This repository contains the code for the COVID-19 epidemiological simulation model as well as supporting data as used in the manuscript:
Forecasting the spread of SARS-CoV-2 is inherently ambiguous given the
current state of virus research
by
- M.F. Koenen
- M. Balvert
- R. Brekelmans
- H.A. Fleuren
- V.F. Stienen
- J.C. Wagenaar
Zero Hunger Lab, Tilburg University
- The
srcfolder contains the Java code of the simulation model. - The
transitionfolder contains a Python module for fitting transition matrices.
Transition matrices and simulation initializations can be found in the input folder in the source code.
Simulation initializations were based on a lower- and an upper bound
on the number of deaths for March 6-20. These bounds can be found in
Deathrates_for_initialization.csv.
Scenario input files are coded according to the following table.
| ID | Symptoms | CFR | Immunity |
|---|---|---|---|
| 1 | 0.375 | Data from NL | All |
| 2 | 0.375 | Literature-E | All |
| 3 | 0.375 | Literature-I-s | All |
| 4 | 0.500 | Data from NL | All |
| 5 | 0.500 | Literature-E | All |
| 6 | 0.500 | Literature-I-s | All |
| 7 | 0.625 | Data from NL | All |
| 8 | 0.625 | Literature-E | All |
| 9 | 0.625 | Literature-I-s | All |
| 10 | 0.750 | Data from NL | All |
| 11 | 0.750 | Literature-E | All |
| 12 | 0.750 | Literature-I-s | All |
| 13 | 0.375 | Data from NL | High |
| 14 | 0.375 | Literature-E | High |
| 15 | 0.375 | Literature-I-s | High |
| 16 | 0.500 | Data from NL | High |
| 17 | 0.500 | Literature-E | High |
| 18 | 0.500 | Literature-I-s | High |
| 19 | 0.625 | Data from NL | High |
| 20 | 0.625 | Literature-E | High |
| 21 | 0.625 | Literature-I-s | High |
| 22 | 0.750 | Data from NL | High |
| 23 | 0.750 | Literature-E | High |
| 24 | 0.750 | Literature-I-s | High |
| 25 | 0.375 | Data from NL | Medium |
| 26 | 0.375 | Literature-E | Medium |
| 27 | 0.375 | Literature-I-s | Medium |
| 28 | 0.500 | Data from NL | Medium |
| 29 | 0.500 | Literature-E | Medium |
| 30 | 0.500 | Literature-I-s | Medium |
| 31 | 0.625 | Data from NL | Medium |
| 32 | 0.625 | Literature-E | Medium |
| 33 | 0.625 | Literature-I-s | Medium |
| 34 | 0.750 | Data from NL | Medium |
| 35 | 0.750 | Literature-E | Medium |
| 36 | 0.750 | Literature-I-s | Medium |
| 37 | 0.375 | Data from NL | Low |
| 38 | 0.375 | Literature-E | Low |
| 39 | 0.375 | Literature-I-s | Low |
| 40 | 0.500 | Data from NL | Low |
| 41 | 0.500 | Literature-E | Low |
| 42 | 0.500 | Literature-I-s | Low |
| 43 | 0.625 | Data from NL | Low |
| 44 | 0.625 | Literature-E | Low |
| 45 | 0.625 | Literature-I-s | Low |
| 46 | 0.750 | Data from NL | Low |
| 47 | 0.750 | Literature-E | Low |
| 48 | 0.750 | Literature-I-s | Low |
The table below shows a conversion table indicating the stage names and abbreviations used in some of the data and source code files that were used during development, and the stage names and abbreviations as they are used in the final report.
| ID | short | long | paper | paper-code |
|---|---|---|---|---|
| 0 | H | HEALTHY | Susceptible | S |
| 1 | INN | INFECTED_NOSYMPTOMS_NOTCONTAGIOUS | Exposed | E |
| 2 | INY | INFECTED_NOSYMPTOMS_ISCONTAGIOUS | Infectious asymptomatic | I-a |
| 3 | IM | INFECTED_SYMPTOMS_MILD | Infectious symptomatic | I-s |
| 4 | ISY | INFECTED_SYMPTOMS_SEVERE_ICpossible | ICU admission | ICU-a |
| 5 | ISN | INFECTED_SYMPTOMS_SEVERE_ICnotpossible | ICU refusal | ICU-r |
| 6 | ISQ | INFECTED_SYMPTOMS_SEVERE_QUEUE | N/A | N/A |
| 7 | C | CURED | Immune | IM |
| 8 | D | DEAD | Deceased | D |