sbionlinfit Grouping Experimental Data Replicates For Parameter Fitting

I'm trying to fit parameters with data that contains multiple data points per time point (replicates) using the PK-PD model and the sbionlinfit function. However, I'm having issues understanding exactly what fields I need to specify within the PKData object to specify which columns of data in the dataset object are replicates. There are fields called GroupID, GroupLabel, and GroupNames. What do I need to specify in order to get a fit with replicates?

Also, the documentation mentions that the data points are not averaged, but are fitted individually. Am I correct in assuming that this will not mean I will get 3 individual parameter fits for my 3 replicate sets?

Answer 1

[Ingrid Tigges]

Are you using the SimBiology Desktop? Do you want to get one set of parameters for all replicates?

For each replicate set the value of the grouping variable to another integer value. In case you want the same model parameters for all conditions, check that the pooled option is set to true in the fitting task. You can find this option under Tasks=> Parameter Fit => Algorithm Settings. You can find screenshots illustrating these two points here: http://www.mathworks.co.uk/support/solutions/en/data/1-LZ6PSB/index.html

At the bottom of the page you can also find a link to a .pdf which explains fitting of parameters using the SimBiology Desktop in detail.

With respect to your question about individual fits, you get individual fits if you have unticked the option pooled fitting mentioned above. I hope this helps. If not, please let me know what is unclear for you.

[Timothy Shih]

I prefer doing it through code. Is there a way to do so? Yes, I would want to get one set of parameters for all replicates.

[Ingrid Tigges]

Yes, there is. Have had a look at this page of the documentation http://www.mathworks.com/help/releases/R2013a/simbio/ug/fitting-pharmacokinetic-model-parameters.html? Those information described under "Performing Individual Fitting" are also valid if you have replicates. If this does not help you might also want to consider contacting the technical support (refer to this thread then).