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Difference between revisions of "Initializing Disease Compartments"

 
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When a certain disease model should be used in scenario, the initial conditions for the isease have to be specified. The following components in STEM enable the user to do so. The Disease Initializer component provides the combined functionality of the Infector and Inoculator components. For initialization from an external file the External Data Source Disease Initializer must be used.
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For a certain disease model to be used in a scenario, the initial conditions for the disease have to be specified. Several components in STEM enable the user to do so. The Disease Initializer component provides the combined functionality of the Infector and Inoculator components. For initialization from an external file, the External Data Source Disease Initializer must be used.
  
 
== Infector ==
 
== Infector ==
 
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[[Image:InnoculatorWiz.png|right]]
In '''[http://wiki.eclipse.org/Creating_a_STEM_Scenario#Create_an_Infector Creating a STEM Scenario]''' it is shown how infectors are used.
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Infectors are a simple and intuitive tool that can be used to set ''initial conditions'' when you want to start a simulation with a specific number or percentage of people in the ''infectious state''.  Please see '''[http://wiki.eclipse.org/Creating_a_STEM_Scenario#Create_an_Infector Creating a STEM Scenario]''' to see a step-by-step example of how infectors can be used.  The infector, at simulation start, takes the specified number from the Susceptible state and moves them to the infectious state. You can configure an inoculator to set the initial condition for a specific regions, at node containing sub-regions (e.g., a state or country) or your entire graph.  The wizard for creating an infector is shown to the right. Infectors also allow you to initialize the disease state from an external file (or a previous set of run files). This is useful when you want to specify specific values for many individual locations (as opposed to the same percentage everywhere). Disease initializers (see below) provide an even more powerful way to specify the initial state for every compartment in one step.
  
 
== Inoculator ==
 
== Inoculator ==
  
There is currently no documentation about inoculators.
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Inoculators are very similar to infectors. They are used to set the initial condition or initial state of a population when you want to set the herd immunity at simulation start. They work by moving a specified number or percentage of people from Susceptible to Recovered. Like infectors, an inoculator can be configured to set the initial condition for a specific regions, at node containing sub-regions (e.g., a state or country) or your entire graph. The wizard for creating an inoculator is the same as the wizard for creating an infector (shown to the right).
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Inoculators also allow you to initialize the disease state from an external file (or a previous set of run files). This is useful when you want to specify specific values for many individual locations (as opposed to the same percentage everywhere). Inoculators also allow you to initialize the disease state from an external file (or a previous set of run files). This is useful when you want to specify specific values for many individual locations (as opposed to the same percentage everywhere).
  
 
== Disease Initializer ==
 
== Disease Initializer ==
  
To create an initializer for a specific disease, the user has to right click on the disease and select "Create new Initializer".
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Disease Initializers are a much more flexible and powerful way to set initial conditions. You can specify and set or target compartments to initialize so a Disease Initializer can play the role of Infector, Inoculator, and more. For example, you can set the initial number of Exposed people in an SEIR model. To create an initializer for a specific disease, you need to right click on the disease and select "Create new Initializer".
  
 
[[Image:StemCreateInitializer.png|500px]]
 
[[Image:StemCreateInitializer.png|500px]]
  
Since initializers also work for diseases with multiple populations, the population to initialize has to be selected. For the selected population the absolute number or percentage of individuals for all compartments can be specified. At last the user has to select a location for the initializer. If for example France is selected, any region in France is initialized with the chosen values. The new initializer will show up under the "Decorators" folder in the Project explorer. You can drag the population initializer right into a scenario.
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Since initializers can work for diseases with multiple populations, you need to select the population to initialize. For the selected population the absolute number or percentage of individuals for all compartments can be specified. At you need to select a location for the initializer. If for example France is selected, any region in France is initialized with the chosen values. The new initializer will show up under the "Decorators" folder in the Project explorer. You can drag the initializer right into a scenario.
  
 
[[Image:StemInitializer.png|450px]]
 
[[Image:StemInitializer.png|450px]]
  
 
== External Data Source Disease Initializer ==
 
== External Data Source Disease Initializer ==
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To create an initializer for a specific disease, you right click on the disease and select "Create new External Data Initializer".
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[[Image:StemCreateDataInitializer.png|350px]]
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Since initializers also work for diseases with multiple populations, you first select the population to be initialized. Next you enter the folder containing the log files for the disease you have specified and the population you've selected. Finally you must specify the number of the row to be used. The new initializer will show up under the "Decorators" folder in the Project explorer. You can drag the initializer right into a scenario.
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[[Image:StemDataInitializer.png|450px]]

Latest revision as of 15:32, 13 September 2012

For a certain disease model to be used in a scenario, the initial conditions for the disease have to be specified. Several components in STEM enable the user to do so. The Disease Initializer component provides the combined functionality of the Infector and Inoculator components. For initialization from an external file, the External Data Source Disease Initializer must be used.

Infector

InnoculatorWiz.png

Infectors are a simple and intuitive tool that can be used to set initial conditions when you want to start a simulation with a specific number or percentage of people in the infectious state. Please see Creating a STEM Scenario to see a step-by-step example of how infectors can be used. The infector, at simulation start, takes the specified number from the Susceptible state and moves them to the infectious state. You can configure an inoculator to set the initial condition for a specific regions, at node containing sub-regions (e.g., a state or country) or your entire graph. The wizard for creating an infector is shown to the right. Infectors also allow you to initialize the disease state from an external file (or a previous set of run files). This is useful when you want to specify specific values for many individual locations (as opposed to the same percentage everywhere). Disease initializers (see below) provide an even more powerful way to specify the initial state for every compartment in one step.

Inoculator

Inoculators are very similar to infectors. They are used to set the initial condition or initial state of a population when you want to set the herd immunity at simulation start. They work by moving a specified number or percentage of people from Susceptible to Recovered. Like infectors, an inoculator can be configured to set the initial condition for a specific regions, at node containing sub-regions (e.g., a state or country) or your entire graph. The wizard for creating an inoculator is the same as the wizard for creating an infector (shown to the right).

Inoculators also allow you to initialize the disease state from an external file (or a previous set of run files). This is useful when you want to specify specific values for many individual locations (as opposed to the same percentage everywhere). Inoculators also allow you to initialize the disease state from an external file (or a previous set of run files). This is useful when you want to specify specific values for many individual locations (as opposed to the same percentage everywhere).

Disease Initializer

Disease Initializers are a much more flexible and powerful way to set initial conditions. You can specify and set or target compartments to initialize so a Disease Initializer can play the role of Infector, Inoculator, and more. For example, you can set the initial number of Exposed people in an SEIR model. To create an initializer for a specific disease, you need to right click on the disease and select "Create new Initializer".

StemCreateInitializer.png

Since initializers can work for diseases with multiple populations, you need to select the population to initialize. For the selected population the absolute number or percentage of individuals for all compartments can be specified. At you need to select a location for the initializer. If for example France is selected, any region in France is initialized with the chosen values. The new initializer will show up under the "Decorators" folder in the Project explorer. You can drag the initializer right into a scenario.

StemInitializer.png

External Data Source Disease Initializer

To create an initializer for a specific disease, you right click on the disease and select "Create new External Data Initializer".

StemCreateDataInitializer.png

Since initializers also work for diseases with multiple populations, you first select the population to be initialized. Next you enter the folder containing the log files for the disease you have specified and the population you've selected. Finally you must specify the number of the row to be used. The new initializer will show up under the "Decorators" folder in the Project explorer. You can drag the initializer right into a scenario.

StemDataInitializer.png