Below are descriptions of the various data files used by the application. Each file has a default file location that can be changed in the config.json file. The default location for the data as well as other details will be noted in each description.
File format: TSV
Default location: "/data/patients.tsv"
This file contains the majority of the data for the application. It consists of a list of patients assigned to various cohorts and additional patient specific information used in the data visualizations.
| Field | Type | Description |
|---|---|---|
| ID | numeric | Unique id of the patient within the dataset |
| PAT_MRN_ID | numeric | Unique id of the patient within the source data |
| FEVER_SYMPTOMS | Yes/No | Did the patient have a fever at the time of collection |
| COUGH_SYMPTOMS | Yes/No | Did the patient have a cough at the time of collection |
| SORE_THROAT_SYMPTOMS | Yes/No | Did the patient have a sore throat at the time of collection |
| GENDER | string | Supported values are: Male/Female/Unknown |
| RACE | string | Currently this field is free text |
| MORTALITY_STATUS | string | Supported values are: Alive/Deceased/[Blank] |
| AGE | numeric | Patient age at the time of collection |
| FACILITY | string | Facility identifier for the dataset |
| DEATH_DATE | date | Time can be included but is currently not used |
| SAMPLE_COLLECTION_DATE | date | Time can be included but is currently not used |
| Latitude | numeric | Latitude coordinate for the patient's home address |
| Longitude | numeric | Longitude coordinate for the patient's home address |
| COHORT | string | The cohort the patient belongs to* |
The values allowed in the COHORT column of this file are defined by the overlays:patients configuration section of the config.json file. This array contains items with a cohort property. Only the values of those properties are allowed in this column. The default configuration provides these values: COVID-19+, COVID-19-, Influenza+, Influenza-. If you require additional cohorts, they will need to be added to the overlays:patients configuration.
File format: CSV
Default location: "/data/medical-facilities.csv"
A list of medical facilities to display as an overlay on the map visualization.
| Field | Type | Description |
|---|---|---|
| ID | numeric | Unique id of the facility within the dataset |
| Name | string | Name of the facility to be used in the UI |
| Date | date | Used to filter facilities based on the date they opened |
| Latitude | numeric | Latitude coordinate for the facility's address |
| Longitude | numeric | Latitude coordinate for the facility's address |
| Type | string | Default supported values are: Hospital/Drive-thru/Testing site* |
| Address | string | Street address of the facility |
The values allowed in the TYPE column of this file are defined by the overlays:medical_facilities configuration section of the config.json file. This array contains items with a type property. Only the values of those properties are allowed in this column. The default configuration provides these values: Hospital, Drive-thru, Testing site. If you require additional cohorts, they will need to be added to the overlays:medical_facilities configuration.
File format: CSV
Default location: "/data/timeline-events.csv"
A file containing a list of events to display in the application UI. These events are shown on the timeline slider and may also be used within various charts.
| Field | Type | Description |
|---|---|---|
| Name | string | Used as the label for the event on the timeline |
| Date | date | Used to display the event at the proper position on the timeline |