Clear Filters
Clear Filters

How to randomly sample output times in Simbiology?

5 views (last 30 days)
In the Simbiology Model Analyzer, 1) how to specify output time point of each run of the model as a random number from a normal distribution? E.g. a random number from a mean of 15min and SD 2min. 2) How to incorporate the output time as one input variable in global sensitivity analysis (Sobol index)? Thank you very much!

Answers (2)

Sulaymon Eshkabilov
Sulaymon Eshkabilov on 10 Feb 2024
To randomly generate values using MEAN and STD values, normrnd() fcn can be used:
MEAN_val = 15; % Mean in minutes
STD_dev = 2; % Standard deviation in minutes
Random_Number = normrnd(MEAN_val, STD_dev, 10, 1);
fprintf('Random number generated: %f \n', Random_Number);
Random number generated: 16.088707 Random number generated: 15.394483 Random number generated: 13.774981 Random number generated: 12.427133 Random number generated: 16.101281 Random number generated: 14.156724 Random number generated: 14.321607 Random number generated: 14.717372 Random number generated: 13.227484 Random number generated: 13.669566

Jeremy Huard
Jeremy Huard on 15 Feb 2024
Edited: Jeremy Huard on 15 Feb 2024
Hi @Wang,
Since your ultimate goal is to run a GSA on the model output, I would recommend the following:
  1. Create parameter outTimeScalar in your model with the relevant unit
  2. Create a parameter that converts the simulation time (which can be different for every simulation program) into the same unit as the parameter outTimeScalar. This can be achieved with a repeated assignment: timeInUnitOfInterest = time
  3. Create an observable that will call an external function that you will implement in the next step, for example: out = getOutput(timeInUnitOfInterest, speciesOfinterest, outTimeScalar)
  4. Create the external function that gives you the output at this specific time:
function out = getOutput(time, speciesOfinterest, outTime)
if all(time==0)
out = speciesOfinterest(end);
[time,idx] = unique(time,'last');
speciesOfinterest = speciesOfinterest(idx);
outTime = outTime(1);
out = interp1(time, speciesOfinterest, outTime,'pchip');
Please note that for this to provide meaningful results, you will need to make sure that timeInUnitOfInterest(1) < outTimeScalar < timeInUnitOfInterest(end).
Now, you can use Sobol GSA or MPGSA with outTimeScalar as an input that is sampled from a normal distribution.
I hope this helps.
Best regards,
Edit: Corrected function.


More Answers in the  SimBiology Community


Find more on Extend Modeling Environment in Help Center and File Exchange




Community Treasure Hunt

Find the treasures in MATLAB Central and discover how the community can help you!

Start Hunting!