covid-19-impact-lab/sid issues and pull requests

#151 - Add immunization waning parameters to the covid epi params

Issue - State: open - Opened by roecla about 3 years ago

#150 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: open - Opened by pre-commit-ci[bot] about 3 years ago - 2 comments

#149 - First draft flexible waning immunity

Pull Request - State: closed - Opened by timmens about 3 years ago - 3 comments

#148 - Is sid prepared for reinfections?

Issue - State: open - Opened by roecla about 3 years ago
Labels: enhancement

#147 - Adjust `calculate_r_zero` to be able to handle non-binary immunity

Issue - State: open - Opened by roecla about 3 years ago
Labels: enhancement

#146 - Fix the deaths in the assortative matching notebook

Issue - State: open - Opened by roecla about 3 years ago
Labels: bug

#145 - Support that simulated moments do not have an empirical equivalent.

Pull Request - State: closed - Opened by roecla over 3 years ago - 2 comments

#144 - Update notebooks

Pull Request - State: closed - Opened by timmens over 3 years ago - 3 comments

#143 - New approach to immunization feature

Pull Request - State: closed - Opened by timmens over 3 years ago - 1 comment

#142 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 3 years ago - 1 comment

#141 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 3 years ago - 1 comment

#140 - Implement non-binary immunity

Pull Request - State: closed - Opened by timmens over 3 years ago - 2 comments

#139 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 3 years ago - 1 comment

#138 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 3 years ago - 1 comment

#137 - Add preprint and new citation.

Pull Request - State: closed - Opened by tobiasraabe over 3 years ago - 1 comment

#136 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 3 years ago - 1 comment

#135 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 3 years ago - 1 comment

#134 - Do not convert last states to dask DataFrame.

Pull Request - State: closed - Opened by roecla over 3 years ago - 1 comment

#133 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 3 years ago - 1 comment

#132 - Set start countdown value to -9999.

Pull Request - State: closed - Opened by roecla over 3 years ago - 1 comment

#131 - Move parsing of virus strain factors to simulation.

Pull Request - State: closed - Opened by tobiasraabe over 3 years ago - 1 comment

#130 - Remove the normalization of seasonality factors

Pull Request - State: closed - Opened by janosg over 3 years ago - 1 comment

#129 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 3 years ago - 1 comment

#128 - Ensure determinacy in the setup of a simulation.

Pull Request - State: closed - Opened by tobiasraabe over 3 years ago - 1 comment

#127 - Implement an empirically more founded version of time-variant sensitivity of rapid tests.

Pull Request - State: closed - Opened by roecla over 3 years ago - 1 comment

#126 - Enhance the plot for the channels of infections.

Pull Request - State: closed - Opened by tobiasraabe over 3 years ago - 1 comment

#125 - Fix bug in inferring which contact models caused which infection.

Pull Request - State: closed - Opened by tobiasraabe over 3 years ago - 1 comment

#124 - Update the release notes.

Pull Request - State: closed - Opened by tobiasraabe over 3 years ago

#123 - Allow for time dependent sensitivity of rapid tests.

Pull Request - State: closed - Opened by roecla over 3 years ago - 1 comment

#122 - Optionally calculate simulated moments every period to reduce memory

Pull Request - State: closed - Opened by janosg over 3 years ago - 1 comment

#121 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 3 years ago - 1 comment

#120 - Add matplotlib to dependencies.

Pull Request - State: closed - Opened by tobiasraabe over 3 years ago - 1 comment

#119 - Fix infection channel plot if called with prepared data.

Pull Request - State: closed - Opened by janosg over 3 years ago - 1 comment

#118 - Make plot for infections per contact model more performant.

Pull Request - State: closed - Opened by tobiasraabe over 3 years ago - 1 comment

#117 - Improve msm

Pull Request - State: closed - Opened by janosg over 3 years ago - 1 comment

#116 - Add plot for infections by contact models.

Pull Request - State: closed - Opened by tobiasraabe over 3 years ago - 1 comment

#115 - Make it possible to have different seasonalities for different contact types

Pull Request - State: closed - Opened by janosg over 3 years ago - 1 comment

#114 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 3 years ago - 1 comment

#113 - Visualize policies with Gantt chart.

Pull Request - State: closed - Opened by tobiasraabe over 3 years ago - 1 comment

#112 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 3 years ago - 1 comment

#111 - Replace versioneer with setuptools_scm.

Pull Request - State: closed - Opened by tobiasraabe over 3 years ago - 1 comment

#110 - Fix setting with copy warning in contacts.py.

Pull Request - State: closed - Opened by roecla over 3 years ago - 1 comment

#109 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 3 years ago - 1 comment

#108 - Improve dtype handling for random contacts.

Pull Request - State: closed - Opened by roecla over 3 years ago - 1 comment

#107 - Derived states

Pull Request - State: closed - Opened by janosg over 3 years ago - 1 comment

#106 - Allow policies to affect all contacts.

Pull Request - State: closed - Opened by tobiasraabe over 3 years ago - 1 comment

#105 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 3 years ago - 1 comment

#104 - Implement seasonality.

Pull Request - State: closed - Opened by tobiasraabe over 3 years ago - 1 comment

#103 - Fix leftovers from #99.

Pull Request - State: closed - Opened by tobiasraabe over 3 years ago - 1 comment

#102 - Separate contact calculation from policies.

Pull Request - State: closed - Opened by tobiasraabe over 3 years ago - 1 comment
Labels: ready-for-review

#101 - Remove `is_active` key for policies.

Pull Request - State: closed - Opened by tobiasraabe over 3 years ago - 1 comment
Labels: ready-for-review

#100 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 3 years ago - 1 comment

#99 - Fix bug in `factorize_assortative_variables` with single `assort_by` variables.

Pull Request - State: closed - Opened by tobiasraabe over 3 years ago - 1 comment
Labels: ready-for-review

#98 - Fix typo that passed the last review.

Pull Request - State: closed - Opened by roecla over 3 years ago - 1 comment

#97 - Improve coverage and tests.

Pull Request - State: closed - Opened by tobiasraabe over 3 years ago - 2 comments
Labels: ready-for-review

#96 - Change initialization of countdowns.

Pull Request - State: closed - Opened by tobiasraabe over 3 years ago - 1 comment

#95 - Enhance the documentation.

Pull Request - State: closed - Opened by tobiasraabe over 3 years ago - 1 comment

#94 - Reimplement vaccination models as a dictionary of models.

Pull Request - State: closed - Opened by tobiasraabe over 3 years ago - 2 comments

#93 - Enhance validation of model functions.

Pull Request - State: closed - Opened by tobiasraabe over 3 years ago - 2 comments

#92 - Add interface for rapid testing.

Pull Request - State: closed - Opened by tobiasraabe over 3 years ago - 1 comment

#91 - Add realistic vaccination countdowns.

Pull Request - State: closed - Opened by roecla over 3 years ago - 1 comment

#90 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 3 years ago - 1 comment

#89 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 3 years ago - 1 comment

#88 - Add vaccination models.

Pull Request - State: closed - Opened by tobiasraabe over 3 years ago - 2 comments

#87 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 3 years ago - 1 comment

#86 - Publish package under sid-dev.

Pull Request - State: closed - Opened by tobiasraabe over 3 years ago - 1 comment

#85 - Add seeds to events.

Pull Request - State: closed - Opened by tobiasraabe over 3 years ago - 1 comment

#84 - Clean up the matching algorithm.

Pull Request - State: closed - Opened by tobiasraabe over 3 years ago - 1 comment

#83 - Add multiple virus strains.

Pull Request - State: closed - Opened by tobiasraabe almost 4 years ago - 1 comment

#82 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] almost 4 years ago - 1 comment

#81 - Fix the default starting date of testing models.

Pull Request - State: closed - Opened by tobiasraabe almost 4 years ago - 1 comment

#80 - Fix the default starting date for testing models.

Issue - State: closed - Opened by tobiasraabe almost 4 years ago
Labels: bug

#79 - Implement multiplier for infection probabilities.

Pull Request - State: closed - Opened by tobiasraabe almost 4 years ago - 2 comments

#78 - Adjust test countdowns

Pull Request - State: closed - Opened by roecla almost 4 years ago - 2 comments

#77 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] almost 4 years ago - 1 comment

#76 - Remove share_known_cases which should be implemented via testing models.

Pull Request - State: closed - Opened by tobiasraabe almost 4 years ago - 1 comment

#75 - Pass sid's seed to testing models.

Pull Request - State: closed - Opened by tobiasraabe almost 4 years ago - 1 comment

#74 - Add seeds for testing models.

Issue - State: closed - Opened by tobiasraabe almost 4 years ago
Labels: enhancement

#73 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] almost 4 years ago - 1 comment

#72 - Add versioneer and PyPI packaging.

Pull Request - State: closed - Opened by tobiasraabe almost 4 years ago - 1 comment

#71 - Separate matching of recurrent and random contacts.

Pull Request - State: closed - Opened by tobiasraabe almost 4 years ago - 1 comment

#70 - Improve the factorization.

Pull Request - State: closed - Opened by tobiasraabe almost 4 years ago - 2 comments

#69 - Add models for vaccination.

Issue - State: closed - Opened by tobiasraabe almost 4 years ago - 1 comment

#68 - Allow for multiple virus strains.

Issue - State: closed - Opened by tobiasraabe almost 4 years ago

#67 - Skip factorization of assortative variables if indicated.

Pull Request - State: closed - Opened by tobiasraabe almost 4 years ago - 1 comment

#66 - Skip factorization of state variables if indicated.

Issue - State: closed - Opened by tobiasraabe almost 4 years ago
Labels: enhancement

#65 - Convert recurrent contact columns to bool.

Issue - State: closed - Opened by tobiasraabe almost 4 years ago - 1 comment
Labels: enhancement

#64 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] almost 4 years ago - 1 comment

#63 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] almost 4 years ago - 1 comment

#62 - Small fixes for estimation of christmas models

Pull Request - State: closed - Opened by janosg almost 4 years ago - 1 comment

#61 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] almost 4 years ago - 1 comment

#60 - More tests and better documentation.

Pull Request - State: closed - Opened by tobiasraabe almost 4 years ago - 1 comment

#59 - Remove optional_state_columns.

Pull Request - State: closed - Opened by tobiasraabe almost 4 years ago - 1 comment

#58 - Add simplified way to account for unknown cases.

Pull Request - State: closed - Opened by tobiasraabe almost 4 years ago - 1 comment

#57 - Skip missing group

Pull Request - State: closed - Opened by janosg almost 4 years ago - 1 comment

#54 - Redesign optional_state_columns.

Issue - State: closed - Opened by tobiasraabe almost 4 years ago
Labels: enhancement

#53 - Add license and citation.

Pull Request - State: closed - Opened by tobiasraabe almost 4 years ago - 1 comment

#52 - Release v0.0.1.

Pull Request - State: closed - Opened by tobiasraabe about 4 years ago - 1 comment

#44 - Implement a msm interface for parallel evaluations.

Pull Request - State: closed - Opened by tobiasraabe about 4 years ago - 1 comment

#39 - Improve the MSM functionality

Issue - State: closed - Opened by janosg about 4 years ago - 3 comments
Labels: enhancement

GitHub / covid-19-impact-lab/sid issues and pull requests