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Python code to analyze data and predict Covid-19 infection

License: Apache License 2.0

Python 7.60% Jupyter Notebook 92.40%
covid-19 infectious-disease-models covid19-data sir covid19 simulation engineering

dataandmodelscovid19's People

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gasilva avatar vinimassis avatar

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vinimassis ats-aerothermal-solutions

dataandmodelscovid19's Issues

SEAIRD_DRS.py: error: argument --S_0: invalid int value: '1000.0' 

python SEAIRD_DRS.py --districtRegions "DRS 08 - Franca" --start-date 2020-04-01 --prediction-days 60 --S_0 1000.0 --E_0 0.0001 --A0 0.0001 --I0 0.0001 --R0 0.0001 --D0 0.0001 --START 0 --RATIO 0.1 --WCASES 0.4 --WREC 0.1
usage: SEAIRD_DRS.py [-h] [--districtRegions DISTRICTREGIONS]
                     [--download-data DOWNLOAD_DATA] [--start-date START_DATE]
                     [--prediction-days PREDICT_RANGE] [--S_0 S_0] [--E_0 E_0]
                     [--A_0 A_0] [--I_0 I_0] [--R_0 R_0] [--D_0 D_0]
                     [--START STARTNCASES] [--RATIO RATIO]
                     [--WCASES WEIGTHCASES] [--WREC WEIGTHRECOV]
SEAIRD_DRS.py: error: argument --S_0: invalid int value: '1000.0'

elif and if

change line from elif to if in DRS_run_all.py

        elif query['s0'][0] == query['s0'][0]:
            command  += " --S_0 {}".format(query['s0'][0])

        if query['s0'][0] == query['s0'][0]:
            command  += " --S_0 {}".format(query['s0'][0])

Things to do

  • update read.me in order to reflect new equations implemented

  • make a plotModels.py to compare results from several models

  • save dataFrame results and load back in plotModels.py

  • make a log plot and daily growth for best/selected model results

  • make weights an input variable for each country (self object)

  • separated data analysis from the model

  • do the optimization for the initial conditions and parameters for each DR

  • make the model available on a web-page

  • include an equation for hospitalization, ITU / Respirator beds

  • include an equation for quarantine

  • make the ODES parameters variable in time

division by zero

make tot minimum as 1 to not have division by zero

    l1=np.sqrt(l1/max(1.,tot))
    l2=np.sqrt(l2/max(1.,tot))
    l3=np.sqrt(l3/max(1.,tot))

SEAIRD_DRS.py: error: unrecognized arguments: 09 - Marília' 

python SEAIRD_DRS.py --districtRegions 'DRS 09 - Marília' --start-date 2020-04-01 --prediction-days 60 --S_0 500.0 --E_0 0.0001 --A_0 0.0001 --I_0 0.0001 --R_0 0.0001 --D_0 0.0001 --START 0 --RATIO 0.1 
--WCASES 0.4 --WREC 0.1
usage: SEAIRD_DRS.py [-h] [--districtRegions DISTRICTREGIONS]
                     [--download-data DOWNLOAD_DATA] [--start-date START_DATE]
                     [--prediction-days PREDICT_RANGE] [--S_0 S_0] [--E_0 E_0]
                     [--A_0 A_0] [--I_0 I_0] [--R_0 R_0] [--D_0 D_0]
                     [--START STARTNCASES] [--RATIO RATIO]
                     [--WCASES WEIGTHCASES] [--WREC WEIGTHRECOV]
SEAIRD_DRS.py: error: unrecognized arguments: 09 - Marília'

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