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add samples examples hub
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@annakrystalli
annakrystalli committed May 17, 2024
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14 changes: 14 additions & 0 deletions inst/testhubs/samples/hub-config/admin.json
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{
"schema_version": "https://raw.githubusercontent.com/Infectious-Disease-Modeling-Hubs/schemas/main/v3.0.0/admin-schema.json",
"name": "US CDC FluSight",
"maintainer": "US CDC",
"contact": {
"name": "Rebecca Borchering",
"email": "[email protected]"
},
"repository_host": "GitHub",
"repository_url": "https://github.com/cdcepi/FluSight-forecast-hub",
"file_format": ["csv"],
"timezone": "US/Eastern",
"model_output_dir": "model-output"
}
134 changes: 134 additions & 0 deletions inst/testhubs/samples/hub-config/model-metadata-schema.json
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{
"$schema": "https://json-schema.org/draft/2020-12/schema",
"title": "Schema for Modeling Hub model metadata",
"description": "This is the schema for model metadata files, please refer to https://github.com/Infectious-Disease-Modeling-Hubs/example-complex-forecast-hub/blob/main/model-metadata/README.md for more information.",
"type": "object",
"properties": {
"team_name": {
"description": "The name of the team submitting the model",
"type": "string"
},
"team_abbr": {
"description": "Abbreviated name of the team submitting the model",
"type": "string",
"pattern": "^[a-zA-Z0-9_+]+$",
"maxLength": 16
},
"model_name": {
"description": "The name of the model",
"type": "string"
},
"model_abbr": {
"description": "Abbreviated name of the model",
"type": "string",
"pattern": "^[a-zA-Z0-9_+]+$",
"maxLength": 16
},
"model_version": {
"description": "Identifier of the version of the model",
"type": "string"
},
"model_contributors": {
"type": "array",
"items": {
"type": "object",
"properties": {
"name": {
"type": "string"
},
"affiliation": {
"type": "string"
},
"email": {
"type": "string",
"format": "email"
},
"orcid": {
"type": "string",
"pattern": "^\\d{4}\\-\\d{4}\\-\\d{4}\\-[\\dX]{4}$"
}
},
"additionalProperties": false,
"required": ["name", "affiliation"]
}
},
"website_url": {
"description": "Public facing website for the model",
"type": "string",
"format": "uri"
},
"repo_url": {
"description": "Repository containing code for the model",
"type": "string",
"format": "uri"
},
"license": {
"description": "License for use of model output data",
"type": "string",
"enum": [
"CC0-1.0",
"CC-BY-4.0",
"CC-BY_SA-4.0",
"CC-BY-NC-SA-4.0",
"PPDL",
"ODC-by",
"ODbL",
"OGL-3.0"
]
},
"designated_model": {
"description": "Team-specified indicator for whether the model should be eligible for inclusion in a Hub ensemble and public visualization. A team may designate up to two models.",
"type": "boolean"
},
"citation": {
"description": "One or more citations for this model",
"type": "string",
"examples": ["Gibson GC , Reich NG , Sheldon D. Real-time mechanistic bayesian forecasts of Covid-19 mortality. medRxiv. 2020. https://doi.org/10.1101/2020.12.22.20248736"]
},
"team_funding": {
"description": "Any information about funding source for the team or members of the team.",
"type": "string",
"examples": ["National Institutes of General Medical Sciences (R01GM123456). The content is solely the responsibility of the authors and does not necessarily represent the official views of NIGMS."]
},
"data_inputs": {
"description": "List or description of data inputs used by the model",
"type": "string"
},
"methods": {
"description": "A brief (200 char.) description of the methods used by this model",
"type": "string",
"maxLength": 200
},
"methods_long": {
"description": "A full description of the methods used by this model. Among other details, this should include whether spatial correlation is considered and how the model accounts for uncertainty.",
"type": "string"
},
"ensemble_of_models": {
"description": "Indicator for whether this model is an ensemble of any separate component models",
"type": "boolean"
},
"ensemble_of_hub_models": {
"description": "Indicator for whether this model is an ensemble specifically of other models submitted to this Hub",
"type": "boolean"
},
"source_notes": {
"description": "Original source of the model output data",
"type": "string"
}
},
"additionalProperties": false,
"required": [
"team_name",
"team_abbr",
"model_name",
"model_abbr",
"model_contributors",
"license",
"designated_model",
"data_inputs",
"methods",
"methods_long",
"ensemble_of_models",
"ensemble_of_hub_models"
]
}
209 changes: 209 additions & 0 deletions inst/testhubs/samples/hub-config/tasks.json
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{
"schema_version": "https://raw.githubusercontent.com/Infectious-Disease-Modeling-Hubs/schemas/main/v3.0.0/tasks-schema.json",
"rounds": [
{
"round_id_from_variable": true,
"round_id": "reference_date",
"model_tasks": [
{
"task_ids": {
"reference_date": {
"required": null,
"optional": [
"2022-10-22", "2022-10-29", "2022-11-05",
"2022-11-12", "2022-11-19", "2022-11-26",
"2022-12-03", "2022-12-10", "2022-12-17",
"2022-12-24", "2022-12-31", "2023-01-07",
"2023-01-14", "2023-01-21", "2023-01-28",
"2023-02-04", "2023-02-11", "2023-02-18",
"2023-02-25", "2023-03-04", "2023-03-11",
"2023-03-18", "2023-03-25", "2023-04-01",
"2023-04-08", "2023-04-15", "2023-04-22",
"2023-04-29", "2023-05-06", "2023-05-13",
"2023-05-20", "2023-05-27"
]
},
"target": {
"required": null,
"optional": ["wk flu hosp rate category"]
},
"horizon": {
"required": null,
"optional": [0, 1, 2, 3]
},
"location": {
"required": null,
"optional": [
"US",
"01",
"02",
"04",
"05"
]
},
"target_end_date": {
"required": null,
"optional": [
"2022-10-22", "2022-10-29", "2022-11-05",
"2022-11-12", "2022-11-19", "2022-11-26",
"2022-12-03", "2022-12-10", "2022-12-17",
"2022-12-24", "2022-12-31", "2023-01-07",
"2023-01-14", "2023-01-21", "2023-01-28",
"2023-02-04", "2023-02-11", "2023-02-18",
"2023-02-25", "2023-03-04", "2023-03-11",
"2023-03-18", "2023-03-25", "2023-04-01",
"2023-04-08", "2023-04-15", "2023-04-22",
"2023-04-29", "2023-05-06", "2023-05-13",
"2023-05-20", "2023-05-27"
]
}
},
"output_type": {
"pmf": {
"output_type_id": {
"required": [
"low",
"moderate",
"high",
"very high"
],
"optional": null
},
"value": {
"type": "double",
"minimum": 0,
"maximum": 1
}
}
},
"target_metadata": [
{
"target_id": "wk flu hosp rate category",
"target_name": "week ahead weekly influenza hospitalization rate category",
"target_units": "rate per 100,000 population",
"target_keys": {
"target": [
"wk flu hosp rate category"
]
},
"target_type": "ordinal",
"description": "This target represents a categorical severity level for rate of new hospitalizations per week for the week ending [horizon] weeks after the reference_date, on target_end_date.",
"is_step_ahead": true,
"time_unit": "week"
}
]
},
{
"task_ids": {
"reference_date": {
"required": null,
"optional": [
"2022-10-22", "2022-10-29", "2022-11-05",
"2022-11-12", "2022-11-19", "2022-11-26",
"2022-12-03", "2022-12-10", "2022-12-17",
"2022-12-24", "2022-12-31", "2023-01-07",
"2023-01-14", "2023-01-21", "2023-01-28",
"2023-02-04", "2023-02-11", "2023-02-18",
"2023-02-25", "2023-03-04", "2023-03-11",
"2023-03-18", "2023-03-25", "2023-04-01",
"2023-04-08", "2023-04-15", "2023-04-22",
"2023-04-29", "2023-05-06", "2023-05-13",
"2023-05-20", "2023-05-27"
]
},
"target": {
"required": null,
"optional": ["wk inc flu hosp"]
},
"horizon": {
"required": null,
"optional": [0, 1, 2, 3]
},
"location": {
"required": null,
"optional": [
"US",
"01",
"02",
"04",
"05"
]
},
"target_end_date": {
"required": null,
"optional": [
"2022-10-22", "2022-10-29", "2022-11-05",
"2022-11-12", "2022-11-19", "2022-11-26",
"2022-12-03", "2022-12-10", "2022-12-17",
"2022-12-24", "2022-12-31", "2023-01-07",
"2023-01-14", "2023-01-21", "2023-01-28",
"2023-02-04", "2023-02-11", "2023-02-18",
"2023-02-25", "2023-03-04", "2023-03-11",
"2023-03-18", "2023-03-25", "2023-04-01",
"2023-04-08", "2023-04-15", "2023-04-22",
"2023-04-29", "2023-05-06", "2023-05-13",
"2023-05-20", "2023-05-27"
]
}
},
"output_type": {
"mean": {
"output_type_id": {
"required": null,
"optional": ["NA"]
},
"value": {
"type": "double",
"minimum": 0
}
},
"median": {
"output_type_id": {
"required": null,
"optional": ["NA"]
},
"value": {
"type": "double",
"minimum": 0
}
},
"sample": {
"output_type_id_params": {
"is_required": true,
"type": "integer",
"min_samples_per_task": 100,
"max_samples_per_task": 100,
"compound_taskid_set" : ["reference_date", "location"]
},
"value": {
"type": "integer",
"minimum": 0
}
}
},
"target_metadata": [
{
"target_id": "wk inc flu hosp",
"target_name": "incident influenza hospitalizations",
"target_units": "count",
"target_keys": {
"target": [
"wk inc flu hosp"
]
},
"target_type": "continuous",
"description": "This target represents the count of new hospitalizations in the week ending on the date [horizon] weeks after the reference_date, on the target_end_date.",
"is_step_ahead": true,
"time_unit": "week"
}
]
}
],
"submissions_due": {
"relative_to": "reference_date",
"start": -6,
"end": -3
}
}
]
}
14 changes: 14 additions & 0 deletions inst/testhubs/samples/hub-config/validations.yml
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default:
validate_model_data:
horizon_timediff:
fn: "opt_check_tbl_horizon_timediff"
pkg: "hubValidations"
args:
t0_colname: "reference_date"
t1_colname: "target_end_date"
counts_lt_popn:
fn: "opt_check_tbl_counts_lt_popn"
pkg: "hubValidations"
args:
targets: !expr list(target = 'wk inc flu hosp')
popn_file_path: "auxiliary-data/locations.csv"
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