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update round documentation
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@LucieContamin
LucieContamin committed Apr 16, 2024
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4 changes: 4 additions & 0 deletions README.md
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Expand Up @@ -316,6 +316,10 @@ The folder contains multiple sub-folders:

- Metadata: We will require a brief meta-data from all teams.

- Filename: the date YYYY-MM-DD should correspond to the **due date**.
For phase 1: the date will be "2024-05-15". For more information,
please consult the [model-output/README](./model-output/README.md)


## Target Data

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176 changes: 156 additions & 20 deletions hub-config/tasks.json
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Expand Up @@ -2,7 +2,7 @@
"schema_version": "https://raw.githubusercontent.com/Infectious-Disease-Modeling-Hubs/schemas/main/v2.0.0/tasks-schema.json",
"rounds": [
{
"round_id": "2024-03-26",
"round_id": "2024-05-15",
"round_id_from_variable": false,
"model_tasks": [
{
Expand Down Expand Up @@ -39,16 +39,6 @@
"max_samples_per_task": 300,
"samples_joint_across": ["horizon", "race_ethnicity"]
},
"value" : {
"type": "double",
"minimum": 0
}
},
"quantile":{
"type_id": {
"required": [0.01, 0.025, 0.05, 0.1, 0.15, 0.2, 0.25, 0.3, 0.35, 0.4, 0.45, 0.5, 0.55, 0.6, 0.65, 0.7, 0.75, 0.8, 0.85, 0.9, 0.95, 0.975, 0.99],
"optional": [0, 1]
},
"value" : {
"type": "numeric",
"minimum": 0
Expand All @@ -70,12 +60,12 @@
},
{
"target_id": "inc inf",
"target_name": "Incident infection",
"target_name": "Incident Infection",
"target_units": "count",
"target_keys": {
"target": "inc inf"
},
"description": "Weekly newly reported infections",
"description": "Weekly new COVID-19 infection.",
"target_type": "discrete",
"is_step_ahead": true,
"time_unit": "week"
Expand All @@ -87,7 +77,7 @@
"target_keys": {
"target": "inc hosp"
},
"description": "Weekly newly reported cases",
"description": "Weekly newly reported COVID-19 cases",
"target_type": "discrete",
"is_step_ahead": true,
"time_unit": "week"
Expand Down Expand Up @@ -129,12 +119,158 @@
"samples_joint_across": ["horizon", "race_ethnicity"]
},
"value" : {
"type": "double",
"type": "numeric",
"minimum": 0
}
}
},
"target_metadata": [
{
"target_id": "inc death",
"target_name": "Incident deaths",
"target_units": "count",
"target_keys": {
"target": "inc death"
},
"description": "Weekly new deaths due to COVID-19 as reported by state and local departments of public health and aggregated in the NCHS data collection system.",
"target_type": "discrete",
"is_step_ahead": true,
"time_unit": "week"
},
{
"target_id": "inc inf",
"target_name": "Incident Infection",
"target_units": "count",
"target_keys": {
"target": "inc inf"
},
"description": "Weekly new COVID-19 infection.",
"target_type": "discrete",
"is_step_ahead": true,
"time_unit": "week"
},
{
"target_id": "inc case",
"target_name": "Incident cases",
"target_units": "count",
"target_keys": {
"target": "inc hosp"
},
"description": "Weekly newly reported COVID-19 cases",
"target_type": "discrete",
"is_step_ahead": true,
"time_unit": "week"
}
]
},
{
"task_ids": {
"origin_date": {
"required": ["2020-11-15"],
"optional": null
},
"scenario_id": {
"required": ["A-2020-05-01"],
"optional": null
},
"quantile": {
"type_id": {
"location": {
"required": ["06"],
"optional": null
},
"race_ethnicity": {
"required": ["latino", "asian", "black", "white", "other", "overall"],
"optional": null
},
"target": {
"required": null,
"optional": ["inc death", "inc inf", "inc case"]
},
"horizon": {
"required": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20],
"optional":null
}
},
"output_type": {
"quantile":{
"output_type_id": {
"required": [0.01, 0.025, 0.05, 0.1, 0.15, 0.2, 0.25, 0.3, 0.35, 0.4, 0.45, 0.5, 0.55, 0.6, 0.65, 0.7, 0.75, 0.8, 0.85, 0.9, 0.95, 0.975, 0.99],
"optional": [0, 1]
},
"value" : {
"type": "numeric",
"minimum": 0
}
}
},
"target_metadata": [
{
"target_id": "inc death",
"target_name": "Incident deaths",
"target_units": "count",
"target_keys": {
"target": "inc death"
},
"description": "Weekly new deaths due to COVID-19 as reported by state and local departments of public health and aggregated in the NCHS data collection system.",
"target_type": "discrete",
"is_step_ahead": true,
"time_unit": "week"
},
{
"target_id": "inc inf",
"target_name": "Incident Infection",
"target_units": "count",
"target_keys": {
"target": "inc inf"
},
"description": "Weekly new COVID-19 infection.",
"target_type": "discrete",
"is_step_ahead": true,
"time_unit": "week"
},
{
"target_id": "inc case",
"target_name": "Incident cases",
"target_units": "count",
"target_keys": {
"target": "inc hosp"
},
"description": "Weekly newly reported COVID-19 cases",
"target_type": "discrete",
"is_step_ahead": true,
"time_unit": "week"
}
]
},
{
"task_ids": {
"origin_date": {
"required": ["2020-11-15"],
"optional": null
},
"scenario_id": {
"required": ["A-2020-05-01"],
"optional": null
},
"location": {
"required": ["37"],
"optional": null
},
"race_ethnicity": {
"required": ["asian", "black", "white", "other", "overall"],
"optional": null
},
"target": {
"required": null,
"optional": ["inc death", "inc inf", "inc case"]
},
"horizon": {
"required": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20],
"optional":null
}
},
"output_type": {
"quantile":{
"output_type_id": {
"required": [0.01, 0.025, 0.05, 0.1, 0.15, 0.2, 0.25, 0.3, 0.35, 0.4, 0.45, 0.5, 0.55, 0.6, 0.65, 0.7, 0.75, 0.8, 0.85, 0.9, 0.95, 0.975, 0.99],
"optional": [0, 1]
},
Expand All @@ -159,12 +295,12 @@
},
{
"target_id": "inc inf",
"target_name": "Incident infection",
"target_name": "Incident Infection",
"target_units": "count",
"target_keys": {
"target": "inc inf"
},
"description": "Weekly newly reported infections",
"description": "Weekly new COVID-19 infection.",
"target_type": "discrete",
"is_step_ahead": true,
"time_unit": "week"
Expand All @@ -176,7 +312,7 @@
"target_keys": {
"target": "inc hosp"
},
"description": "Weekly newly reported cases",
"description": "Weekly newly reported COVID-19 cases",
"target_type": "discrete",
"is_step_ahead": true,
"time_unit": "week"
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15 changes: 9 additions & 6 deletions model-output/README.md
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Expand Up @@ -93,8 +93,8 @@ arrow::read_parquet(filename)
```

For the disparities round, the date YYYY-MM-DD should correspond to the
**due date**, for example: "`2024-03-26`" from
"Phase 1 projections due: March 26, 2024" as noted in the scenario
**due date**, for example: "`2024-05-15`" from
"Phase 1 projections due: mid-May" as noted in the scenario
description on the main
[README, Submission Information](https://github.com/midas-network/rsv-scenario-modeling-hub)).

Expand Down Expand Up @@ -125,8 +125,8 @@ The output file must contain eleven columns (in any order):

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

#### Column format

Expand Down Expand Up @@ -169,7 +169,7 @@ The submission can contain multiple output type information:
will call this format "sample" output type. For more information, please
consult the [sample](./data-processed#sample)
section.
- A set of quantiles value for all the targets.
- An optional set of quantiles value for all the targets.
We will call this format "quantile" output type. For more information,
please consult the [quantile](./data-processed#quantile)
section.
Expand Down Expand Up @@ -292,7 +292,7 @@ identifier for each group containing all the possible value for `"race_ethnicity
and `"horizon"`.

Fore more information and examples, please consult the
[Sample Format Wiki page](https://github.com/midas-network/rsv-scenario-modeling-hub/wiki/Sample-File-Format).
[Sample Format Documentation page](https://scenariomodelinghub.org/documentation/sample_format.html).

For example:

Expand Down Expand Up @@ -324,6 +324,9 @@ 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` quantile can also be provided.


For example:

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