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CFA Forecast Tools (Python)
================
# CFA Forecast Tools (Python)


<!-- To learn more about using Quarto for
render a GitHub README, see
Expand Down Expand Up @@ -31,6 +31,10 @@ Install `forecasttools` via:

# Datasets

``` python
import forecasttools
```

`forecasttools` contains several datasets. These datasets aid with
experimentation or are directly necessary to some of `forecasttools`
utilities.
Expand All @@ -41,28 +45,35 @@ The location table contains abbreviations, codes, and extended names for
the US jurisdictions for which the FluSight and COVID forecasting hubs
require users to generate forecasts.

Shape: (58, 3)

| location_code | short_name | long_name |
|---------------|------------|-----------------------------|
| str | str | str |
| ————— | ———— | —————————– |
| US | US | United States |
| 1 | AL | Alabama |
| 2 | AK | Alaska |
| 4 | AZ | Arizona |
| 5 | AR | Arkansas |
| 6 | CA | California |
| 8 | CO | Colorado |
| 9 | CT | Connecticut |
| … | … | … |
| 56 | WY | Wyoming |
| 60 | AS | American Samoa |
| 66 | GU | Guam |
| 69 | MP | Northern Mariana Islands |
| 72 | PR | Puerto Rico |
| 74 | UM | U.S. Minor Outlying Islands |
| 78 | VI | U.S. Virgin Islands |
``` python
forecasttools.location_table
```

<div><style>
.dataframe > thead > tr,
.dataframe > tbody > tr {
text-align: right;
white-space: pre-wrap;
}
</style>
<small>shape: (58, 3)</small>

| location_code | short_name | long_name |
|---------------|------------|-------------------------------|
| str | str | str |
| "US" | "US" | "United States" |
| "01" | "AL" | "Alabama" |
| "02" | "AK" | "Alaska" |
| "04" | "AZ" | "Arizona" |
| "05" | "AR" | "Arkansas" |
| … | … | … |
| "66" | "GU" | "Guam" |
| "69" | "MP" | "Northern Mariana Islands" |
| "72" | "PR" | "Puerto Rico" |
| "74" | "UM" | "U.S. Minor Outlying Islands" |
| "78" | "VI" | "U.S. Virgin Islands" |

</div>

The location table is stored in `forecasttools` as a `polars` dataframe
and is accessed via:
Expand All @@ -86,31 +97,35 @@ make_census_dataset(
The example FluSight submission comes from the [following 2023-24
submission](https://raw.githubusercontent.com/cdcepi/FluSight-forecast-hub/main/model-output/cfa-flumech/2023-10-14-cfa-flumech.csv).

Shape: (4_876, 8)

| reference_date | target | horizon | target_end_date | location | output_type | output_type_id | value |
|----------------|------------|---------|-----------------|----------|-------------|----------------|------------|
| 2023-10-14 | wk inc flu | -1 | 2023-10-07 | 01 | quantile | 0.01 | 7.670286 |
| | hosp | | | | | | |
| 2023-10-14 | wk inc flu | -1 | 2023-10-07 | 01 | quantile | 0.025 | 9.968043 |
| | hosp | | | | | | |
| 2023-10-14 | wk inc flu | -1 | 2023-10-07 | 01 | quantile | 0.05 | 12.022354 |
| | hosp | | | | | | |
| 2023-10-14 | wk inc flu | -1 | 2023-10-07 | 01 | quantile | 0.1 | 14.497646 |
| | hosp | | | | | | |
| 2023-10-14 | wk inc flu | -1 | 2023-10-07 | 01 | quantile | 0.15 | 16.119813 |
| | hosp | | | | | | |
| 2023-10-14 | wk inc flu | -1 | 2023-10-07 | 01 | quantile | 0.2 | 17.670122 |
| | hosp | | | | | | |
| 2023-10-14 | wk inc flu | -1 | 2023-10-07 | 01 | quantile | 0.25 | 19.125462 |
| | hosp | | | | | | |
| 2023-10-14 | wk inc flu | -1 | 2023-10-07 | 01 | quantile | 0.3 | 20.443282 |
| | hosp | | | | | | |
| … | … | … | … | … | … | … | … |
| 2023-10-14 | wk inc flu | 2 | 2023-10-28 | US | quantile | 0.75 | 1995.98533 |
| | hosp | | | | | | 6 |
| 2023-10-14 | wk inc flu | 2 | 2023-10-28 | US | quantile | 0.99 | 4761.75738 |
| | hosp | | | | | | 5 |
``` python
forecasttools.example_flusight_submission
```

<div><style>
.dataframe > thead > tr,
.dataframe > tbody > tr {
text-align: right;
white-space: pre-wrap;
}
</style>
<small>shape: (4_876, 8)</small>

| reference_date | target | horizon | target_end_date | location | output_type | output_type_id | value |
|----|----|----|----|----|----|----|----|
| str | str | i64 | str | str | str | f64 | f64 |
| "2023-10-14" | "wk inc flu hosp" | -1 | "2023-10-07" | "01" | "quantile" | 0.01 | 7.670286 |
| "2023-10-14" | "wk inc flu hosp" | -1 | "2023-10-07" | "01" | "quantile" | 0.025 | 9.968043 |
| "2023-10-14" | "wk inc flu hosp" | -1 | "2023-10-07" | "01" | "quantile" | 0.05 | 12.022354 |
| "2023-10-14" | "wk inc flu hosp" | -1 | "2023-10-07" | "01" | "quantile" | 0.1 | 14.497646 |
| "2023-10-14" | "wk inc flu hosp" | -1 | "2023-10-07" | "01" | "quantile" | 0.15 | 16.119813 |
| … | … | … | … | … | … | … | … |
| "2023-10-14" | "wk inc flu hosp" | 2 | "2023-10-28" | "US" | "quantile" | 0.85 | 2451.874899 |
| "2023-10-14" | "wk inc flu hosp" | 2 | "2023-10-28" | "US" | "quantile" | 0.9 | 2806.928588 |
| "2023-10-14" | "wk inc flu hosp" | 2 | "2023-10-28" | "US" | "quantile" | 0.95 | 3383.74799 |
| "2023-10-14" | "wk inc flu hosp" | 2 | "2023-10-28" | "US" | "quantile" | 0.975 | 3940.392536 |
| "2023-10-14" | "wk inc flu hosp" | 2 | "2023-10-28" | "US" | "quantile" | 0.99 | 4761.757385 |

</div>

The example FluSight submission is stored in `forecasttools` as a
`polars` dataframe and is accessed via:
Expand Down Expand Up @@ -169,16 +184,42 @@ The fitting data is stored in `forecasttools` as a `polars` dataframe
and is accessed via:

``` python
import forecasttools


# access COVID data
covid_nhsn_data = forecasttools.nhsn_hosp_COVID

# access flu data
flu_nhsn_data = forecasttools.nhsn_hosp_flu

# display flu data
flu_nhsn_data
```

<div><style>
.dataframe > thead > tr,
.dataframe > tbody > tr {
text-align: right;
white-space: pre-wrap;
}
</style>
<small>shape: (81_713, 3)</small>

| state | date | hosp |
|-------|--------------|------|
| str | str | str |
| "AK" | "2020-03-23" | null |
| "AK" | "2020-03-24" | null |
| "AK" | "2020-03-25" | null |
| "AK" | "2020-03-26" | null |
| "AK" | "2020-03-27" | null |
| … | … | … |
| "WY" | "2024-04-23" | "1" |
| "WY" | "2024-04-24" | "1" |
| "WY" | "2024-04-25" | "0" |
| "WY" | "2024-04-26" | "0" |
| "WY" | "2024-04-27" | "0" |

</div>

The data was created by placing a csv file called
`NHSN_RAW_20240926.csv` (the full NHSN dataset) into `./forecasttools`
and running, in `data.py`, the following:
Expand Down Expand Up @@ -250,12 +291,8 @@ make_forecast(

The forecast looks like:

<figure>
<img src="./assets/example_forecast_w_dates.png" style="width:75.0%"
alt="Example NHSN-based Influenza forecast" />
<figcaption aria-hidden="true">Example NHSN-based Influenza
forecast</figcaption>
</figure>

------------------------------------------------------------------------

Expand All @@ -270,7 +307,9 @@ CDC use of GitHub does not imply an endorsement of any one particular
service, product, or enterprise.

<details>

<summary>

Rules, Policy, And Collaboration
</summary>

Expand All @@ -282,10 +321,14 @@ Rules, Policy, And Collaboration
- [Code of Conduct](./rules-and-policies/code-of-conduct.md)

</details>

<details>

<summary>

Public Domain Standard Notice
</summary>

This repository constitutes a work of the United States Government and
is not subject to domestic copyright protection under 17 USC § 105. This
repository is in the public domain within the United States, and
Expand All @@ -296,8 +339,11 @@ contributions to this repository will be released under the CC0
dedication. By submitting a pull request you are agreeing to comply with
this waiver of copyright interest.
</details>

<details>

<summary>

License Standard Notice
</summary>

Expand All @@ -320,18 +366,25 @@ http://www.apache.org/licenses/LICENSE-2.0.html
The source code forked from other open source projects will inherit its
license.
</details>

<details>

<summary>

Privacy Standard Notice
</summary>

This repository contains only non-sensitive, publicly available data and
information. All material and community participation is covered by the
[Disclaimer](DISCLAIMER.md) and [Code of Conduct](code-of-conduct.md).
For more information about CDC’s privacy policy, please visit
[http://www.cdc.gov/other/privacy.html](https://www.cdc.gov/other/privacy.html).
</details>

<details>

<summary>

Contributing Standard Notice
</summary>

Expand All @@ -349,19 +402,27 @@ through CDC including this GitHub page may be subject to applicable
federal law, including but not limited to the Federal Records Act, and
may be archived. Learn more at <http://www.cdc.gov/other/privacy.html>.
</details>

<details>

<summary>

Records Management Standard Notice
</summary>

This repository is not a source of government records, but is a copy to
increase collaboration and collaborative potential. All government
records will be published through the [CDC web
site](http://www.cdc.gov).
</details>

<details>

<summary>

Additional Standard Notices
</summary>

Please refer to [CDC’s Template
Repository](https://github.com/CDCgov/template) for more information
about [contributing to this
Expand Down

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