3 ms·

Building a command line tool to simulate the spread of an infection

19 points by kaunta 7y ago

vegetablepotpie 7y ago
I also wrote a very simple model of infection growth based on a system of non-linear differential equations [1]. My model has not at all followed the curve of the real infection in the US. John’s model is looks much more sophisticated. [1] https://github.com/eggsactly/corona/blob/master/corona.py https://github.com/eggsactly/corona/blob/master/corona.py
- bunje 7y ago
  Are you sure it's nonlinear? Looks like a system of linear ODE's to me.
  - bunje 7y ago
    Oops. Of course it's nonlinear. My bad.
- photonemitter 7y ago
  Small note on this. You should probably check some on numerical integration methods and solving ode’s. Specifically try the midpoint method or Runge-Kutta 4. (Rk4) which is easily implemented from the wiki-page.
- kaunta 6y ago
  Garrett, thank you. * * * My inspiration for writing this came from watching 3Blue1Brown's YouTube video, "Simulating an epidemic": https://www.youtube.com/watch?v=gxAaO2rsdIs https://www.youtube.com/watch?v=gxAaO2rsdIs His simulations cover several scenarios: - Simulating social distancing. - Having people travel to a central location (e.g. a grocery store). - What if the government is able to identify and isolate cases? - Simulating multiple communities with travel, that put quarantine measures in place. - What happens when people get tired of social distancing. * * * Thanks for sharing your code. I see that you are using gnuplot to visualize the output of the script. Have you considered using the csv module (https://docs.python.org/3/library/csv.html https://docs.python.org/3/library/csv.html) to output the data, instead of using the print() function? That way, you wouldn't have to manually add in spaces around the data and stringify the numeric data. >>> import csv, sys >>> writer = csv.writer(sys.stdout, delimiter=" ") >>> writer.writerow(["#", "T", "S", "I", "R"]) # T S I R In the script, usage would look something like this: import csv import sys ... writer = csv.writer(sys.stdout, delimiter=" ") writer.writerow(["#", "T", "S", "I", "R"]) writer.writerow([T, S, I, R]) while I > 1000: ... writer.writerow([T, S, I, R])
tromp 7y ago
Coincidentally this month's IBM Ponder This challenge calls for a similar tool: https://www.research.ibm.com/haifa/ponderthis/challenges/April2020.html https://www.research.ibm.com/haifa/ponderthis/challenges/Apr...

19 points by kaunta 7y ago

I also wrote a very simple model of infection growth based on a system of non-linear differential equations [1]. My model has not at all followed the curve of the real infection in the US. John’s model is looks much more sophisticated. [1] https://github.com/eggsactly/corona/blob/master/corona.py https://github.com/eggsactly/corona/blob/master/corona.py

bunje 7y ago
Are you sure it's nonlinear? Looks like a system of linear ODE's to me.
- bunje 7y ago
  Oops. Of course it's nonlinear. My bad.
photonemitter 7y ago
Small note on this. You should probably check some on numerical integration methods and solving ode’s. Specifically try the midpoint method or Runge-Kutta 4. (Rk4) which is easily implemented from the wiki-page.
kaunta 6y ago
Garrett, thank you. * * * My inspiration for writing this came from watching 3Blue1Brown's YouTube video, "Simulating an epidemic": https://www.youtube.com/watch?v=gxAaO2rsdIs https://www.youtube.com/watch?v=gxAaO2rsdIs His simulations cover several scenarios: - Simulating social distancing. - Having people travel to a central location (e.g. a grocery store). - What if the government is able to identify and isolate cases? - Simulating multiple communities with travel, that put quarantine measures in place. - What happens when people get tired of social distancing. * * * Thanks for sharing your code. I see that you are using gnuplot to visualize the output of the script. Have you considered using the csv module (https://docs.python.org/3/library/csv.html https://docs.python.org/3/library/csv.html) to output the data, instead of using the print() function? That way, you wouldn't have to manually add in spaces around the data and stringify the numeric data. >>> import csv, sys >>> writer = csv.writer(sys.stdout, delimiter=" ") >>> writer.writerow(["#", "T", "S", "I", "R"]) # T S I R In the script, usage would look something like this: import csv import sys ... writer = csv.writer(sys.stdout, delimiter=" ") writer.writerow(["#", "T", "S", "I", "R"]) writer.writerow([T, S, I, R]) while I > 1000: ... writer.writerow([T, S, I, R])

tromp 7y ago

Coincidentally this month's IBM Ponder This challenge calls for a similar tool: https://www.research.ibm.com/haifa/ponderthis/challenges/April2020.html https://www.research.ibm.com/haifa/ponderthis/challenges/Apr...