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Data submission instructions

This page is intended to provide teams with all the information they need to submit scenarios.

All scenarios should be submitted directly to the data-processed/ folder. Data in this directory should be added to the repository through a pull request.

Due to file size limitation, the file can be submitted in a .parquet or .gz.parquet.

The submission file format has been updated starting round 17 (April 2023). For information on previous file format please refer to past version of this README file.

Example

See this file for an illustration of part of a (hypothetical) submission file.

Subdirectory

Each subdirectory within the data-processed/ directory has the format

team-model

where

  • team is the teamname and
  • model is the name of your model.

Both team and model should be less than 15 characters, and not include hyphens nor spaces.

Within each subdirectory, there should be a metadata file, a license file (optional), and a set of scenarios.

Metadata

The metadata file name should have the following format

metadata-team-model.txt

where

  • team is the teamname, usually the name of the submitting institution.
  • model is the name of your model, used to distinguish between multiple models from a single institution.

The metadata file must follow the documented description. An example hypothetical metadata file has been posted in the data-processed directory.

License (optional)

License information for data sharing and reuse is requested in the metadata, including a link to the license text. If you cannot link to the text of a standard license and have specific license text, include a license file named

LICENSE.txt

Date/Epiweek information

For week-ahead scenarios, we will use the specification of epidemiological weeks (EWs) defined by the US CDC which run Sunday through Saturday.

There are standard software packages to convert from dates to epidemic weeks and vice versa. E.g. MMWRweek for R and pymmwr and epiweeks for python.

Model Results

Each model results file within the subdirectory should have the following name

YYYY-MM-DD-team-model.parquet

where

  • YYYY is the 4 digit year,
  • MM is the 2 digit month,
  • DD is the 2 digit day,
  • team is the teamname, and
  • model is the name of your model.

"parquet" files format from Apache is "is an open source, column-oriented data file format designed for efficient data storage and retrieval". Please find more information on the parquet.apache.com website.

The "arrow" library can be used to read/write the files in Python and R. Other tools are also accessible, for example parquet-tools

For example, in R:

# To write "parquet" file format:
filename <- ”path/data-processed/YYYY-MM-DD-team_model.parquet”
arrow::write_parquet(df, filename)
# with "gz compression"
filename <- ”path/data-processed/YYYY-MM-DD-team_model.gz.parquet”
arrow::write_parquet(df, filename, compression = "gzip", compression_level = 9)

# To read "parquet" file format:
arrow::read_parquet(filename)

The date YYYY-MM-DD should correspond to the start date for scenarios projection ("first date of simulated transmission/outcomes" as noted in the scenario description on the main README, Submission Information).

The team and model in this file must match the team and model in the directory this file is in. Both team and model should be less than 15 characters, alpha-numeric and underscores only, with no spaces or hyphens.

If the size of the file is larger than 100MB, it should be submitted in a .gz.parquet format. If the 100MB limit is not solved by compression the submission file can also be partitioned.

Partitioning

The submission files can be partitioned with the "arrow" library and should be partitioned by origin_date and target.

The basename template should match the previous standard ( "YYYY-MM-DD-team-model.parquet") with the a date and the aggregation of the team and model abbreviation name.

For example, in R:

team_folder <- ”path/data-processed/<team_model>/”

# Without compression
arrow::write_dataset(df, team_folder, partitioning = c("origin_date", "target"),
                     hive_style = FALSE,
                     basename_template = "YYYY-MM-DD-tteam_model{i}.parquet")

# With GZIP Compression
arrow::write_dataset(df, team_folder, partitioning = c("origin_date", "target"),
                     hive_style = FALSE, compression = "gzip", compression_level = 9,
                     basename_template = "YYYY-MM-DD-team_model{i}.gz.parquet")

For example, in Python:

import pyarrow.dataset as ds

team_folder <- ”path/data-processed/<team_model>/”


# Without compression
ds.write_dataset(table, team_folder, partitioning=["origin_date", "target"],
                 format="parquet", partitioning_flavor=None, 
                 basename_template="YYYY-MM-DD-team_model{i}.parquet")

# Compression options
fs = ds.ParquetFileFormat().make_write_options(compression='gzip', compression_level=9)
# With GZIP Compression
ds.write_dataset(table, team_folder, partitioning=["origin_date", "target"],
                 format="parquet", partitioning_flavor=None, file_options=fs,
                 basename_template="YYYY-MM-DD-team_model{i}.gz.parquet")

Please note that the hive_style or partitioning_flavor should be set to FALSE or None, so all the teams have the same output style.

The submission file columns used for the partitioning (origin_date and target) should not be present in the .parquet file.

Model results file format

The file must be a parquet file with the following columns (in any order):

The output file should contains multiple columns:

  • origin_date
  • scenario_id
  • target
  • horizon
  • location
  • age_group
  • output_type
  • output_type_id
  • run_grouping
  • stochastic_run
  • value

No additional columns are allowed.

Each row in the file is a specific type for a scenario for a location on a particular date for a particular target.

Column format

Column Name Accepted Format
origin_date character, date (datetime not accepted)
scenario_id character
target character
horizon numeric, integer
location character
age_group character
output_type character
output_type_id numeric, character, logical (if all NA)
value numeric
run_grouping numeric, integer
stochastic_run numeric, interger

origin_date

Values in the origin_date column must be a date in the format

YYYY-MM-DD

The origin_date is the start date for scenarios (first date of simulated transmission/outcomes). The "origin_date" and date in the filename should correspond.

scenario_id

The standard scenario id should be used as given in in the scenario description in the main Readme. Scenario IDs include a captitalized letter and date as YYYY-MM-DD, e.g., A-2020-12-22.

target

The submission can contain multiple output type information:

  • From 100 to 300 representative trajectories from the model simulations. We will call this format "sample" type output. For more information, please consult the sample section.
  • A set of quantiles with an optional "mean" value for all the tarquets. We will call this format "quantile" type output. For more information, please consult the quantile section.

The requested targets are (for "sample" type output):

  • weekly incident deaths
  • weekly incident hospitalizations

Optional target (for "quantile" type output):

  • cumulative deaths
  • cumulative incident hospitalizations
  • weekly incident deaths
  • weekly incident hospitalizations

Values in the target column must be one of the following character strings:

  • "inc death"
  • "inc hosp"
  • "cum death"
  • "cum hosp"

inc death

This target is the incident (weekly) number of deaths predicted by the model during the week that is N weeks after origin_date.

A week-ahead scenario should represent the total number of new deaths on the dates they occurred, not on the date they were reported (from Sunday through Saturday, inclusive).

Predictions for this target will be evaluated compared to the number of new deaths, as recorded by the National Center for Health Statistics (NCHS) as distributed by the COVIDcast Epidata API.

inc hosp

This target is the incident (weekly) number of hospitalized cases predicted by the model during the week that is N weeks after origin_date.

A week-ahead scenario should represent the total number of new hospitalized cases reported during a given epiweek (from Sunday through Saturday, inclusive).

Predictions for this target will be evaluated compared to the number of new hospitalized cases, as reported by the HHS and distributed by the COVIDcast Epidata API.

cum death

This target is the cumulative number of deaths predicted by the model during the week that is N weeks after origin_date (since start of the simulation).

A week-ahead scenario should represent the cumulative number of deaths reported on the Saturday of a given epiweek.

Predictions for this target will be evaluated compared to the cumulative of the number of new deaths, as recorded by the National Center for Health Statistics (NCHS) as distributed by the COVIDcast Epidata API.

cum hosp

This target is the cumulative number of incident (weekly) number of hospitalized cases predicted by the model during the week that is N weeks after origin_date (since start of the simulation).

A week-ahead scenario should represent the cumulative number of hospitalized cases reported on the Saturday of a given epiweek.

Predictions for this target will be evaluated compared to the cumulative of the number of new hospitalized cases, as reported by the HHS and distributed by the COVIDcast Epidata API.

horizon

Values in the horizon column must be an integer (N) between 1 and last week horizon value representing the associated target value during the N weeks after origin_date.

For example, between 1 and 104 for Round 17 ("Simulation end date: April 19, 2025 (104-week horizon)") and in the following example table, the first row represent the number of incident death in the US, for the 1st epiweek (epiweek ending on 2023-04-22)after 2023-04-16 for the scenario A-2023-04-16.

origin_date scenario_id location target horizon ...
2023-04-16 A-2023-04-16 US inc death 1 ...

location

Values in the location column must be one of the "locations" in this FIPS numeric code file which includes numeric FIPS codes for U.S. states, counties, territories, and districts as well as "US" for national scenarios.

Please note that when writing FIPS codes, they should be written in as a character string to preserve any leading zeroes.

output_type

Values in the output_type column are either

  • "sample" or
  • "quantile" (optional) or
  • "mean" (optional)

This value indicates whether that row corresponds to a "sample" scenario or a quantile scenario.

Scenarios must include "sample" scenario for every scenario-location-target-horizon(-age_group) group.

output_type_id

sample

For the simulation samples format only. Value in the output_type_id column is NA

The id sample number is input via two columns:

  • run_grouping: This column specifies any additional grouping if it controls for some factor driving the variance between trajectories (e.g., underlying parameters, baseline fit) that is shared across trajectories in different scenarios. I.e., if using this grouping will reduce overall variance compared to analyzing all trajectories as independent, this grouping should be recorded by giving all relevant rows the same number. If no such grouping exists, number each model run independently.
  • stochastic_run : a unique id to differentiate multiple stochastic runs. If no stochasticity: the column will contain an unique value

Both columns should only contain integer number.

The submission file is expected to have 100 simulation samples (or trajectories) for each "group".

For round 18, it is required to have the trajectories grouped at least by "age_group" and "horizon", so it is required that the combination of the run_grouping and stochastic_run columns contains at least an unique identifier for each group containing all the possible value for "age_group" and "horizon".

Fore more information and examples, please consult the Sample Format Documentation page.

For example:

origin_date scenario_id location target horizon age_group output_type output_type_id run_grouping stochastic_run value
2024-04-28 A-2024-03-01 US inc hosp 1 0-64 sample NA 1 1
2024-04-28 A-2024-03-01 US inc hosp 2 0-64 sample NA 1 1
2024-04-28 A-2024-03-01 US inc hosp 3 0-64 sample NA 1 1
2024-04-28 A-2024-03-01 US inc hosp 1 0-64 sample NA 2 1
2024-04-28 A-2024-03-01 US inc hosp 2 0-64 sample NA 2 1

quantile and mean

Values in the quantile column are quantiles in the format

0.###

For quantile scenarios, this value indicates the quantile for the value in this row.

Teams should provide the following 23 quantiles:

0.010 0.025 0.050 0.100 0.150 0.200 0.250 0.300 0.350 0.400 0.450 0.500
0.550 0.600 0.650 0.700 0.750, 0.800 0.850 0.900 0.950 0.975 0.990

An optional 0 and 1 value can also be provided.

An optional mean value can also be provided with mean as "type" value and NA as "type_id" value.

For example:

origin_date scenario_id location target horizon age_group output_type output_type_id run_grouping stochastic_run value
2024-04-28 A-2024-03-01 US inc death 1 0-64 quantile 0.010 NA NA
2024-04-28 A-2024-03-01 US inc death 1 0-64 quantile 0.025 NA NA
2024-04-28 A-2024-03-01 US inc death 1 0-64 mean NA NA NA

value

Values in the value column are non-negative numbers integer or with one decimal place indicating the "sample" or "quantile" prediction for this row.

For a "quantile" prediction, value is the inverse of the cumulative distribution function (CDF) for the target,horizon, location, and quantile associated with that row.

age_group

Accepted values in the age_group column are:

  • "0-64" (required)
  • "65-130" (required)
  • "0-130" (required)

Scenario validation

To ensure proper data formatting, pull requests for new data or updates in data-processed/ will be automatically validated.

Pull request scenario validation

When a pull request is submitted, the data are validated by running the scripts in validation.R. The intent for these tests are to validate the requirements above and all checks are specifically enumerated on the wiki. Please let us know if the wiki is inaccurate.

Workflow

When a pull request is submitted, the validation will be automatically triggered.

  • If the pull request (PR) contains update on metadata and/or abstract file(s):

    • These files are manually validated, the automatic validation will only returns a message indicating it did not run any validation.

  • If the PR contains model output submission file(s). The validation automatically runs and output a message:

    • The validation has 3 possible output:
      • "Error": the validation has failed and returned a message indicating the error(s). The error(s) should be fixed to have the PR accepted
      • "Warning": the PR can be accepted. However, it might be necessary for the submitting team to validate if the warning(s) is expected or not before merging the PR.
      • "Success": the validation did not found any issue and returns a message indicating that the validation is a success and the PR can be merged.

Run checks locally

To run these checks locally rather than waiting for the results from a pull request, follow these instructions (section File Checks Run Locally).