snlls: allow extrapenalty to take linear parameters as input
#175
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luisfabib
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stestoll
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May 10, 2021
luisfabib
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* deploy_ghpages.yml: add missing dependency (#161) * Bump VERSION to v0.14.0-dev (#162) * bump VERSION to 0.14.0-dev * add Python 3.9 to conda build * Removed Ctot from second order term in chemicalequalibrium polynomial (#163) * Fix prescaling of data and vanishing confidence intervals in `snlls` (#166) * parse_multidatasets: fix bug in parsing so that prescaling works also for single signals * tests: fix snlls test * fitregmodel: adapt to changes in parse_multidatasets * tests: refactor test as relative assertion * Update README.md (#167) * deerload: Fix bug when loading BES3T files with entries in manipulation history layer (#164) * deerload: fix bug when loading BES3T files with entries in manipulation history layer * add unit tests for deerload * deerload: fix error in parsing of XGF files * rename test data files consistently * fix tests Co-authored-by: Stefan Stoll <stestoll@users.noreply.github.com> * Fix behavior of weights in global fitting (#171) * fitregmodel: fix behaviour of weights in global fitting * fitparamodel: add test for global weights behaviour * lsqcomponents: fix usage of global weights * fitmultimodel: fix behaviour of weights in global fitting * fitmultimodel: return list of fitted signals instead of single array, fix scaling of output fit signals and UQ, fix plotting * fitmultimodel: fix scaling issue in global fitting * snlls: fix behaviour of weights in global fitting * fitmodel: add tests to check behaviour of weights in global fitting * fitmultimodel: fix error when plotting single dataset fits * fitmultimodel: fix bug in plottin of single dataset fits * fitmultimodel: fix error in previous commit * fitmodel: Fix uncertainty quantification when fitting dipolar evolution functions (#172) * fitmodel: fix errors in uncertainty quantification for dipolar evolution functions * modify tests that missed the error * fitmodel: fixed error found by tests * fitparamodel: fix scale of output fit.model and its uncertainty (#173) * snlls: allow `extrapenalty` to take linear parameters as input (#175) * snlls: allow `extrapenalty` to take linear parameters as input * snlls: fix order of concatenation of Jacobians * Optimize default weights in global fitting according to the datasets noise levels (#174) * optimize default weights in global fitting according to the datasets noise levels * add tests * fix bug in calculation of default weights for arbitrary scales * refactor DER_SNR method, add reference Co-authored-by: Stefan Stoll <stestoll@users.noreply.github.com> * VERSION: bump to v0.13.1 * CHANGELOG: update for v0.13.1 * CHANGELOG: minor edits * fix GHA to run on a PR to merge into any branch * fix GHA to run docs CI on PR to merge into any branch Co-authored-by: Maxx Tessmer <mhtessmer@gmail.com> Co-authored-by: Stefan Stoll <stestoll@users.noreply.github.com>
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The optional argument
extrapenaltyallows the specification of custom penalties to be added to the residual vector insnlls. However, at the moment it only takes nonlinear parameters as an input. This PR enhances the functionality to allow also to define penalties depending on the linear parameters.The new syntax takes two positional arguments for the penalty function:
It also fixes an error in the documentation of
snllswhereextrapenaltyargument is listed ascustom_penalty.