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PEtab-dev / libpetab-python

Python package for working with PEtab files
https://libpetab-python.readthedocs.io
MIT License
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add: plotting STD if the column noiseParameter has values and no replicates available #3

Open erikadudki opened 5 years ago

erikadudki commented 5 years ago

e.g. the Chen model has specified noiseParameters in the measurement data, and no replicate measurement data is available. (so, standard deviation cant be calculated from replicates) For plotting the standard deviation if no measurement replicates are available, and the column noiseParameters has values, plot these values as standard deviation.

paulstapor commented 4 years ago

That has to some degree already been implemented in PEtab-dev/PEtab#120 . If you want the standard deviation from the measurement file to be plotted, you can specify "provided" in the visualization sheet, and it will take the values from the measurement table, if they are numeric.

If the standard deviation is parametric, however, things are a bit more complicated: Technically, the standard deviation is an assignment rule, which one would have to read out from the SBML file. In 95% of the cases, this assignment rule is just the parameter value. Those cases one could cover with just using the parameter value. However, the assignment rule cases are more or less beyond direct reach, I'm afraid...