benchmark algorithms for predicting the location of dark matter halos are, for the most part, all over the map. Most of the test skies look something like this: There are, however, some skies with rather strong halo signals that get a decent amount of agreement: The Lenstool MLE ... [Read more...]

Some people like to do crossword puzzles. I like to do machine learning puzzles. Lucky for me, a new contest was just posted yesterday on Kaggle. So naturally, my lazy Saturday was spent getting elbow deep into the data. The training set consists of a series of ‘skies’, each containing ... [Read more...]

How to choose the right *apply function: This is an amazing stackoverflow answer to help you decide which of the many *apply functions (apply, lapply, sapply, vapply, mapply, rapply, tapply) is appropriate for the task at hand. I’m planning on doing... [Read more...]

Whenever possible, I try to save R graphic output in a vector format, typically pdf(). I also like to use the handy ggsave() function to do so, as it streamlines the process, and makes it easy to be consistent across formats. However, at times it is n... [Read more...]

I only rarely have the occasion to need the convex hull of a set of points, but I love chull(), so I’d like to share an example of how to use it. This Gist also offers a pretty straightforward application of the Split-Apply-Combine strategy (see... [Read more...]

I don’t really care for the name “marimekko” or “mosaic,” but I do like this type of plot as a means of illustrating proportions in nested categorical data, or as an alternative to the parallel time series plots discussed... [Read more...]

Here’s an example of how to color your plot shapes and pch using an ifelse() statement. Ifelse() is handy as it creates an easy way to branch a function. The syntax is: ifelse(logical.condition, option1, option2). Meaning, if the logical condi... [Read more...]

The problem: We often want to plot data and assign plot attributes based on characteristics of the data. For example, if we have a group of students with the following IQs, we might want to indicate who is an outlier in the statistical sense. I like... [Read more...]

This Gist is mostly for my future self, as a reminder of how to find distances between each row in two different matrices. To create a distance matrix from a single matrix, the function dist(), from the stats package is sufficient. There are times, ho... [Read more...]

This is another of those confluence style posts, where a handful of things I’ve read in quick succession seem to phase lock in my mind: (brought to mind in part via @downes a week or so ago: How to Synch 32 Metronomes) The first was a post by Alan Levine ... [Read more...]

A long title, but there are a couple of handy things in this Gist. The first, and more obscure, is the conversion of a data.frame of categorical variables into a matrix of dummy/binary/indicator variables, one for each category of each original variab... [Read more...]

In developing plots, I often use color (or “colour” in ggplot2 parlance) to reflect values of a third, non-X/Y, variable. Depending on the distribution of this Z variable, however, the effective color range can be narrow, making it difficul... [Read more...]