Assign asymptomatic prevalence by age range, like probability of death Done following Chang et al., i.e. ~13% sym in children (<=18) and ~67% sym in adults (>18). We may have to add more references for that, and maybe even raise asym infectiousness to 30% like Chang et al. does
Add protection-compliance to determine what percentage of agents adopts personal protection
Reduce the risk of exposure from agents with personal protection, like for asymptomatics - this implies that PP needs to be extended to all breeds
Add an isolation-compliance-traced for traced contacts
Ensure naming convention is consistent (e.g. test-coverage-sym instead of sym-test-coverage)
Turn isoltion-threshold into isolation-sym-threhsold to specify measure
Introduce separate isolation duration for contacts vs symptomatics
Find better name for imported-infection (maybe unusual-infection or extraneous-infection)
Expand countdown names (iso-countdown to isolation-countdown etc.)
Add a neighbours-met-per-day slider and make it so that each agent only interacts with that fixed percentage of their neighbourhood every tick
Test possible ways to only record contacts from x days before
^ Figure out what to do with the contact history once active cases dip below the threshold
Test using an external file to set age ranges, their prevalence, and relative asymptomatic percentages and risk of death -> in progress, however this could be very difficult to do in a clean way (e.g. would have to read the number of lines in csv to figure out how many brackets there are etc.) and may be more trouble than it's worth
Move threshold calculation from setup-globals to modify-measures so that the threshold is updated as agents die (or could there be a way to only do this when agents die?)
Introduce an agentset called todays-contacts to slim up the process of counting and recording contacts, and exposing susceptibles. This would be a subset of the neighbours that an agent actually made contact with. The count of contacts would then just be the sum of agentset counts / 2 and would ensure that if an agent is only interacting with a percentage of its neighbourhood, that the agents chosen are consistent throughout a tick.
Find a name for the random duration of the period between incubation and development of symptoms
Change contact lists to agentsets
Instead of using a random p value and comparing it to the parameter value, use n-of where n is the number of agents calculated from the % compliance for that measure (e.g. lockdown or shielding) (doesn't support floats, left old system in place)
Explain to the user that the order of procedures in modify-measures is critical to ensure that lockdown and shielding don't release agents that are being isolated for other reasons (i.e. isolation of symptomatics and test and trace)
Make the isolate procedure less convoluted
Prevent the while loop of the normal distribution from looping infinitely
Ensure that symptomatics who finish isolation before recovering don't start a new course of isolation due to isolation of symptomatics
Make infectiousness of asymptomatics a global parameter
Make infectiousness of symptomatics with masks a global parameter (Not necessary, it's regulated by protection strength)
Change wording of extraneous to exogenous
Change reporters on infections and deaths to use the csv-data (change name to pop-data) to store and retrieve the counts
Implementation summary
Week 1
21/5
Added a num-contacts plot to keep track of the total number of contacts over time
Implemented initial SEIR model, adding exposed people in-between susceptibles and infecteds
22/5
Exposed people can now infect others
Removed people now lose immunity after 30-35 days
Updated contact counts to include exposeds
Infecteds are now removed either with probability p-remove or after a certain number of ticks
Infected people have a chance to become dead instead of removed
Added sliders to control the range of infection, removal and immunity countdowns
Temporarely removed the option for susceptibles to be aware of surrounding removeds
Changed cyan indicator for lockdown into black outline
Week 2
26/5
Found sources that indicated an initial probability of infection of 20%
27/5
Reintroduced option for susceptibles to be aware of surrounding removeds
Implemented log-normal distribution for incubation period, mean and stdev as global variables
Found sources that indicated an average probability of death of ~2%
Adjusted initial probability of infection to 30% to account for other sources
28/5
Implemented poisson distribution for loss of immunity countdown, mean to be varied in simulations
Implemented normal distribution for recovery countdown, with absolute result to prevent negative durations
Implemented imposed lockdown threshold with strictness level parameter, removed risk awareness and awareness neighbourhood systems
Removed all contact weighing
29/5
Created variables list
Implemented control measures to reduce probability of transmission triggered after first lockdown, with effectiveness parameter
Implemented an option to open the system, allowing susceptibles to be infected by outside sources depending on travel strictness when not into lockdown
Week 3
1/6
Implemented two separate start/end lockdown procedures to ensure stable percentages of quarantined population and help readability
Impemented three age ranges, 0-29, 30-59, and 60+, assigned to people based on demographics of the UK population
Implemented modified probability of death depending on age range, 0.6x for under 30 and 5.1x for over 60
2/6
Created github repo
Changed global variable probabilities from decimals to integers for ease of understanding
Separated recurring processed into dedicated procedures
3/6
Added a minimum value for duration of recovery equal to mean - stdev, unless that value is below 0, in which case the minimum is 1 day
4/6
Implemented pareto distribution for variation of initial contact neighbourhood size, i.e. z-contact-ini, with alpha = 2
Added two possible methods to ensure the minimum value for initial contact neighbourhood is equal to the value of z-contact-min
Changed naming convention of exposeds into latents, as they are infectious but not yet symptomatic
Created a separate countdown for infecteds that will die instead of recover, as the mean duration of infection is different between these two categories
Created asymptomatic breed, not yet integrated in the model
5/6
Implemented isolation for infected individuals, currently with isolation-strictness % of people isolating for iso-countdown-max days, and the rest isolating for half that time (applies after first lockdown)
Changed already-locked? variable to currently-locked? for clarity
Integrated asymptomatic infecteds in the model, who behave exactly like infecteds but with no isolation option
Week 4
8/6
Fixed the distribution of isolation duration for infected individuals
Set up a test experiment for headless running and distributed processing
Renamed infecteds to symptomatics and removeds to recovereds
Removed possibility of death for asymptomatic infecteds
Reduced infectiousness of asymptomatic infecteds by only counting 10% of the actual asymptomatic agents in the contact radius
9/6
Set up a test0 experiment for testing with Condor cluster
Started commenting model code
10/6
Set up tests for different world sizes
Finished commenting code
Various naming and procedure fixes
11/6
Decoupled the lockdown and control measures options, so that each can be switched on independently from the other
Added a number of contacts variable to report during tests
12/6
Added reporters for age of deads to use in tests
Edited tests to find an ideal world size between 100x100 and 500x500
Week 5
15/6
Changed initial-inf and lockdown-threshold from absolute values to population percentages to help scaling during world size tests
Changed initial infecteds from symptomatics to latents
Renamed modify-p-infect? as control-measures? for clarity
Decoupled isolation of symptomatics from lockdown, now isolation begins above a threshold and continues indefinitely. Note: fix occurence agents recover before the end of isolation period and continue isolating indefinitely (happens when lockdown off but isolation on)
Added separate thresholds for lockdown, control measures, and isolation of symptomatics
16/6
Created experiments for extremes validation
17/6
Fixed contacts number bug where a spike in contacts happened before second lockdown
Changed contact variable names from E for exposeds to L for latents
18/6
Cleaned up and updated R visualisation script
19/6
Implemented full test and trace, applied to the asymptomatic or pre-symptomatic infecteds with probability test-coverage, and to symptomatics with probability symp-test-coverage, with contacts isolating in the same fashion as the isolate-symptomatics? procedure
Week 6
23/6
Changed visualisation to use number of cases against threshold to determine whether lockdown is on instead of number of isolated agents
26/6
Implemented shelter in place system for agents in the 60+ range
Designed experiments for testing different combinations of control measures
Reintroduced count of locked agents as a reporter
Week 7
29/6
Renamed R script to base_vis
Streamlined R script options so only first line has to be changed
30/6
Created an R script to streamline visualisation of varying parameter experiments
1/7
Changed wording of shelter-at-risk mechanism to shield-at-risk to be more coherent with UK terminology
Added reporters of number of infecteds by age
2/7
Edited script for visualisation of varying parameter experiments to support two varying parameters by using a heatmap instead of a line chart
Changed the name of the mechanic describing the use of masks/social distancing/hand washing from control measures to personal protection
Week 8
6/7
Added code to create the classic breeds plot for vary-type experiments as well
7/7
Added caption line for number of deaths in the first year and total number of infections (where available)
8/7
Fixed wrong caption
10/7
Added a switch to turn off loss of immunity for runs not involving that mechanic
Fixed a bug where contacts would keep isolating indefinitely since the isolation check only kicked in above the threshold
Restored Exposed breed instead of Latent, made them non-infectious
Renamed shield-at-risk as shield-vulnerable
Changed breed progression so that E become A right before the end of their incubation period, then they can either remain A until recovery, or become I after a few ticks and progress from there
Week 9
Added a visualisation for the log of cases vs time to analyse the effect of varying p-inf-init
Fixed the random number generators to include floats, this will ensure that float parameters (especially those between 0 and 1) actually work instead of just effectively being 0
Week 10
Fixed a bug that did not exclude isolated susceptibles from travelling, now only susceptibles with z-contant higher than 0 can be infected by the travel mechanic
Added and fixed comments
Ensured all measures could operate independently of one another
Week 11 onwards: write-up and minor code fixes
Post-dissertation
11/9
Added profiler button to test speed of different procedures
Changed count-contacts system for a faster one that does not separate different types of contats, but simply counts all contacts per tick
Changed system regulating agent neighbourhood: instead of checking agents within n-radius every time it's necessary, each agent is now assigned an agentset of "neighbours" at setup based on their radius, which is interrogated when necessary. Instead of z-contact-init and z-contact, now the agent has a simple boolean that flags them as isolating or not
In modify-measures, number of cases is now only checked once at the beginning instead of at every measure
Optimised logical checks for lockdown and isolation of symptomatics to skip code where possible
Fixed shield-vulnerable mechanic, as it re-interrogated S agents over 60 at each tick instead of only when the threshold is first surpassed, leading to a change in which agents were shielding every tick. Now agents are only interrogated at first, and ALL over 60 are isolated, not just susceptibles
Ensured all isolation checks depend on "isolated?" flag and not agent shape anymore, to prepare for a version of the model that can toggle off visual elements to speed up headless simulations (not fully implemented yet)
Updated check-isolation to ensure 60+ agents who leave isolation for other reasons don't get released if shielding is in progress, not only if a lockdown is happening
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