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covid

COVID-19 tool development

An open collaboration between the Cleveland Clinic and SAS Institute.

What this Code Does

This code takes a set of input parameters and uses them in infectious disease models (SIR & SEIR). Model output is used to calculate useful metrics for each day of an epidemic, such as the number of hospitalizations.

Documentation

In addition to the information shared within this readme and the commenting within the code, you can also review the documentation on the implementation of the models in SAS.

For a good understanding of the SIR and SEIR model approaches, we recommend this very well written blog post from the folks at TRIPLEBYTE.

Getting Started

  • PREPARE
    • Download COVID_19.sas to your SAS environment
      • Also, download the run_scenario.csv file for an example submission file to run many scenarios in batch
  • SETUP
    • Edit line 10 to a local directory you want to save datasets with model output and scenario information to
    • If you do not have SAS/ETS then edit line 16 to 'NO'
      • This option causes the SIR/SEIR models to run with a SAS Data Step version only
      • If you are unsure then you can run PROC PRODUCT_STATUS; run; in SAS and view the log for this information
    • If you have the latest analytical release of SAS, 15.1, then set line 17 to YES
      • This option swaps out PROC MODEL for PROC TMODEL
      • If you are unsure then you can run PROC PRODUCT_STATUS; run; in SAS and view the log for this information
  • RUN
    • Make calls to the macro %EasyRun. Example scenarios are at the end of the file.
    • Submit many scenarios in batch by using an input file. An example file, run_scenarios.csv, is provided. Each row of this file will feed individual calls to the %EasyRun macro.
  • REVIEW
    • All model output for each call to %EasyRun saves in the dataset STORE.MODEL_FINAL
    • All of the parameters that lead to the results in STORE.MODEL_FINAL save in STORE.SCENARIOS, and all inputs to the macro also save to STORE.INPUTS. The variable SCENARIOINDEX links these files.
  • ADJUST inputs to your population
    • Change the input parameters to match the population you are working with. If their is a wide range of scenarios you want to run then use the run_scenarios.csv method to easily submit all the combinations.

Explore the Inputs, Outputs and Details in the Wiki

Explore the wiki

Development Notes

  • The current locked version of the project is in COVID_19.sas.
  • Progress towards the next locked version is in the /progress folder
  • the COVID_19.sas file is built from modular parts in /build/parts into the /build/public folder by /build/build.py and then copied here

Example Scenario Visuals

With the option plots=yes, the COVID_19.sas program will create diagnostic visuals for each scenario. Some example of these visuals follow. The output data is also available in SAS Visual Analytics with user interface to drive the running of scenarios is in the works.

All Approaches Fitting Approaches

Example User Interface (Coming Soon)

Our goal is to allow users to visualize and run scenarios from a user interface. Take a look at our current prototype: