Implement mass-metallicity relations #58
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This commit implements most of the functionality developed in the test notebook. Tomorrow need to write tests for `fg_mzr!` and start on fitting function.
This should be moved into the model interface when we update the AMR models.
Want to support unsorted `logAge` arguments in `fg_mzr!`, will require some alterations.
Also adds `logdensity_and_gradient` definition that takes care of variable transformations, with optional Jacobian corrections.
`fittable_params` to retrieve the values of the fittable parameters out of models.
Not sure I want these to live here forever but can always move them later.
Implements random sampling and some other StatsBase methods
Contains MLE and MAP result from BFGS optimization. Also hoist transformation out of `_rand!` calls and into `exptransform_samples!` in hierarchical_models.jl to enable reuse of this code for HMC samples.
Warmup steps were fairly unsuccessful, so just check convergence after running and warn if poor.
Moved docs on hierarchical models from fitting/ to fitting/hierarchical to reflect structure in source code directory. Added `try/catch` block in `fit_sfh` to deal with inverse Hessian approximations in MLE results that are not positive definite. Added `calculate_coeffs` method to return types `BFGSResult` and `CompositeBFGSResult` with tests. Added docstring for `fit_sfh` in generic `fitting/hierarchical/hierarchical_models.jl` where it will probably be moved eventually.
Reduces runtime by 25%
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #58 +/- ##
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- Coverage 88.60% 70.12% -18.49%
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Files 18 25 +7
Lines 1536 2122 +586
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+ Hits 1361 1488 +127
- Misses 175 634 +459 ☔ View full report in Codecov by Sentry. |
Still triggers `Test.detect_unbound_args` because of the `Vararg` but don't care right now.
New `tups_to_mat` function results in unbound type parameters because of `Vararg`, trying to fix. See [Aqua.jl #316](JuliaTesting/Aqua.jl#316) and [#86](JuliaTesting/Aqua.jl#86).
Seems to be passing Aqua checks now.
All tests passing, including Aqua
Update SFH fitting section
Having `N` in the method signature forces specialization, which recompiles for every different `N`, blows up compilation time for large `N` but is fine when using repeatedly with same, small `N`. Going to try removing specialization; tests indicate it does not really hurt performance.
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This PR implements mass-metallicity relations (MZRs) as an alternative to previously implemented age-metallicity relations (AMRs). In order to simplify implementation of these models, the hierarchical fitting API was overhauled so that
fit_sfhis now the recommended entry point for hierarchical fitting andsample_sfhis the entry point for HMC sampling for hierarchical fitting.calculate_coeffsreplacescalculate_coeffs_mdf.Most of the old functions that are superceded by this new API still exist in this PR, but should issue deprecation warnings. These should eventually be removed in the 1.0 release.
Also fixes #51 and #52.