{"id":21048205,"url":"https://github.com/podusowski/covid-simulations","last_synced_at":"2025-03-13T22:42:07.977Z","repository":{"id":71845265,"uuid":"362948423","full_name":"podusowski/covid-simulations","owner":"podusowski","description":"Couple of COVID-19 related simulations.","archived":false,"fork":false,"pushed_at":"2021-09-23T10:55:13.000Z","size":7599,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-03-07T16:09:16.432Z","etag":null,"topics":["coronavirus","covid-19","simulation"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/podusowski.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2021-04-29T21:11:15.000Z","updated_at":"2021-09-23T10:55:16.000Z","dependencies_parsed_at":null,"dependency_job_id":"3e2ea275-61b4-4d17-8b96-974026c73241","html_url":"https://github.com/podusowski/covid-simulations","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/podusowski%2Fcovid-simulations","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/podusowski%2Fcovid-simulations/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/podusowski%2Fcovid-simulations/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/podusowski%2Fcovid-simulations/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/podusowski","download_url":"https://codeload.github.com/podusowski/covid-simulations/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":243495489,"owners_count":20299921,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["coronavirus","covid-19","simulation"],"created_at":"2024-11-19T14:42:34.333Z","updated_at":"2025-03-13T22:42:07.957Z","avatar_url":"https://github.com/podusowski.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"How does it work\n----------------\nThe simulation is written in Python and it was tested under Ubuntu 20.04 with\nPython 3.8.5. `requirements.txt` contains a list of dependencies.\n\nThe basic building block o the simulation is a model of a population.\nIndividuals in a population have features which can evolve as the summation\nruns, and thus creating subpopulations. Randomly picked individuals can be then\n_affected_ (one or more of their features can change) in each simulation cycle.\n\n\nData\n----\nThe data about daily cases, deaths and vaccinations was taken from\nhttps://ourworldindata.org/ and added to the repository.\n\nIt can be updated with:\n\n```\nwget https://covid.ourworldindata.org/data/owid-covid-data.csv\n```\n\n\nHow many time-correlated deaths are expected during a vaccination campain?\n--------------------------------------------------------------------------\n**Summary: Considerable number of time-correlated deaths are expected, but vaccine is not the cause.**\n\nWhile it is obvious that no vaccine makes you immortal and therefore some\nvaccinated people will die shorty after getting a shot. This simulation tries\nto estimate a number of such occurrences to see whether number of serious\nadverse events can be based on the time correlation alone.\n\nThe algorithm works as follow. First, it constructs a virtual population of around 40M\npeople. Then, for each day the data exists for, it randomly picks two groups of\npeople. First group is getting vaccinated and the second dies. Number of\nvaccinated people is taken from OWID data, and number of people who die is\nalways 1000, which is a understated number of daily deaths in Poland.\n\nDates for both events are recoded for each affected person and two sets are\nbuilt out of them: people who died within a week after taking a vaccine and\npeople who died next day after.\n\nThe simulation can be started with:\n\n```\n./how-people-would-die.py --plot plot.png\n```\n\nThese are the result for a simulation for the OWID data up to 17 Aug 2021:\n\n![](plots/how-people-would-die.png)\n\n\nHow many people are expected to get infected after vaccination?\n---------------------------------------------------------------\nThis COVID-19 simulation tries to asses how many vaccinated people might still\nget infected and die before the immunity system fully kicks in.\n\nIt can be started by:\n\n```\n./simulate.py --location Poland --plot plot.png\n```\n\n`--plot` can be skipped to see the raw computed data instead.\n\n\nThere are number of known (and probably some unknown) limitations that you\nshould be aware of. Make sure you understand them before interpreting any of\nthis.\n\nThings that might cause the numbers to be underestimated:\n\n- For the program, a _protected_ person is everyone two weeks after the first\n  dose of the vaccine. In other words, no one can be infected two weeks after\n  vaccination, which obviously isn't the case in the real world.\n\n- In many countries, people in the high risk groups were prioritized to take\n  jabs first, making them overrepresented in the vaccinated subpopulation.\n\n- By default, infected people are not vaccinated. This is only partially true\n  because there might be people who did catch the infection say a day before\n  the vaccination. You can change this behavior to vaccinate despite the \n  infection by `--vaccinate-despite-infection`.\n\n\nSimulation performed with data from the beginning of the pandemic\nto 28 April 2021:\n\n![](plots/plot1.png)\n\nThis is what happens if we allow infected people to be vaccinated:\n\n![](plots/plot2.png)\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpodusowski%2Fcovid-simulations","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpodusowski%2Fcovid-simulations","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpodusowski%2Fcovid-simulations/lists"}