Website for COVID-19 ORC Research Effort

This website presents the results of our work.

Link to website: http://www.covidanalytics.io/

Getting Started

After cloning/being up to date with the repo, run (preferably from a virtual environment):

pip install -r requirements.txt

Workflow

To run the app locally, run from your command line:

python index.py

Then in your browser, insert the address shown in your terminal.

(To exit, CTRL+C)

Once you are done and have checked your changes locally, make a pull request.

COVIDAnalytics REST API

For easy integration, we provide a RESTful HTTP API.

Functionality

As of now, we only expose our models to calculate patient risk. The base path for this API is https://covidanalytics.io/api/ and we provide the following functionality:

As of now, we only expose our models to calculate patient risk. The base path for this API is https://covidanalytics.io/api/ with these endpoints:

Endpoint	Function
mortality_calc_no_labs	Runs the mortality risk calculator model without lab values
mortality_calc_labs	Runs the mortality risk calculator model with lab values
infection_calc_no_labs	Runs the infection risk calculator model without lab values
infection_calc_labs	Runs the infection risk calculator model with lab values

Parameters

Parameter	Description
age	Age
sao2-labs	ABG: Oxygen Saturation (SaO2)
sao2-nolabs	SaO2
cardiac_freq	Cardiac Frequency
alt	Alanine Aminotransferase (ALT)
creat	Blood Creatinine
sodium	Blood Sodium
bun	Blood Urea Nitrogen (BUN)
temp	Body Temperature
crp	C-Reactive Protein (CRP)
hemo	CBC: Hemoglobin
leuko	CBC: Leukocytes
mcv	CBC: Mean Corpuscular Volume (MCV)
ast	Aspartate Aminotransferase (AST)
platel	CBC: Platelets
glyc	Glycemia
pot	Potassium Blood Level
inr	Prothrombin Time (INR)
gender	Gender
dysrh	Cardiac dysrhythmias
kidney	Chronic kidney disease
atheros	Coronary atherosclerosis and other heart disease
diabetes	Diabetes
bili	Total Bilirubin
rdw	CBC: Red cell Distribution Width (RDW)
resp_freq	Respiratory Frequency
calcium	Blood Calcium

Example

From the browser go to:

# Run the mortality calculator without labs on a male, age 50, oxygen saturation 98%:
https://covidanalytics.io/api/mortality_calc_no_labs?age=50&gender=0.0&sao2=98.0

# Run the infection calculator with lab values on a diabetic female, age 50, oxygen saturation 98%, blood glucose 500mg/dL:
https://covidanalytics.io/api/mortality_calc_no_labs?age=50&gender=1.0&sao2=98.0&glyc=500&diabetes=true

Or from Python:

import requests
print(requests.get('https://covidanalytics.io/api/mortality_calc_no_labs', params={'age': 50, 'gender': 0, 'diabetes': True, 'sao2': 98}).json())

All Parameters

Here is a table of all available parameters. Note that not all parameters are available for all models. You can refer to the website calculator to see if a parameter is available for a particular model.

GET Parameter	Feature Name	Datatype	Value Range	Explanation
age	Age	numeric	0.0 - 100.0	Age of the patient. Modeled only for adults.
temp	Body Temperature	numeric	34 - 104.0	Body temperature measurement. Use the dropdown to select the unit (Fahrenheit or Celsius).
cardiac_freq	Cardiac Frequency	numeric	40.0 - 171.0	Number of Beats per Minute.
resp_freq	Respiratory Frequency	numeric	14.0 - 40.0	Number of Breaths per Minute
sao2-nolabs	SaO2	numeric	80 - 100.0	Oxygen Saturation (SaO2) in %
sao2-labs	ABG: Oxygen Saturation (SaO2)	numeric	80 - 100.0	Oxygen Saturation (SaO2) in %
crp	C-Reactive Protein (CRP)	numeric	0.0 - 567.0	C-Reactive Protein (CRP) in mg/L
leuko	CBC: Leukocytes	numeric	0.0 - 36.0	Leukocytes in 10^3/muL
calcium	Blood Calcium	numeric	6.0 - 12.0	Blood Calcium in mg/dL
platel	CBC: Platelets	numeric	20.0 - 756.0	Platelets in 10^3/muL
creat	Blood Creatinine	numeric	0.0 - 11.0	Blood Creatinine in mg/dL
mcv	CBC: Mean Corpuscular Volume (MCV)	numeric	58.0 - 116.0	Mean Corpuscular Volume (MCV) in fL
inr	Prothrombin Time (INR)	numeric	0.0 - 17.0	Prothrombin Time Ratio (INR)
sodium	Blood Sodium	numeric	115.0 - 166.0	Blood Sodium in mmol/L
rdw	CBC: Red cell Distribution Width (RDW)	numeric	10 - 27	Red cell Distribution Width in %
ast	Aspartate Aminotransferase (AST)	numeric	9.0 - 941.0	Aspartate Aminotransferase (AST) in U/L
bun	Blood Urea Nitrogen (BUN)	numeric	4.0 - 174.0	Blood Urea Nitrogen (BUN) in mg/dL
alt	Alanine Aminotransferase (ALT)	numeric	2.0 - 929.0	Alanine Aminotransferase (ALT) in U/L
bili	Total Bilirubin	numeric	0.0 - 5.0	Total Bilirubin in mg/dL
hemo	CBC: Hemoglobin	numeric	6.0 - 19.0	Hemoglobin in g/dL
glyc	Glycemia	numeric	57.0 - 620.0	Blood Glucose in mg/dL
pot	Potassium Blood Level	numeric	2.0 - 7.0	Potassium Blood Level in mmol/L
gender	Gender	category	[0.0, 1.0]	Select the gender of the patient. 0.0 -> male; 1.0 -> female
dysrh	Cardiac dysrhythmias	boolean	true/false	Disease
kidney	Chronic kidney disease	boolean	true/false	Disease
atheros	Coronary atherosclerosis and other heart disease	boolean	true/false	Disease
diabetes	Diabetes	boolean	true/false	Disease