I found this article: Modeling the COVID-19 Outbreak with J <https://datakinds.github.io/2020/03/15/modeling-the-coronavirus-outbreak-with-j>
I took the author's code, which is a modified SEIR model (The_SEIR_model <https://en.wikipedia.org/wiki/Compartmental_models_in_epidemiology#The_SEIR_model>), and updated some of the data and recalculated the variables. I then pilfered some of Michal's (Tangentstorm, you rock!) code for animating things in J from his talks. This is helping me to push my learning of J, and keep it interesting. Two disclaimers: The author of the linked article doesn't claim to be an epidemiologist, and I am only doing this to learn J, and cannot comment on any of the validity of the algorithm or simulations it produces. Now, on to my two issues (full code at end): 1. I know I have to figure out a way to have the* infect_display^:144 starting population* call feed the *update* loop, otherwise it is trying to run all 144 days of simulation in one call to update at a frequency set by *wd 'timer 600'*. I am working on this, and realize I somehow have to run it outside of update, and then feed update "a day at a time". The goal is to see the same person (grid location) evolve over the simulation. I know this is simple, but i haven't gotten there yet. Any tips will be appreciated! 2. When I had initially set up the code to run 25 people instead of 144, the color index I had setup with the DSEIR variable exhibit two strange glitches. First, squares that were supposed to be 1=White, were rendering as 0=Black=Dead, and sometimes colors appeared "blended". An yellowish, off-white for yellow, and at times bright yellow. When I went to 144 people and it is trying to run in update, the grid appears to be correctly indexing and not moving askew from frame to frame, but the colors are inconsistent. BTW, thanks to Linda's article in Journal of J - Vol.4, No.1 for the RGB list to then pull my desired colors from in the DSEIR variable (Dead, Susceptible, Exposed, Infectious, Recovered): *RGB=: (#:i.8) { 0 255* *DSEIR =: (0 7 6 4 2 { RGB)* Here is my integration of the two sources of code to try and animate the outbreak per the article, and thanks!: *load 'viewmat'* *coinsert'jgl2'* *wd 'pc Covid-19-Sim closeok' NB. parent control (window) named 'w0'* *wd 'minwh 500 500; cc g0 isidraw;' NB. add an 'isidraw' child control named 'g0'* *wd 'pshow; pmove 40 510 0 0' NB. show the window at the given coordinates.* *wd 'sm focus term' NB. session manager: bring terminal to front* *wd 'psel Covid-19-Sim; ptop' NB. bring our window to front* *vmcc =: viewmatcc_jviewmat_ NB. viewmat to a child control* *step =: render @ update NB. each step, we'll call those two in sequence* *RGB=: (#:i.8) { 0 255* *DSEIR =: (0 7 6 4 2 { RGB)* *update =: verb define* * im =: 12 12 $ infect_display^:144 starting_pop* *)* *render =: verb define* * DSEIR vmcc im;'g0'* * glpaint''* *)* *sys_timer_z_ =: step_base_* *wd 'timer 600'* *ppl =: 144 NB. How many people are in our simulation?* *Beta =: 0.106271 NB. The rate at which susceptible people become exposed. RPH - dependent on R0 = 2.2 3/25/2020* *Sigma =: 0.066967 NB. The rate at which exposed people become infectious. RPH - (1-sigma)^10=0.5, 10 is incubation period.* *Gamma =: 0.056126 NB. The rate at which infectious people recover. RPH - adjusted to 12 days, so (1-Gamma)^12=0.5.* *Xi =: 0.02284 NB. The rate at which recovered people lose immunity and become susceptible. RPH - 30 days* * NB. is partially based upon man on Diamond Princess who presented symptoms around 30 days otherwise made up.* *R =: 2.2 NB. How many people will 1 person infect? RPH - based on latest CDC estimate 3/25/2020* *CFR =: 0.015 NB. Case Fatality Rate - RPH based upon 0.25% to 3% from CDC, so 1.5% is higher than average.* *D =: 0.0011619 NB. Death rate per day while symptomatic - RPH based upon 13 days to death as seen and per CDC.* *ClosenessStdDev =: 5 % 3* *ClosenessMean =: 1* *rand_norm =: 3 : '(2&o. 2p1 * ? y) * %: _2 * ^. ? y'* *closeness =: 4 %~ 2 %~ (+ |:) ClosenessMean + ClosenessStdDev * rand_norm (ppl,ppl) $ 0* *risk =: closeness - closeness * =i.ppl * *NB. risk =: (ppl,ppl)$0* *NB. 0 = Dead* *NB. 1 = Susceptible* *NB. 2 = Exposed* *NB. 3 = Infectious* *NB. 4 = Recovered* *starting_pop =: 2 , (ppl - 1) $ 1* *infect =: 3 : 0* * can_spread =. (1&< *. 4&>) y* * susceptible =. y = 1* * exposed =. y = 2* * infectious =. y = 3* * recovered =. y = 4* * infectiousness =. can_spread ,./ . * risk* * susceptible_to_exposed =. (Beta * susceptible) * (+/ can_spread) %~ +/ |: susceptible * infectiousness* * exposed_to_infectious =. Sigma * exposed* * infectious_to_recovered =. Gamma * infectious* * infectious_to_dead =. D * infectious* * recovered_to_susceptible =. Xi * recovered* * 1 (I.recovered_to_susceptible>?ppl$0)} 4 (I.infectious_to_recovered>?ppl$0)} 0 (I.infectious_to_dead>?ppl$0)} 3 (I.exposed_to_infectious>?ppl$0)} 2 (I.susceptible_to_exposed>?ppl$0)} y* *)* *infect_display =: 3 : 0* * out =. infect y* * smoutput out* * smoutput ('Susceptible';'Exposed';'Infectious';'Recovered';'Dead'),:(+/1=out);(+/2=out);(+/3=out);(+/4=out);(+/0=out)* * out* *)* ---------------------------------------------------------------------- For information about J forums see http://www.jsoftware.com/forums.htm
