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sys-bio / SBstoat

Parameter optimization using Tellurium
MIT License
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Improvements to plots of fitted values #7

Closed joseph-hellerstein closed 3 years ago

joseph-hellerstein commented 3 years ago
  1. Include prediction intervals using data collected from bootstrapping on the variance of fitted values.
  2. Plotting fitted values can be done with a user-specified number of points to get a smoother curve.
joseph-hellerstein commented 3 years ago

Feedback from Predici on Observed & Fitted curves that include mean and standard deviations of fitted values from bootstrap.

As an added feature, would it be possible to surround this third (optimum) curve with a shaded area, representing (in some sense) the "95% confidence interval" ? This would be a measure most medical doctors and biologists would readily understand, and the results could be easier to publish in more publications, even those less mathematically savy . Again, this is just a suggestion for the package to be, and maybe useful for a larger group, not a requirement.

joseph-hellerstein commented 3 years ago

What is being requested is a confidence interval around the fitted values. This can be done using a bootstrap approach in which residuals for the simulation for a set of parameters are used to estimate standard deviations. The desired output is a shaded region, not error bars.

joseph-hellerstein commented 3 years ago

Other possible plots can be seen in Chapter 11.6 of Herbert's Pathways Modeling Book.

Screen Shot 2020-10-21 at 8 36 51 AM
joseph-hellerstein commented 3 years ago

Implemented band plots to describe confidence regions for fitted values.