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Stochastic Epidemiology Models with Applications to the COVID-19

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Stochastic simulation of SEIR model

POSTED BY: Robert Nachbar
11 Replies

To run the notebook for this post in version 12.0 of Mathematica make the following changes:

1) Replace the first input

<<CompartmentalModeling`

with

Get@CloudObject["https://www.wolframcloud.com/obj/rnachbar/Published/CompartmentalModeling.wl"]

2) Replace all instances of stochasticSolve with StochasticSolve

3) Don't evaluate the input in the section "Simulation loop"

POSTED BY: Robert Nachbar

Thank you for your help.

POSTED BY: Moustafa Salama

The stochastic simulation is not running properly because it's trying to use the CreateDataStructure function which is not in version 12.0.

Let me see what it takes to run the notebook in version 12.0, and then send you either a short list of changes, or a new notebook. I might not be able to get to this until Wednesday, however.

POSTED BY: Robert Nachbar

also in comparison plotting the charts of stochastic are empty

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POSTED BY: Moustafa Salama
POSTED BY: Moustafa Salama

Try using the StochatsticSolve function in my package

CloudObject["https://www.wolframcloud.com/obj/rnachbar/Published/CompartmentalModeling.wl"]

instead of stochasticSolve used in the Community post notebook. Use the option Compiled -> True (the default), and it should use the fixed-length memory version of the Gillespie algorithm.

POSTED BY: Robert Nachbar

First I 'd like to thank you for you kind reply. Really I have version 12. How can I fix the problem in version 12 ?

POSTED BY: Moustafa Salama

What version of Mathematica are you using?

Version 12.1 or newer is required to use the new built-in data structures that are used by the stochastic simulation code (for example, CreateDataStructure).

POSTED BY: Robert Nachbar

Please I have the following error while evaluating you notebook

In[369]:= SeedRandom[1425367]
solnsCME = 
   Table[stochasticSolve[modelData["Rates"] /. paramsN, 
     modelData["StoichiometricMatrix"], 
     Through@modelData["Variables"][0] /. Rule @@@ inits /. paramsN, 
     modelData["Variables"], {t, 0, tmax}], 500]; // Timing

During evaluation of In[369]:= Set::shape: Lists {times$25658,states$25658} and Transpose[CreateDataStructure[DynamicArray]] are not the same shape.

During evaluation of In[369]:= $RecursionLimit::reclim2: Recursion depth of 1024 exceeded during evaluation of Transpose[states$25658].

During evaluation of In[369]:= $RecursionLimit::reclim2: Recursion depth of 1024 exceeded during evaluation of Transpose[states$25658].

During evaluation of In[369]:= Set::shape: Lists {times$25667,states$25667} and Transpose[CreateDataStructure[DynamicArray]] are not the same shape.

During evaluation of In[369]:= $RecursionLimit::reclim2: Recursion depth of 1024 exceeded during evaluation of Transpose[states$25667].

During evaluation of In[369]:= General::stop: Further output of $RecursionLimit::reclim2 will be suppressed during this calculation.

During evaluation of In[369]:= Set::shape: Lists {times$25682,states$25682} and Transpose[CreateDataStructure[DynamicArray]] are not the same shape.

During evaluation of In[369]:= General::stop: Further output of Set::shape will be suppressed during this calculation.

Out[370]= {78.5, Null}
POSTED BY: Moustafa Salama

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