June 11, 2020

1684 words 8 mins read



Projections of COVID-19, in standardized format

repo name reichlab/covid19-forecast-hub
repo link https://github.com/reichlab/covid19-forecast-hub
language JavaScript
size (curr.) 1076159 kB
stars (curr.) 200
created 2020-04-09
license Other

COVID-19 Forecast Hub

The goal of this repository is to create a standardized set of data on forecasts from teams making projections of cumulative and incident deaths and incident hospitalizations due to COVID-19 in the United States. This repository is the data source for the official CDC COVID-19 Forecasting page. This project to collect, standardize, visualize and synthesize forecast data has been led by the CDC-funded UMass-Amherst Influenza Forecasting Center of Excellence based at the Reich Lab, with contributions from many others.

This README provides an overview of the project. Additional specific links can be found in the list below:

Data license and reuse

We are grateful to the teams who have generated these forecasts. They have spent a huge amount of time and effort in a short amount of time to operationalize these important real-time forecasts. The groups have graciously and courageously made their public data available under different terms and licenses. You will find the licenses (when provided) within the model-specific folders in the data-processed directory. Please consult these licenses before using these data to ensure that you follow the terms under which these data were released.

All source code that is specific to this project, along with our d3-foresight visualization tool is available under an open-source MIT license. We note that this license does NOT cover model code from the various teams (maybe available from them under other licenses) or model forecast data (available under specified licenses as described above).

What forecasts we are tracking, and for which locations

Different groups are making forecasts at different times, and for different geographic scales. The specifications below were created by consulting with collaborators at CDC and looking at what models forecasting teams were already building.

What do we consider to be “gold standard” death data? We will use the daily reports containing death data from the JHU CSSE group as the gold standard reference data for deaths in the US. These data are the time-series version of the JHU data that do occasionally contain “revisions” of previous daily reports. Note that there are not insignificant differences (especially in daily incident death data) between the JHU data and another commonly used source, from the New York Times. The team at UTexas-Austin is tracking this issue on a separate GitHub repository.

When will forecast data be updated? We will be storing any new forecasts from each group as they are either provided to us directly (by pull request) or available for download online. We will attempt to make every version of each team’s forecasts available in “processed” form in the GitHub repo. Teams are encouraged to submit data as often has they have it available, although we only support one upload for each day. In general, “updates” to forecasts will not be permitted. Teams are responsible for checking that their forecasts are ready for public viewing upon submission. This can be done locally using our interactive visualization tool.

What locations will have forecasts? Currently, forecasts may be submitted for any state in the US and the US at the national level. At a future date, we may expand to include smaller geographic scales within the US and/or other international locations.

How will probabilistic forecasts be represented? Forecasts will be represented in a standard format using quantile-based representations of predictive distributions. We encourage all groups to make available the following 23 quantiles for each distribution: c(0.01, 0.025, seq(0.05, 0.95, by = 0.05), 0.975, 0.99). One goal of this effort is to create probabilistic ensemble forecasts, and having high-resolution component distributions will provide data to create better ensembles.

What forecast targets will be stored? We will store forecasts on 0 through 130 day-ahead incident and cumulative deaths, 1 through 20 week-ahead incident and cumulative deaths, and 0 through 130 day-ahead incident hospitalizations. The targets should be labeled in files as, e.g., "1 day ahead inc death", "1 day ahead cum death", "1 wk ahead inc death", "1 wk ahead cum death", or "1 wk ahead inc hosp". Please refer to the technical README for details on aligning targets with forecast dates.

Ensemble model

Every Monday at 6pm ET, we will update our COVID Forecast Hub ensemble forecast and interactive visualization using the most recent forecast from each team as long as it was submitted before 6pm ET on Monday and has a forecast_date of Sunday or Monday. All models meeting the above criteria will be considered for the ensemble. For inclusion in the ensemble, we additionally require that forecasts include a full set of 23 quantiles to be submitted (see technical README for details), and that the 10th quantile of the predictive distribution for a 1 week ahead forecast is not below the most recently observed data. Additionally, we perform manual visual inspection checks to ensure that forecasts are in alignment with the ground truth data. Details on which models were included each week in the ensemble are available in the ensemble metadata folder.

Depending on how the project evolves, we may add additional weekly builds for the ensemble and visualization. Currently, our ensemble is created by taking the arithmetic average of each quantile for all models that submit 1- through 4-week ahead cumulative death targets for a given location. Ensemble methods and inclusion criteria may evolve as more data becomes available.

Data model

Most groups are providing their forecasts in a quantile-based format. We have developed a general data model that can be used to represent all of the forecasts that have been made publicly available. The tabular version of the data model is a simple, long-form data format, with six required columns and several optional columns.

  • forecast_date: the date on which the submitted forecast data was made available in YYYY-MM-DD format. In general, this will typically be the date on which the model finishes running and produces the standard formatted file. forecast_date should correspond and be redundant with the date in the filename, but is included here by request from some analysts. We will enforce that the forecast_date for a file must be either the date on which the file was submitted to the repository or the previous day. Exceptions will be made for legitimate extenuating circumstances.
  • target: a unique id for the target
  • target_end_date: the date corresponding to the end time of the target, in YYYY-MM-DD format. E.g. if the target is "1 wk ahead inc hosp" and this forecast is submitted on Monday 2020-04-20, then this field should correspond to the Saturday that ends the current week 2020-04-25. See details about date formatting in the technical README.
  • location: a unique id for the location (we have standardized to FIPS codes, see details in the technical README.)
  • location_name: (optional) if desired to have a human-readable name for the location, this column may be specified. Note that the location column will be considered to be authoritative and for programmatic reading and importing of data, this column will be ignored.
  • type: one of either "point" or "quantile".
  • quantile: a value between 0 and 1 (inclusive), stating which quantile is displayed in this row. if type=="point" then NA.
  • value: a numeric value representing the value of the quantile function evaluated at the probability specified in quantile

For example, if quantile is 0.3 and value is 10, then this row is saying that the 30th percentile of the distribution is 10. If type is "point" and value is 15, then this row is saying that the point estimate from this model is 15.

Forecast file format

All forecast data should be submitted to a team’s subfolder in the data-processed directory. All files must follow the format outlined above. Teams can use this file as an example or template to follow.

Each file must have a specific naming scheme that represents when the forecast was made and what model made the forecast. Files will follow the following name scheme: YYYY-MM-DD-[team]-[model].csv. Where YYYY-MM-DD is the forecast_date as defined above. Teams are welcome to submit up to one file a day to be stored in the repository.

Teams and models

So far, we have identified a number of groups that are creating forecasts of COVID-19-related deaths in the US and globally. Our list of groups whose forecasts are currently standardized and in the repository are (with data reuse license):

Participating teams must provide a metadata file (see example), including methodological detail about their approach and a link to a file (or a file itself) describing the methods used.

The COVID Forecast Hub Team

Carefully curating these datasets into a standard format has taken a Herculean team effort. The following lists those who have helped out, in reverse alphabetical order:

  • Nutcha Wattanachit (ensemble model, data processing)
  • Nicholas Reich (project lead, ensemble model, data processing)
  • Evan Ray (ensemble model)
  • Jarad Niemi (data processing and organization)
  • Khoa Le (validation, automation)
  • Katie House (visualization, validation, project management)
  • Matt Cornell (validation, Zoltar integration)
  • Andrea Brennen (metadata curation)
  • Johannes Bracher (evaluation, data processing)
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