Tag Archives: human development index

MCMC in Python: PyMC for Bayesian Model Selection

(Updated 9/2/2009, but still unfinished; see other’s work on this that I’ve collected)

I never took a statistics class, so I only know the kind of statistics you learn on the street. But now that I’m in global health research, I’ve been doing a lot of on-the-job learning. This post is about something I’ve been reading about recently, how to decide if a simple statistical model is sufficient or if the data demands a more complicated one. To keep the matter concrete (and controversial) I’ll focus on a claim from a recent paper in Nature that my colleague, Haidong Wang, choose for our IHME journal club last week: Advances in development reverse fertility declines. The title of this short letter boldly claims a causal link between total fertility rate (an instantaneous measure of how many babies a population is making) and the human development index (a composite measure of how “developed” a country is, on a scale of 0 to 1). Exhibit A in their case is the following figure:

An astute observer of this chart might ask, “what’s up with the scales on those axes?” But this post is not about the visual display of quantitative information. It is about deciding if the data has a piecewise linear relationship that Myrskyla et al claim, and doing it in a Bayesian framework with Python and PyMC. But let’s start with a figure where the axes have a familiar linear scale! Continue reading


Filed under MCMC, statistics