Archive

Archive for January, 2011

Using PEST to Calibrate Models

January 14th, 2011 21 comments

There are times when it is helpful to calibrate, or fit, your model to historical data. This capability is not built into the iThink/STELLA program, but it is possible to interface to external programs to accomplish this task. One generally available program to calibrate models is PEST, available freely from www.pesthomepage.org. In this blog post, I will demonstrate how to calibrate a simple STELLA model using PEST on Windows. Note that this method relies on the Windows command line interface added in version 9.1.2 and will not work on the Macintosh. The export to comma-separated value (CSV) file feature, added in version 9.1.2, is also used.

The model and all files associated with its calibration are available by clicking here.

The Model

The model being used is the simple SIR model first presented in my blog post Limits to Growth. The model is shown again below. There are two parameters: infection rate and recovery rate. Technically, the initial value for the Susceptible stock is also a parameter. However, since this is a conserved system, we can make an excellent guess as to its value and do not need to calibrate it.

image

The Data Set

We will calibrate this model to two data sets. The first is the number of weekly deaths caused by the Hong Kong flu in New York City over the winter of 1968-1969 (below).

clip_image004

The second is the number of weekly deaths per thousand people in the UK due to the Spanish flu (H1N1) in the winter of 1918-1919 (shown later).

In both cases, I am using the number of deaths as a proxy for the number of people infected, which we do not know. This is reasonable because the number of deaths is directly proportional to the number of infected individuals. If we knew the constant of proportionality, we could multiply the deaths by this constant to get the number of people infected.

Read more…