COVIDcases

Various files with models and graphs concerning COVID-19.

Accessible at https://share.streamlit.io/rcsmit/covidcases/main/covid_menu_streamlit.py

Sorry, sourcecode, input and outputfiles are mixed in one directory. If I'd do it again, I would split it up and make an utils.py file also.

Interesting files/scripts

• 1) covid_dashboard_rcsmit.py - aggregates a lot of information and statistics from the Netherlands. Shows correlations and graphs.

• 2) Plot_hosp_ic_streamlit.py - Plot the number of hospital and ICU admissions per age in time in the Netherlands

[](https://share.streamlit.io/rcsmit/covidcases/main/grafiek_pos_testen_per_leeftijdscategorie_streamlit.py)

3) calculate_false_positive_rate_covid_test.py - HOE BETROUWBAAR ZIJN DE TESTEN ?

• 4) number_of_cases_interactive.py - Plotting the number of COVID cases with different values. Contains a SIR-graph and a classical SIR-model. Including immunity

5) calculate_ifr_prevalence.py - calculate percentage of population who had covid and the IFR from the prevalence

6)fit_to_data_streamlit.py - FIT THE DATA

• 7) SEIR_hobbeland.py - Make an interactive version of the SEIR model, inspired by Hobbeland - https://twitter.com/MinaCoen/status/1362910764739231745

• 8) Show contact matrix

• 9) r getal per provincie

• 10) Cases from suspectibles

• 11) Fit to data OWID

• 12) Calculate R per country owid

• 13) Covid dashboard OWID/Google or Waze

• 14) Dag verschillen per leeftijd

• 15) Calculate spec)/abs) humidity from rel) hum

• 16) R getal per leeftijdscategorie

• 17) Show rioolwaardes

• 18) SIR model met leeftijdsgroepen

• 19) grafiek_pos_testen_per_leeftijdscategorie_streamlit)py - draw graphs of positieve cases per age in time** githubusercontent)com/1609141/112730260-e0f09f00-8f30-11eb-9bff-a835c2f965f7)png)** streamlit)io/badges/streamlit_badge_black_white)svg)streamlit)io/rcsmit/covidcases/main/grafiek_pos_testen_per_leeftijdscategorie_streamlit)py)**

• 20) per provincie per leeftijd

• 21) kans om covid op te lopen

• 22) Data per gemeente

• 23) VE Israel

• 24) Hosp/death NL

• 25) VE Nederland

• 26) Scatterplots QoG OWID - Combine a lot of information of Qog and Our World in Data

• 

• 27) VE & CI calculations

• 28) VE scenario calculator

• 29) VE vs inv. odds

Help files

• grafiek_pos_testen_per_leeftijdscategorie_PREPARE)py
• prepare_casuslandelijk.py

Required files

• mobilityR.csv - Contains google- and apple mobility data for masterfile_covid.py
• requirements.txt - required to use number_of_cases_interactive.py at share.streamlit.io

DATA FILES

• knmi2.csv - weather info
• mobility.csv - mobility info
• pos_test_leeftijdscat_wekelijks.csv - table 14 from 'wekelijks rapport RIVM' with tested/tested positive with different ageclasses -from 2020/8/1
• postestennaarleeftijd2.csv - table 14 from 'wekelijks rapport RIVM' with tested/tested positive with different ageclasses - from 2021/1/1
• input_latest_age_pos_test_kids_seperated.csv - table 14 from 'wekelijks rapport RIVM' with tested/tested positive with different ageclasses - from 2021/1/1 >20 in 10 years cohorts and kids still separated
• input_latest_age_pos_tests.csv - table 14 from 'wekelijks rapport RIVM' with tested/tested positive with different ageclasses - from 2021/1/1 >20 in 10 years cohorts and kids in one chohort
• restrictions.csv - restrictions in NL
• SWEDEN_our_world_in_data.csv - info about sweden
• weektabel.csv - all data from the dashboard aggregated per week - 2021

Installing

Just download or copy paste. Do not forget the required files

Built With

• Python
• Streamlit - Streamlit

Tutorial

See explanation how to make interactive graphs with Streamlit here https://rcsmit.medium.com/making-interactive-webbased-graphs-with-python-and-streamlit-a9fecf58dd4d

License

MIT

Acknowledgments

• Thanks to Han-Kwang Nienhuys for his help on several topics and some code snippets (MIT-licensed)
• Thanks to Josette Schoenmakers and Maarten van den Berg for their inspiration, help and feedback

Contact

• Twitter @rcsmit