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README.Rmd

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@@ -145,13 +145,13 @@ Below the fold, we pull the dataset from the epidata API and clean it.
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<summary> Creating the dataset using `{epidatr}` and `{epiprocess}` </summary>
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This section is intended to demonstrate some of the ubiquitous cleaning operations needed to be able to forecast.
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A subset of this dataset prepared here is also included ready-to-go in [`{epipredict}`](https://cmu-delphi.github.io/epipredict/) as `covid_case_death_rates`.
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A subset of the dataset prepared here is also included ready-to-go in [`{epipredict}`](https://cmu-delphi.github.io/epipredict/) as `covid_case_death_rates`.
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First we pull both `jhu-csse` cases and deaths data from the
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[Delphi API](https://cmu-delphi.github.io/delphi-epidata/api/covidcast.html) using the
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[`{epidatr}`](https://cmu-delphi.github.io/epidatr/) package:
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```{r case_death, warning = FALSE, eval = FALSE}
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```{r case_death, warning = FALSE, eval = TRUE}
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cases <- pub_covidcast(
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source = "jhu-csse",
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signals = "confirmed_7dav_incidence_prop",
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four_week_ahead
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```
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In our model setup, we are defining as our predictors case rate lagged 0-3
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In our model setup, we are defining as predictors case rate lagged 0-3
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days, one week, and two weeks, and death rate lagged 0-2 weeks.
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The result `four_week_ahead` is both a fitted model object which could be used
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any time in the future to create different forecasts, and a set of predicted
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accurate, with the true data being at least within the 10-90% interval.
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A couple of things to note:
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1. Our methods are primarily direct forecasters; this means we don't need to
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predict 1, 2,..., 27 days ahead to then predict 28 days ahead
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1. `epipredict` methods are primarily direct forecasters; this means we don't need to
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predict 1, 2,..., 27 days ahead to then predict 28 days ahead.
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2. All of our existing engines are geo-pooled, meaning the training data is
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shared across geographies. This has the advantage of increasing the amount of
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available training data, with the restriction that the data needs to be on

README.md

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@@ -86,7 +86,7 @@ Creating the dataset using `{epidatr}` and `{epiprocess}`
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</summary>
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This section is intended to demonstrate some of the ubiquitous cleaning
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operations needed to be able to forecast. A subset of this dataset
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operations needed to be able to forecast. A subset of the dataset
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prepared here is also included ready-to-go in
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[`{epipredict}`](https://cmu-delphi.github.io/epipredict/) as
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`covid_case_death_rates`.
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four_week_ahead
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#> ══ A basic forecaster of type ARX Forecaster ════════════════════════════════
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#>
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#> This forecaster was fit on 2025-03-03 14:43:07.
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#> This forecaster was fit on 2025-03-04 12:12:54.
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#>
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#> Training data was an <epi_df> with:
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#> • Geography: state,
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#>
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```
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In our model setup, we are defining as our predictors case rate lagged
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0-3 days, one week, and two weeks, and death rate lagged 0-2 weeks. The
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In our model setup, we are defining as predictors case rate lagged 0-3
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days, one week, and two weeks, and death rate lagged 0-2 weeks. The
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result `four_week_ahead` is both a fitted model object which could be
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used any time in the future to create different forecasts, and a set of
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predicted values (and prediction intervals) for each location 28 days
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#> # A tibble: 20 × 5
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#> geo_value values quantile_levels forecast_date target_date
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#> <chr> <dbl> <dbl> <date> <date>
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#> 1 ca 0.0425 0.1 2021-08-01 2021-08-29
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#> 2 ca 0.0803 0.25 2021-08-01 2021-08-29
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#> 3 ca 0.115 0.5 2021-08-01 2021-08-29
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#> 4 ca 0.150 0.75 2021-08-01 2021-08-29
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#> 5 ca 0.187 0.9 2021-08-01 2021-08-29
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#> 6 ma 0 0.1 2021-08-01 2021-08-29
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#> 1 ca 0.199 0.1 2021-08-01 2021-08-29
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#> 2 ca 0.285 0.25 2021-08-01 2021-08-29
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#> 3 ca 0.345 0.5 2021-08-01 2021-08-29
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#> 4 ca 0.405 0.75 2021-08-01 2021-08-29
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#> 5 ca 0.491 0.9 2021-08-01 2021-08-29
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#> 6 ma 0.0285 0.1 2021-08-01 2021-08-29
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#> # ℹ 14 more rows
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```
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relatively accurate, with the true data being at least within the 10-90%
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interval. A couple of things to note:
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1. Our methods are primarily direct forecasters; this means we don’t
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need to predict 1, 2,…, 27 days ahead to then predict 28 days ahead
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1. `epipredict` methods are primarily direct forecasters; this means we
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don’t need to predict 1, 2,…, 27 days ahead to then predict 28 days
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ahead.
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2. All of our existing engines are geo-pooled, meaning the training
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data is shared across geographies. This has the advantage of
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increasing the amount of available training data, with the

man/figures/README-date-1.png

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