Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Calib continued #830

Merged
merged 38 commits into from
Dec 20, 2024
Merged

Calib continued #830

merged 38 commits into from
Dec 20, 2024

Conversation

cliffckerr
Copy link
Contributor

Description

Checklist

  • Code commented & docstrings added
  • New tests were needed and have been added
  • A new version number was needed & changelog has been updated
  • A new PyPI version needs to be released

@daniel-klein
WIP - allowing for replicates within build_sim towards better likelih…
d9aba7f 
…ood functions.
@daniel-klein
Multi reps are running with beta binomial
a66e180
@daniel-klein
Separated plotting. Feels like we need a class for each likelihood form.
30c71e7
@daniel-klein
Scipy likelihoods (!), fixed gamma-poisson, better plotting
cb12cf1
@daniel-klein
Creating separate components for likelihood forms. Improved robustnes…
28dc752 
…s. GammaPoisson still WIP. eval_kwargs is now eval_kw.
@daniel-klein
Fixing syntax.
3c0f725
@daniel-klein
Working on the GammaPoisson likelihood component, still a WIP.
895e149
@daniel-klein
Finally fixed GammaPoisson!
ceab532 
Also added all optuna visualizations, which requires scikit-learn, (torch), and plotly so may remove later.
@daniel-klein
Addressing Bug in identifying parent for units #800
5c6e081
@daniel-klein
Merge branch 'fix-time-parent' into calib-continued
5a73384
@daniel-klein
WIP on Dirichlet Multinomial component
e9d1758
@daniel-klein
Dirichlet-Multinomial component seems to be working!
49747c5
@daniel-klein
Adding a Normal (Gaussian) likelihood component. This serves as a "su…
107b26f 
…m of squared error" component as well with various normalizations made possible through specification of sigma2.
@daniel-klein
* Moving CalibComponents into calib_components.py.
f08300f 
* Improved tests
* Fixed a few bugs
@daniel-klein
Improved tests and plotting
8800cd5
@daniel-klein
* Added a test of a custom likelihood function.
737db11 
* Improved plotting, but still needs work
* Removed unneeded translate_pars
@daniel-klein
Better handling of builders that return a sim when an msim was ex…
f37d66e 
…pected, primarily for checking and plotting.
@daniel-klein
Addressing #820 and improving warning message
b86a096
@daniel-klein
Addressing #821
deb6dfb
@daniel-klein
Addressing #822, relabeling the infected state to Infected.
9d7dad8
@daniel-klein
Fixing #821 changes baselines!
16c1f35
@daniel-klein
* Adding "include_fn" to selectively include simulations in a component.
6e01637 
* Also adjusting how labels are carried through to component plots.
@daniel-klein
Small improvement to check_fit, now with optional plotting and reload…
8836142 
…ing of best_pars
@daniel-klein
Improved plotting
b08f1be
@daniel-klein
Fixing bug caught by tests. The Normal component test is still failin…
8131be5 
…g due to _s2, need a clever solution.
@daniel-klein
Adding a random sleep to mitigate database collisions. Improving plot…
2d5254a 
…ting for Normal.
@daniel-klein
Removing unnecessary sleep. Instead increasing mysql `max_connections…
5deb511 
…` does the trick!
@daniel-klein
* Checking datatype for Gamma Poisson
c593f98 
* GammaPoisson: Combining expected and actual in case of multiple simulations per rand_seed. Need to do the same for other components.
@daniel-klein
Adding "step_containing" conform method
2486954
@daniel-klein
Fixing Dirichlet-Multinomial plotting
5502387
@daniel-klein
* Fixing Dirichlet-Multinomial plotting
40e131b 
* merging expected and actual in case user has multiple levels of each expected value, for example if running "control" and "intervention" arms and want to use both prior to the start of the intervention.
@daniel-klein
Trying optional bootstrap
3050369
@daniel-klein
New bootstrap plots and database loading improvements.
53bf00c
@daniel-klein
* Adding Binomial
6df38dd 
* Removing boot_size option, len(seeds) is technically superior
@daniel-klein
Allowing Binomial to be specified by x and n instead of p, which aids…
f685423 
… in bootstrap aggregation
@daniel-klein
Cleaning
d3f26de
@daniel-klein
Incorporating feedback from @pausz, WIP.
d8c9acd
@daniel-klein
Merge branch 'calib-continued-bootstrap' into calib-continued-bootstr…
4e9029e 
…ap-merge
@cliffckerr cliffckerr merged commit 4e9029e into rc2.3 Dec 20, 2024
0 of 5 checks passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@cliffckerr @daniel-klein