SimBiology

Follow

When the number of groups are so high, using plot with sbiopredictionci object, it plots all the groups left to righ in a single column, is it possible to change this output?. Thanks

I don't know if I accidentally changed some plotting configuration, but in the past weeks I have been having an issue with the subplots generated by sbiopredictionci. I can edit the data normally in the subplots and I can delete subplots as I wish, but for some reason I can't move the subplots around in the Figure window. It's like they have been fixed in place somehow. Is this configurable? Thanks!

Hello everyone, I am trying to plot the results of the confidence intervals for the model predictions. Since I have 17 ResponseNames, my figure is overloaded with images (see attached picture). How do I separate the various plots from the figure? I am using this function: sbioparameterci ciPredPooled = sbiopredictionci(pooledFit); plot(ciPredPooled); Thank you in advance for your help. Best regards, Valentina

Hello team, I was trying to comput the prediction confident interval for my parameter estimation results. I first used sbioparameterci to check with my estimated parameters. The estimattions are not perfect, but all of the status for my estimated parameters were either estimatable or constrained. Thus, I further use sbiopredictionci to get the prediction confident interval. By excuting the following code for defults setting, I was able to get prediction CI, but the results were not ideal. ciPred = sbiopredictionci(fitWeightFunction); Thus, I tried to use bootstrap method with following code to see if I could get better results. ciPred = sbiopredictionci(fitWeightFunction, 'Alpha', 0.1, 'Type', 'bootstrap', 'NumSamples', 1000, 'UseParallel', true,'Display','final') However, the ciPred I got is an empty output '0x0 PredictionConfidenceInterval' Please find the OptimResults of my fitWeightFunction data in the attachment file. Thank you very much. Best, Jesse

Hello team, I asked a question yesterday considering using the sbiopredictionci. (plz find in the following link) https://fr.mathworks.com/matlabcentral/answers/1830703-sbiopredictionci-return-empty-result I am kind of resolve the probelm but not completely. After applying the code for passing user defined function to the parellel computing and rerun the code as below. addAttachedFiles(gcp,"calculate_P_A2B_factor.m") ciPred = sbiopredictionci(fitWeightFunction, 'Alpha', 0.1, 'Type', 'bootstrap', 'NumSamples', 1000, 'UseParallel', true,'Display','final') I got another warning, and the code ran forever nonstop. (warning and code shown as below) ciPred = sbiopredictionci(fitWeightFunction, 'Alpha', 0.1, 'Type', 'bootstrap', 'NumSamples', 3, 'UseParallel', true,'Display','final'); Warning: Observation data contains NaN. This may cause the computation of 'bootstrap' confidence intervals to error. > In SimBiology.fit/LeastSquaresResults/validateDataForBootstrapping (line 2685) In SimBiology.fit/LeastSquaresResults/validatePredictionCIInput (line 2633) In SimBiology.fit/LeastSquaresResults/predictionci (line 1052) In sbiopredictionci (line 68) Computing 90% bootstrap prediction confidence intervals ------------------------------------------------------- Warning: You have passed PARTICLESWARM options to LSQNONLIN. LSQNONLIN will use the common options and ignore the PARTICLESWARM options that do not apply. To avoid this warning, convert the PARTICLESWARM options using OPTIMOPTIONS. > In optim.options/SolverOptions/convertForSolver (line 777) In SimBiology.fit.internal.validateOptions>convertOptionsForMethod (line 167) In SimBiology.fit.internal.validateOptions (line 15) In SimBiology.fit.internal/FitObject/initializeReRun (line 376) In SimBiology.fit.internal/FitObject/rerunFit (line 314) In SimBiology.fit.LeastSquaresResults.createBootFun/getBootstrapSample (line 1806) In SimBiology.fit.LeastSquaresResults>@(x)getBootstrapSample(x,numGroups,groupIdx,groupSize,resampleWeights,refIdx,obj.Data,obj.Weights,obj.ConfidenceIntervalData.EstimInfo,restartData,obj.Beta.Estimate,exitFlag,fcn) (line 1764) In bootci (line 146) In SimBiology.fit/LeastSquaresResults/predCIBootstrap (line 1576) In SimBiology.fit.LeastSquaresResults>@(obj)predCIBootstrap(obj,alpha,numSamples,useParallel) (line 1060) In SimBiology.fit/LeastSquaresResults/dispatchConfidenceIntervalComputation (line 1880) In SimBiology.fit/LeastSquaresResults/predictionci (line 1068) In sbiopredictionci (line 68) Warning: You have passed PARTICLESWARM options to LSQNONLIN. LSQNONLIN will use the common options and ignore the PARTICLESWARM options that do not apply. To avoid this warning, convert the PARTICLESWARM options using OPTIMOPTIONS. > In optim.options/SolverOptions/convertForSolver (line 777) In SimBiology.fit.internal.validateOptions>convertOptionsForMethod (line 167) In SimBiology.fit.internal.validateOptions (line 15) In SimBiology.fit.internal/FitObject/initializeReRun (line 376) In SimBiology.fit.internal/FitObject/rerunFit (line 314) In SimBiology.fit.LeastSquaresResults.createBootFun/getBootstrapSample (line 1806) In SimBiology.fit.LeastSquaresResults>@(x)getBootstrapSample(x,numGroups,groupIdx,groupSize,resampleWeights,refIdx,obj.Data,obj.Weights,obj.ConfidenceIntervalData.EstimInfo,restartData,obj.Beta.Estimate,exitFlag,fcn) (line 1764) In bootstrp (line 178) In bootci>bootper (line 207) In bootci (line 167) In SimBiology.fit/LeastSquaresResults/predCIBootstrap (line 1576) In SimBiology.fit.LeastSquaresResults>@(obj)predCIBootstrap(obj,alpha,numSamples,useParallel) (line 1060) In SimBiology.fit/LeastSquaresResults/dispatchConfidenceIntervalComputation (line 1880) In SimBiology.fit/LeastSquaresResults/predictionci (line 1068) In sbiopredictionci (line 68) From the warning, I suspect that it is the observation data contains NaN which caused the problem. Is there anyway to resolve it? In addition to that, I also found that the bootci() function has more options could be accessed such as define different bootfun or types of confident interval. Is there anyway I couid change the settign for the sbiopredictionci ? Thank you in advance. Best, Jesse

Hello team, I am currently working with simbiology. After using sbiofit for fitting the experimental data (pooled), I would like to further calculate the confidence interval with sbiopredictionci. fit_result = sbiofit(...) preci = sbiopredictionci(fit_result) plot(preci) I have successfully calculated the confidence interval, as shown in the photo below. Since I am working with pooled fitting, I am thinking about combining all group data into one figure with only one confident interval plotted with the experimental data points. And also, since I have multiple compartments (14) that were fitted, I would like to reorganize them into my ideal subplot layout (4*4). Is there any way to do it? If I have any misunderstanding, please also correct me. Thank you very much. Best, Jesse