Simulated day-of-week effect #90
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zsusswein
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Nov 29, 2024
The current timeseries doesn't have a day of week effect, which makes it hard to test how the day of week effect implementation is performing. This modifies the simulated timeseries to add a large-ish day of week reporting effect. In implementing this change, I converted the timeseries over to using a `data-raw` script for reproducibility. I moved the original Gostic "Practical considerations" dataset into an RDS object in `data-raw`. This change makes the dataset tracked and available for re-generation of the package dataset, but doesn't expose it to or ship it with the package. It's not 100% reproducible because I don't implement the git clone of the "Practical considerations" repo, but I think it gets us a fair but further than before. I also clean up the package-provided `stochastic_sir_rt` datset. I rename the `obs_incidence` col to `obs_cases`, add a `obs_cases_no_dow` for testing, and rename `date` to `reference_date` in anticipation of a future `report_date`. Closes #90
zsusswein
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Dec 2, 2024
The current timeseries doesn't have a day of week effect, which makes it hard to test how the day of week effect implementation is performing. This modifies the simulated timeseries to add a large-ish day of week reporting effect. In implementing this change, I converted the timeseries over to using a `data-raw` script for reproducibility. I moved the original Gostic "Practical considerations" dataset into an RDS object in `data-raw`. This change makes the dataset tracked and available for re-generation of the package dataset, but doesn't expose it to or ship it with the package. It's not 100% reproducible because I don't implement the git clone of the "Practical considerations" repo, but I think it gets us a fair but further than before. I also clean up the package-provided `stochastic_sir_rt` datset. I rename the `obs_incidence` col to `obs_cases`, add a `obs_cases_no_dow` for testing, and rename `date` to `reference_date` in anticipation of a future `report_date`. Closes #90
zsusswein
added a commit
that referenced
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Dec 2, 2024
The current timeseries doesn't have a day of week effect, which makes it hard to test how the day of week effect implementation is performing. This modifies the simulated timeseries to add a large-ish day of week reporting effect. In implementing this change, I converted the timeseries over to using a `data-raw` script for reproducibility. I moved the original Gostic "Practical considerations" dataset into an RDS object in `data-raw`. This change makes the dataset tracked and available for re-generation of the package dataset, but doesn't expose it to or ship it with the package. It's not 100% reproducible because I don't implement the git clone of the "Practical considerations" repo, but I think it gets us a fair but further than before. I also clean up the package-provided `stochastic_sir_rt` datset. I rename the `obs_incidence` col to `obs_cases`, add a `obs_cases_no_dow` for testing, and rename `date` to `reference_date` in anticipation of a future `report_date`. Closes #90
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Add a simulated day of week effect to the simulated data timeseries.
I'm pushing handling a full data simulator to #42.
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