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Posts Tagged ‘h1n1’

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.

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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).

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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.

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Limits to Growth

December 3rd, 2009 5 comments

This is the first of a three-part series on the Limits to Growth Archetype.  The second part can be accessed here and the third part here.

The Limits to Growth Systems Archetype, also known as Limits to Success, combines growth with an exogenous or endogenous limit.  This Systems Archetype was formally identified in Appendix 2 of The Fifth Discipline by Peter Senge (1990), but made its first prominent appearance in World Dynamics by Jay Forrester (1971) and then The Limits to Growth by Meadows, Meadows, Randers, and Behrens (1972).  The Causal Loop Diagram (CLD) is shown below.

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Real growth processes have inherent limits to growth.  Identifying these limits can help avoid problems in the future, whether the problem is overpopulation, increasing demand for a product that cannot be met, or growing a business in a mature market.  When growth is desired, but limited, it is always better to find ways to increase the limit before pushing for more growth.  Excessive growth in the face of a limit often leads to collapse.  Driving the system to the point of collapse can erode the ability to continue after the collapse, for example, by reducing the production capability of a piece of farmland or destroying the reputation of a company.

Classic examples of limits to growth include:

  • The collapse of the deer population on the Kaibab plateau and on St. Matthew Island due to overpopulation and the attendant overgrazing of their habitat
  • The overshoot and collapse of the human population on Easter Island
  • Overgrazing in the Sahel region of Africa by cattle herders
  • Overfishing of the oceans by fishermen
  • The collapse of People Express due to sharp customer growth combined with slow personnel growth
  • The sharp exodus of America Online subscribers after an intense marketing campaign increased the number of subscribers far beyond their capacity
  • The contraction of the world economy in 2008 due to limiting oil supplies
  • The productivity of staff deteriorating as a company grows, due to increased interactions and reporting overhead
  • Business growth limited by the size of the potential market
  • Yeast cells in the fermentation process, who suffer from both the loss of exogenously supplied sugar and the increase of endogenously produced pollution

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Incorporating STELLA into STEM Education

November 18th, 2009 2 comments

MODSIM 2009Jeremy and I recently attended the MODSIM 2009 Conference in Virginia Beach where we facilitated a pre-conference workshop with the help of Mark Clemente, a local high school science teacher.

We’ve been working with Mark over the past year to incorporate dynamic modeling and computer-based simulation into the STEM curriculum at Ocean Lakes High School in Virginia Beach.  Ocean Lakes is serving as a demonstration school for a broader initiative in Virginia to use Modeling and Simulation (MODSIM) as an engine for 21st Century workforce development.

One of our goals for the pre-conference workshop was to provide participants with STELLA models and lessons that they could use immediately in their classrooms.  To attain this we put together a packet of sample lessons that would cover the spectrum of STEM education courses—Science, Technology, Engineering and Mathematics.

Science: Exploring an H1N1 flu outbreak model

Educators at all levels have found that physical activities or games can often be a good way to introduce students to STELLA models. Activities can be a lot of fun and provide a physical model for kids to make the connection with the more abstract computer-based simulation.

In our workshop, we decided to introduce a STELLA model of the H1N1 flu outbreak by first engaging the class in a simple exercise that demonstrates the spread of infectious disease using cups of water.  Each student was given a cup of water and a pipette.  One cup of water however, was contaminated with sodium hydroxide.   We then began the process of walking around and dropping a pipette filled with liquid from our own cup into the cups of fellow students.  At the end of several rounds, Mark (our teacher) put a drop of phenolphthalein solution into everyone’s cup.  If the liquid turned pink, we were infected.

With a new understanding of how quickly infection can spread, the class was ready to be introduced to a STELLA model of the H1N1 flu outbreak.  The core structure of the model is based on the same model that epidemiologists use to track a population through the various stages of infection including Susceptible, Exposed, Infected and Recovered (SEIR).

The simulation provided several controls for students to experiment with different policy options for controlling the spread of the virus.   Along with the model, we provided a sample lesson with a set of questions to help guide students through their exploration.  To download the H1N1 model and sample lesson, click here.

Technology: Inquiry-based learning with STELLA simulations

It was fascinating to watch how each student in our workshop experimented differently with the model and began asking their own set of questions.  STELLA simulations and computer technology provide the perfect platform for students to learn using an inquiry-based approach.  Rather than being told how something works, students can discover for themselves by exploring “what-if” scenarios and finding out what happens. For teachers, this can mean shifting from a traditional teacher role to that of a facilitator or coach, guiding students in their inquiry without knowing in advance the path they’ll choose.

Engineering/Physics: The Pendulum Story

pendulumAnother STELLA model that we introduced to workshop participants was one that Mark and I modified for the Physics Flexbook project earlier this year.  The original version was developed by Diana Fisher in her book Lessons in Mathematics: A Dynamic Approach. The model provides a practice field for learning how the variables of simple harmonic motion are related.  Controls in the simulation allow you to explore what effect, if any, string length, initial displacement, and pendulum ball mass have on the amplitude, period, and frequency of the pendulum’s motion.  To download the pendulum model and sample lesson, click here.

Mathematics: Algebra Word Problems

You may remember from your own experience in math class that word problems typically give students a lot of trouble!  It is especially difficult to understand what is important in the problem and how to translate words into mathematical equations.  STELLA can help by allowing students to create a visual representation of the problem and making it easier to understand the symbolic representation.

For the workshop, we used the following word problem as an example of a typical Algebra I assignment:

Imagine your class is going to try to raise $400 by making school T-shirts. There is a $150 set-up charge for the T-shirt design that you have designed. Once the design is set, it costs $4 for each T-shirt. You feel it is possible to charge $10 for each T-shirt. How many T-shirts do you have to sell before you break even, i.e., make enough money to cover your costs?

Together we created a STELLA model that provided a visual representation of the word problem and gave everyone some hands-on experience building models from scratch.  It also inspired some participants to think about ways they could expand or change the model to answer additional questions that weren’t part of their immediate assignment. 

Tshirt

To download the T-shirt model and lesson, click here.

We’d love to expand our library of STELLA lessons and models so that we can share them with teachers.  If you’ve got any ideas of things you’d like to try in your classroom, please feel free to contact us – we’re here to help!

Modeling H1N1 Flu Outbreak

November 13th, 2009 3 comments

H1N1 Virus It seems like everyone has been talking about H1N1 (swine flu) the last couple of months.  If you have children in school, then you are probably very aware of how fast the virus is spreading.  Schools are the perfect environment for a virus to spread.  To help understand why, we created a STELLA model of a high school that introduces the H1N1 virus.  You can experiment with vaccination and “stay at home” policies to limit the spread of the flu.

The STELLA model is based on the SEIR compartmental model that epidemiologists use to model the progress of an epidemic.  SEIR models divide the population into compartments: Susceptible, Exposed, Infected and Recovered.  These ‘compartments’ translate nicely into stocks within the STELLA model where we can observe the dynamics of the spreading virus.

While developing the model we decided to explore some strategies that schools are pursuing to limit the virus’ spread.  We wanted to know if the “stay at home” (when you are sick) policy would be effective in the case where vaccines are not available quickly enough, (which as of November 2009 is the case).

Take a look:

Click the ‘Simulate’ link on the home screen above and try some different scenarios.  Be sure to click the ‘How does this simulation work?’ link for a guided tour of the model behind the simulation.

As you experiment with the simulation, consider the following:

  • How does varying “% vaccinated” effect the number of sick students?
  • How many days do infected students need to stay home to have a significant impact on the spread of the virus within the school?
  • What impact does the “% effectiveness of vaccine” have on the flu outbreak?
  • What combination of decisions results in the lowest number of sick students?  Are these decisions realistic in a real-world setting?

Note: Each time you dial in parameters and press run, a new plot will be added to the graph so you can compare the effectiveness of the different decisions.  Clicking on the blue reset button will clear the graph and reset all Knobs to their default value.

If you think this simple model is useful, feel free to share it or embed it on your own website; just click the sharing icon in the lower right corner.  If you want to dig deeper into the STELLA model you can download the model by clicking here.  You can open the model with STELLA 9.1, or the free isee Player.