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api: Start to explore major changes we may need to make to the model input API. #53

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api: Start to explore major changes we may need to make to the model input API. #53

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2 changes: 1 addition & 1 deletion packages/api/package.json
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
{
"name": "@covid-modeling/api",
"version": "0.10.0",
"version": "0.11.0",
"main": "dist/src/index",
"types": "dist/src/index.d.ts",
"scripts": {
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130 changes: 106 additions & 24 deletions packages/api/schema/input.json
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,66 @@
"$ref": "#/definitions/ModelInput",
"$schema": "http://json-schema.org/draft-07/schema#",
"definitions": {
"Actual": {
"additionalProperties": false,
"properties": {
"cases": {
"type": "number"
},
"cumulativeCases": {
"type": "number"
},
"cumulativeDeaths": {
"type": "number"
},
"date": {
"$ref": "#/definitions/ISODate"
},
"deaths": {
"type": "number"
},
"mobility": {
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Is mobility just a single number? Or do we need something more complex than this?

"type": "number"
}
},
"required": [
"date",
"cases",
"cumulativeCases",
"deaths",
"cumulativeDeaths"
],
"type": "object"
},
"HistoricalData": {
"additionalProperties": false,
"properties": {
"actuals": {
"items": {
"$ref": "#/definitions/Actual"
},
"type": "array"
},
"endDate": {
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Is this the last date for which we have data?

"$ref": "#/definitions/ISODate"
},
"totalCases": {
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How is totalCases different from cumulativeCases? Could we just assume that endDate is the latest date in the actuals array?

"description": "The total number of confirmed cases in the region before the calibration date.",
"type": "number"
},
"totalDeaths": {
"description": "The total number of deaths in the region before the calibration date.",
"type": "number"
}
},
"required": [
"endDate",
"totalCases",
"totalDeaths",
"actuals"
],
"type": "object"
},
"ISODate": {
"type": "string"
},
Expand All @@ -13,40 +73,68 @@
],
"type": "string"
},
"InterventionPeriod": {
"Intervention": {
"additionalProperties": false,
"properties": {
"caseIsolation": {
"$ref": "#/definitions/Intensity",
"description": "The level to which individuals with symptoms self-isolate."
"intensity": {
"$ref": "#/definitions/Intensity"
},
"reductionPopulationContact": {
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A little confused how this will work if the reductionPopulationContact is associated with an intervention, rather than an interventionPeriod. Are we expecting that everything is additive?

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Or...I think this should just be removed...

"description": "The estimated reduction in population contact resulting from\nall of the above interventions. Some models require this generalized\nparameter instead of the individual interventions.",
"type": "number"
},
"schoolClosure": {
"$ref": "#/definitions/Intensity",
"description": "The level of school closure in the region."
"type": {
"$ref": "#/definitions/InterventionType"
}
},
"required": [
"type"
],
"type": "object"
},
"InterventionPeriod": {
"additionalProperties": false,
"properties": {
"endDate": {
"$ref": "#/definitions/ISODate"
},
"socialDistancing": {
"$ref": "#/definitions/Intensity",
"description": "The level of social distancing in the region."
"inteventions": {
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Suggested change
"inteventions": {
"interventions": {

"items": {
"$ref": "#/definitions/Intervention"
},
"type": "array"
},
"reductionPopulationContact": {
"description": "The estimated reduction in population contact resulting from\nall of the above interventions. Some models require this generalized\nparameter instead of the individual interventions.",
"type": "number"
},
"startDate": {
"$ref": "#/definitions/ISODate",
"description": "An ISO-8601 string encoding the date that these interventions begin."
},
"voluntaryHomeQuarantine": {
"$ref": "#/definitions/Intensity",
"description": "The level to which entire households self-isolate when one member\nof the household has symptoms."
}
},
"required": [
"startDate",
"endDate",
"inteventions",
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Suggested change
"inteventions",
"interventions",

"reductionPopulationContact"
],
"type": "object"
},
"InterventionType": {
"enum": [
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Can you use text instead of numbers here?

0,
1,
2,
3,
4,
5,
6,
7,
8,
9
],
"type": "number"
},
"ModelInput": {
"additionalProperties": false,
"description": "A generalized description of the input to an epidemiological model.",
Expand All @@ -70,18 +158,13 @@
"ModelParameters": {
"additionalProperties": false,
"properties": {
"calibrationCaseCount": {
"description": "The total number of confirmed cases in the region before the calibration date.",
"type": "number"
"calibrationData": {
"$ref": "#/definitions/HistoricalData"
},
"calibrationDate": {
"$ref": "#/definitions/ISODate",
"description": "An ISO-8601 string encoding the date of the most recent case data in the region."
},
"calibrationDeathCount": {
"description": "The total number of deaths in the region before the calibration date.",
"type": "number"
},
"interventionPeriods": {
"description": "A list of time periods, each with a different set of interventions.",
"items": {
Expand All @@ -99,8 +182,7 @@
},
"required": [
"calibrationDate",
"calibrationCaseCount",
"calibrationDeathCount",
"calibrationData",
"r0",
"interventionPeriods"
],
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130 changes: 106 additions & 24 deletions packages/api/schema/output.json
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,66 @@
"$ref": "#/definitions/ModelOutput",
"$schema": "http://json-schema.org/draft-07/schema#",
"definitions": {
"Actual": {
"additionalProperties": false,
"properties": {
"cases": {
"type": "number"
},
"cumulativeCases": {
"type": "number"
},
"cumulativeDeaths": {
"type": "number"
},
"date": {
"$ref": "#/definitions/ISODate"
},
"deaths": {
"type": "number"
},
"mobility": {
"type": "number"
}
},
"required": [
"date",
"cases",
"cumulativeCases",
"deaths",
"cumulativeDeaths"
],
"type": "object"
},
"HistoricalData": {
"additionalProperties": false,
"properties": {
"actuals": {
"items": {
"$ref": "#/definitions/Actual"
},
"type": "array"
},
"endDate": {
"$ref": "#/definitions/ISODate"
},
"totalCases": {
"description": "The total number of confirmed cases in the region before the calibration date.",
"type": "number"
},
"totalDeaths": {
"description": "The total number of deaths in the region before the calibration date.",
"type": "number"
}
},
"required": [
"endDate",
"totalCases",
"totalDeaths",
"actuals"
],
"type": "object"
},
"ISODate": {
"type": "string"
},
Expand All @@ -13,40 +73,68 @@
],
"type": "string"
},
"InterventionPeriod": {
"Intervention": {
"additionalProperties": false,
"properties": {
"caseIsolation": {
"$ref": "#/definitions/Intensity",
"description": "The level to which individuals with symptoms self-isolate."
"intensity": {
"$ref": "#/definitions/Intensity"
},
"reductionPopulationContact": {
"description": "The estimated reduction in population contact resulting from\nall of the above interventions. Some models require this generalized\nparameter instead of the individual interventions.",
"type": "number"
},
"schoolClosure": {
"$ref": "#/definitions/Intensity",
"description": "The level of school closure in the region."
"type": {
"$ref": "#/definitions/InterventionType"
}
},
"required": [
"type"
],
"type": "object"
},
"InterventionPeriod": {
"additionalProperties": false,
"properties": {
"endDate": {
"$ref": "#/definitions/ISODate"
},
"socialDistancing": {
"$ref": "#/definitions/Intensity",
"description": "The level of social distancing in the region."
"inteventions": {
"items": {
"$ref": "#/definitions/Intervention"
},
"type": "array"
},
"reductionPopulationContact": {
"description": "The estimated reduction in population contact resulting from\nall of the above interventions. Some models require this generalized\nparameter instead of the individual interventions.",
"type": "number"
},
"startDate": {
"$ref": "#/definitions/ISODate",
"description": "An ISO-8601 string encoding the date that these interventions begin."
},
"voluntaryHomeQuarantine": {
"$ref": "#/definitions/Intensity",
"description": "The level to which entire households self-isolate when one member\nof the household has symptoms."
}
},
"required": [
"startDate",
"endDate",
"inteventions",
"reductionPopulationContact"
],
"type": "object"
},
"InterventionType": {
"enum": [
0,
1,
2,
3,
4,
5,
6,
7,
8,
9
],
"type": "number"
},
"ModelInput": {
"additionalProperties": false,
"description": "A generalized description of the input to an epidemiological model.",
Expand Down Expand Up @@ -132,18 +220,13 @@
"ModelParameters": {
"additionalProperties": false,
"properties": {
"calibrationCaseCount": {
"description": "The total number of confirmed cases in the region before the calibration date.",
"type": "number"
"calibrationData": {
"$ref": "#/definitions/HistoricalData"
},
"calibrationDate": {
"$ref": "#/definitions/ISODate",
"description": "An ISO-8601 string encoding the date of the most recent case data in the region."
},
"calibrationDeathCount": {
"description": "The total number of deaths in the region before the calibration date.",
"type": "number"
},
"interventionPeriods": {
"description": "A list of time periods, each with a different set of interventions.",
"items": {
Expand All @@ -161,8 +244,7 @@
},
"required": [
"calibrationDate",
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Should we remove this too, since calibrationData has a sequence of dates? Then models can choose the relevant date to calibrate against.

"calibrationCaseCount",
"calibrationDeathCount",
"calibrationData",
"r0",
"interventionPeriods"
],
Expand Down
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