ecsendmail / covidsimvl-code Goto Github PK

The routine Mtabulate L2559 in simulation.js contains the calculation of R0 for the multiverse, in L2571 ff (this means following....) ....

Please note that both M.xxx (the multiverse) and U.xxxx (the Universes) each keep their own count of R0

and this is done by finding the ORANGE count (persons that have become INERT), and adding the kill=count M.susCt (the count of susceptible which have been infected by the infective transmitter....

This determination is done in P[x].susCt.......in the routine VLtransfer L1918 and the part that deals with infection is in L.1966, L 1972

If you do the math, then at the end when everyone is INERT, the total number of infectives divided by the total number of oranges is near 1...

I suppose that what I should be doing is not dividing by total number of oranges but only those oranges that have non-zero P.susct......

This is probably an error in calculation, and should be tested to see what the difference is between oranges that have no history of infection, and the total number...

Ernie

• added primary CovidSIMVL code
• confirmed that browser based operation works

Hi @ecsendmail, please add admin privileges to this repo for @kmoselle, @MahdiHajiabadi and myself (like you did for the other one)?
cheers
Ash

An open issue until closed! :-D

won't be easy....for me, Miles

cant assign to Ken till he accepts...
Ernie

an issue to be assigned to Ken
somehow only Ash shows up when I pull up the list of persons that I can assign to....will try to empower this repository again....

Develop MVP to estimate compartmental model parameters...
cf eg
towardsdatascience article

This type of function can be used to:

fit compartmental model parameters to "real data"
fit compartmental model parameters to "simulated data"

FYI @kmoselle

and possibly identifying who the agents are, as they move around......Mahdi, if you would like this, or need it, we can work together to change the code on say, Thursday afternoon, or Wed afternoon....will probably take 1 to 2 hours....might be a bit complex and have to test it sorted out from the sliders, because I want the totals per generation, which is not being totalled,,,,,though I just thought of a sweet way to get that....

anyway, let me know

Hi @MahdiHajiabadi,
A warm up exercise @kmoselle suggested: with code available already so no need to implement from scratch...Trying the code in the article and adding some adaptation of this code to our repo would be a great resource! Possible modifications could include:
adding an option to run in non-interactive mode...which is a step that (to be confirmed by @ecsendmail and @kmoselle) would support the work plan

Thoughts?
cheers

Reference:

Shukla, A. Simulating Compartmental Models in Epidemiology using Python and Jupyter Widgets Implement and simulate SEIR and SEIRD models in Jupyter Notebooks. April 11, 2020.

• starting from Ernie's revised version