/COVIDcases

10+ scripts about the COVID-statistics in the Netherlands, accessibile at https://share.streamlit.io/rcsmit/covidcases/main/covid_menu_streamlit.py

Primary LanguagePythonMIT LicenseMIT

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. image

Open in Streamlit

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

plothospIC

[![Open in Streamlit](https://static.streamlit.io/badges/streamlit_badge_black_white.svg)](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 ? image image

  • 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

image

Open in Streamlit

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

6)fit_to_data_streamlit.py - FIT THE DATA image

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

  • 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** imagegithubusercontent)com/1609141/112730260-e0f09f00-8f30-11eb-9bff-a835c2f965f7)png)** Open in Streamlitstreamlit)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 image

  • 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

  • image

  • 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

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

Contact