--- tags: Debug --- # Debugging HeuristicV1 Revision 1 ### Description The goal of this work is to debug the simulator by viewing chains of infections and information about each person in the chain. We use the Heuristic because it has many rules which will allow us to identify (and reason about) issues where risk / recommendation level do not align with the epidemiology or heuristic algorithm. Please refer to this googledoc for a high-level description of the heuristic (v1): https://docs.google.com/document/d/1_J1jcn5b0h7h5_bzjH-qx4LerWNFRJOzBI2vCm1n3AA/edit?usp=sharing Please refer to [the wiki](https://hackmd.io/N-g61aZLQaSB_cz5SttM6Q) for information on how to read the plots. ### Infection Chains ![](https://i.imgur.com/gJ0pG0c.png) Observations: - Humans 605, 947, and 29 all live together. - Humans 470 and 714 live together. - Therefore, the primary infection that we wish we could have stopped was human 605. Questions: - We should show severity of most severe symptom, because this is what drives the heuristic setting of risk/rec level. - why is h470 sending 62 update messages to the next guy? weird. - Q: shouldn't H470 have gone to R=7 earlier than March 11th, since he had symptoms since March 7th? - Q: Person 714 works from home, and human 605 works from a workplace. How did human 714 infect 605? - Q: Why is human 470 green on 03-09 while human 605 is yellow? - A: I think it's because human 470 didn't report their symptoms while 605 did. - The next day (03-10) human 470 was _still_ green. They reported symptoms and were still green, and were tested negative... maybe the negative test over-ruled the positive? - Why is Human 470 only Orange on March 12th even though they got a positive test result? - why does it take 6 days for the app to kick in (when intervention day is 5) Changes: - need to show the severity of the most severe symptoms - need to show the observed symptoms, not true ones ![](https://i.imgur.com/VUEvVlo.png) Questions: - why is h503 getting infected ONE DAY after h404 got infected? it seems too quick. At least 2 days of incubation, no? - why is h404 doing a test (with + answer) for so many consecutive days??? - maybe try INTERVENTION_DAY=0 or 1 ### Baseball Cards ![](https://i.imgur.com/82TH2Dd.png) ![](https://i.imgur.com/AC4Gfqb.png) ![](https://i.imgur.com/35WyyVO.png) ![](https://i.imgur.com/LLKiKcz.png) ![](https://i.imgur.com/k4mZ3MO.png) ![](https://i.imgur.com/a0V8TEX.png) ![](https://i.imgur.com/YPMJO0w.png) ![](https://i.imgur.com/z3umGnP.png) ![](https://i.imgur.com/V49q85v.png) ### Simulation Logs ######## DEMOGRAPHICS ######### age distribution 0 count 1000.000000 mean 42.025000 std 23.473419 min 1.000000 25% 23.000000 50% 41.000000 75% 60.000000 max 101.000000 house age distribution 0 count 386.000000 mean 41.544344 std 15.098008 min 16.000000 25% 30.500000 50% 39.250000 75% 50.729167 max 101.000000 house size distribution 0 count 386.000000 mean 2.528497 std 1.214829 min 1.000000 25% 2.000000 50% 2.000000 75% 3.000000 max 5.000000 Fraction of asymptomatic 0.229 ######## COVID PROPERTIES ######### Avg. incubation days 5.48 Avg. recovery days 18.99 Avg. infectiousnes onset days 3.27 ######## COVID SPREAD ######### human-human transmissions 129 environment-human transmissions 59 environmental transmission ratio 0.457 Ro 1.7628571428571427 Generation times 6.016636904761904 Cumulative Incidence [0.0, 0.0010050251256281408, 0.004024144869215292, 0.00101010101010101, 0.011122345803842264, 0.0010224948875255625, 0.008188331627430911, 0.0041279669762641896, 0.0051813471502590676, 0.004166666666666667, 0.005230125523012552, 0.006309148264984227, 0.007407407407407408, 0.0031982942430703624, 0.0021390374331550803, 0.0053590568060021436, 0.005387931034482759, 0.0021668472372697724, 0.0054288816503800215, 0.002183406113537118, 0.006564551422319475, 0.006607929515418502, 0.0022172949002217295, 0.0033333333333333335, 0.006688963210702341, 0.003367003367003367, 0.0022522522522522522, 0.010158013544018058, 0.009122006841505131] R : [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2.0, 2.0, 1.5, 1.6, 1.7142857142857142, 2.0, 1.9090909090909092, 1.5714285714285714, 1.3333333333333333, 1.2272727272727273, 1.0, 1.0344827586206897, 1.0909090909090908, 0.9473684210526315] ******** R0 ********* Asymptomatic R0 1.2 Presymptomatic R0 1.6153846153846154 Symptomatic R0 1.2222222222222223 ******** Transmission Ratios ********* % asymptomatic transmission 4.65% % presymptomatic transmission 32.56% % symptomatic transmission 17.05% ******** R0 LOCATIONS ********* household R0 1.4827586206896552 workplace R0 1.4545454545454546 school R0 1.4285714285714286 hospital R0 1.0 ######## SYMPTOMS ######### P(symptoms = x | covid patient), where x is: sneezing : 0.3467 nausea_vomiting : 0.3467 heavy_trouble_breathing : 0.3333 moderate_trouble_breathing : 0.2533 runny_nose : 0.2133 confused : 0.1333 lost_consciousness : 0.0267 extremely-severe : 0.0267 unusual : 0.0267 severe_chest_pain : 0.0133 P(symptoms = x | human had some sickness e.g. cold, flu, allergies, covid), where x is: sneezing : 0.1769 nausea_vomiting : 0.1769 heavy_trouble_breathing : 0.1701 moderate_trouble_breathing : 0.1293 runny_nose : 0.1088 confused : 0.0680 lost_consciousness : 0.0136 extremely-severe : 0.0136 unusual : 0.0136 severe_chest_pain : 0.0068 ######## MOBILITY ######### Day - Mon #avg: 9.30375 %:16.22 Tue #avg: 9.36975 %:16.33 Wed #avg: 7.49875 %:13.07 Thurs #avg: 6.87175 %:11.98 Fri #avg: 8.9152 %:15.54 Sat #avg: 7.786 %:13.57 Sun #avg: 7.62025 %:13.28 Average Daily Contacts (1, 10) #avg: 24.142810670136623 %:15.57 (11, 20) #avg: 21.472100313479615 %:14.37 (21, 30) #avg: 13.139959432048684 %:10.87 (31, 40) #avg: 13.364817591204398 %:11.22 (41, 50) #avg: 13.49030172413793 %:10.50 (51, 60) #avg: 13.63423645320197 %:11.61 (61, 70) #avg: 13.26044294925708 %: 9.92 (71, 80) #avg: 16.834845735027226 %: 7.78 (81, 101) #avg: 31.19326383319968 %: 8.16 ######## COVID Testing Statistics ######### Proportion infected : 13.400% Positivity rate: 26.160% Total Tests: 237 Total positive tests: 62 Total negative tests: 175 Maximum tests given to an individual: 5 Proportion of population tested until end: 23.700% Proportion of population tested daily Avg: 0.741% Proportion of population tested daily Max: 1.100% Proportion of population tested daily Min: 0.000% P(tested | symptoms = x), where x is extremely-severe 0.000 severe 0.607 moderate 1.000 mild 0.558 P(symptoms = x | tested), where x is: sneezing : 0.1097 headache : 0.1055 moderate_trouble_breathing : 0.0759 heavy_trouble_breathing : 0.0717 severe : 0.0717 chills : 0.0422 light_trouble_breathing : 0.0380 unusual : 0.0127 lost_consciousness : 0.0084 confused : 0.0042 ######## Effective Contacts & % infected ######### Eff. contacts: 5.853 % infected: 12.900% ### Analysis - Maximum tests given to an individual: 5 is too high ### Todo - run with event logging - run experiment which has intervention_day start with 0 -