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ICB-DCM / PESTO

PESTO: Parameter EStimation TOolbox, Bioinformatics, btx676, 2017.
https://doi.org/10.1093/bioinformatics/btx676
BSD 3-Clause "New" or "Revised" License
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Undefined function or variable 'getParameterSamples'. #2

Closed dweindl closed 8 years ago

dweindl commented 8 years ago

When running the conversion reaction example runEstimation__CR

Undefined function or variable 'getParameterSamples'.

Error in runEstimation__CR (line 103)
parameters = getParameterSamples(parameters,logL,options_par);
FFroehlich commented 8 years ago

I think that function should actually exist. Must have been accidently deleted at some point. I will check if I can find it somewhere.

FFroehlich commented 8 years ago

Okay there is a getParameterSamples in the PESTO version in the CANPATHPRO folder but it contains a lot of unpublished methods developed by Benni, so not including it here might be intentional. Better check with @JanHasenauer .

dweindl commented 8 years ago

@JanHasenauer can you please add an appropriate version of the file when convenient?

paulstapor commented 8 years ago

Does anyone know if plotParameterUncertainty depends on getParamterSamples? I think it shouldn't necessarily, but in the CR example, it's in the sampling block (l.194f., below % Scatter plots). Can someone explain what it does exactly? The first plot seems to be exactly the profile likelihoods, the second seems to be the profile paths...

FFroehlich commented 8 years ago

no plotParameterUncertainty should not depend on getParamterSamples, but in the current implementation it might. plotParameterUncertainty can plot uncertainty from getMultiStarts (via hessian matrix returned from optimization), getParameterSamples and getParameterProfiles. Last time I checked, the checking whether a certain analysis was not done correctly.

dweindl commented 8 years ago

Added the missing file.