COVIDcases

Various files with models and graphs concerning COVID-19.

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

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

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

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

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

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