Contains:
- BA12 for US BA12 scenario projections
- R14 for round 14 of the SMH
- Scripts to generate data (vaccination, cases, hospitalizations, deaths, school and work closures calendar, variant proportions,...)
##CODE IMPLEMENTATION (FOR BA12 CASE)::
###Prepare: scripts to prepare vaccination- https://data.cdc.gov/Vaccinations/COVID-19-Vaccinations-in-the-United-States-Jurisdi/unsk-b7fc DONE scripts to process cases, hospital admission, deaths https://raw.githubusercontent.com/nytimes/covid-19-data/master/us-states.csv https://raw.githubusercontent.com/nytimes/covid-19-data/master/us.csv https://healthdata.gov/Hospital/COVID-19-Reported-Patient-Impact-and-Hospital-Capa/g62h-syeh
DONE scripts to get work/school data DONE scripts with demographics, states, DONE scripts for variants fitting, https://covid.cdc.gov/covid-data-tracker/#variant-proportions DONE
things to do to prepare data: update the date files: date-fit.xlsx and date-vacc.xlsx download updated data for hospitalizations, cases, deaths, and vaccination Update vaccination data in vacc.ipynb script. Run vaxx.ipynb, fit_data.ipynb, fitter_variant.ipynb,
command to send data to TACC: scp data/* abouchni@frontera.tacc.utexas.edu:/work2/08090/abouchni/frontera/seir-austin/seir_regression/ImmunoSEIRS/US-BA12/data/
###Model_function: DONE Improved interaction between booster immunity and primary vaccination
###HPC deployment: parallelize and launch on TACC?? DONE save status file and import DONE
###command to download results:
scp abouchni@frontera.tacc.utexas.edu:/work2/08090/abouchni/frontera/seir-austin/seir_regression/ImmunoSEIRS/US-BA12/saved_data_test/* /media/multiphysics/0A3AF5863AF56ED7/Users/HINNOVIS/Pictures/NN-classification/data/vax_data/BA12/saved_data_test
###TEST;
Scenario assumptions;
2 immune waning, 2 booster 2 BA.12 transmissibility: 10% more transmissible and 25% immune escape