wfmackey
commented
4 years ago Any thoughts on why @HughParsonage ?
Closed wfmackey closed 4 years ago
wfmackey
commented
4 years ago Any thoughts on why @HughParsonage ?
HughParsonage
commented
4 years ago It’s hard to see why it would be a problem with the core model itself, though it could be. It could also be an issue with the formation of workplaces (perhaps they are too small?)
Ideas for diagnosis: Turn off contact tracing and school lockdown triggers Bulk up the number of infected at the start
HughParsonage
commented
4 years ago One can also use the Source column in the Statuses list element of a returner = 0 to get a better idea. One issue is that supermarkets dominate infections but I can’t work out which assumption drives that
On Thu, 4 Jun 2020 at 11:50 am, HughParsonage notifications@github.com wrote:
It’s hard to see why it would be a problem with the core model itself, though it could be. It could also be an issue with the formation of workplaces (perhaps they are too small?)
Ideas for diagnosis: Turn off contact tracing and school lockdown triggers Bulk up the number of infected at the start
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/grattan/covid19.model.sa2/issues/58#issuecomment-638553029, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB54MDBCLOVX7ZPWIBVCJJDRU34WZANCNFSM4NSFXTBA .
wfmackey
commented
4 years ago It’s hard to see why it would be a problem with the core model itself, though it could be. It could also be an issue with the formation of workplaces (perhaps they are too small?)
as in the workplace sizes from ABS Businesses in Australia are small, so the upper limit from workplace_size_max is somewhat redundant? If so, that's really interesting.
wfmackey
commented
4 years ago Number of colleagues is median ~25, so q_workplace = 0.2 should still have a pretty strong effect:
library(covid19.model.sa2)
d <- simulate_sa2()
hist(d$Statuses$nColleagues)
Created on 2020-06-04 by the reprex package (v0.3.0)
wfmackey
commented
4 years ago One can also use the Source column in the Statuses list element of a returner = 0 to get a better idea. One issue is that supermarkets dominate infections but I can’t work out which assumption drives that
I'll look at this today.
HughParsonage
commented
4 years ago There are a couple of phenomena at play that are a bit counter to my intuition.
First most people work close to home and I’m guessing a plurality work in the same sa2, so if supermarkets do all the infecting within an sa2 then that soaks up a lot of the workplace’s potency
Second most workplaces are small, and while we think of policies around working from home as applying to big offices, perhaps most people’s exposure doesn’t decrease that much
wfmackey
commented
4 years ago Closing supermarkets doesn't change:
rebuild_runs <- TRUE
run_days <- 30
repeat_times <- 5
library(tidyverse)
options(dplyr.summarise.inform = FALSE)
library(purrr)
library(data.table)
#>
#> Attaching package: 'data.table'
#> The following objects are masked from 'package:dplyr':
#>
#> between, first, last
#> The following object is masked from 'package:purrr':
#>
#> transpose
library(covid19.model.sa2)
library(fst)
library(glue)
#>
#> Attaching package: 'glue'
#> The following object is masked from 'package:dplyr':
#>
#> collapse
library(lubridate)
#>
#> Attaching package: 'lubridate'
#> The following objects are masked from 'package:data.table':
#>
#> hour, isoweek, mday, minute, month, quarter, second, wday, week,
#> yday, year
#> The following objects are masked from 'package:base':
#>
#> date, intersect, setdiff, union
library(janitor)
#>
#> Attaching package: 'janitor'
#> The following objects are masked from 'package:stats':
#>
#> chisq.test, fisher.test
library(strayr)
repeat_simulation <- function(.name,
.rebuild = rebuild_runs,
.repeat = repeat_times,
.days = run_days,
EpiPars = set_epipars(),
PolicyPars = set_policypars(),
...) {
file_path <- glue("output/{.name}.fst")
if (!.rebuild & file.exists(file_path)) {
message("Run found; loading")
return(read_fst(file_path))
}
# is true otherwise, so proceed
# Show epi settings
message("Using epi parameters:")
print(EpiPars)
# Show policy settings
message("Using policy parameters:")
print(PolicyPars)
return_simulation <- function(x,
to_return = .to_return,
.PolicyPars = PolicyPars,
.EpiPars = EpiPars,
...) {
rep_each <- function(x, len) {
rep(x, each = len / length(x), length.out = len)
}
d <-
simulate_sa2(days_to_simulate = .days,
returner = 3,
PolicyPars = .PolicyPars,
EpiPars = .EpiPars,
...)
# Status
Status12 <- d[["Status12"]]
DT <- data.table(N = Status12)
DT[, day := rep_each(1:.days, .N)]
DT[, state := rep_each(1:9, .N), by = .(day)]
DT[, status := rep_each(-2:3, .N), by = .(day, state)]
DT[, isolated := rep_len(0:1, .N)]
DT[, runid := x]
# New infections
NewInfectionsByState <- d[["NewInfectionsByState"]]
DT2 <- data.table(new_infections = NewInfectionsByState)
DT2[, day := rep_each(1:.days, .N)]
DT2[, state := rep_each(1:9, .N), by = .(day)]
return(left_join(DT, DT2))
}
d <- map_dfr(1:.repeat, return_simulation) %>%
mutate(state_code = state,
state = strayr(state),
conditions = .name)
if (!dir.exists("output")) dir.create("output")
write_fst(d, file_path)
}
# Run
loose_open_workplaces <-
repeat_simulation("loose_open_workplaces",
EpiPars = set_epipars(
q_workplace = 0.2,
),
PolicyPars = set_policypars(
supermarkets_open = FALSE,
workplaces_open = 1,
workplace_size_max = 2000
)
)
#> Using epi parameters:
#> $CHECKED
#> [1] TRUE
#>
#> $a_household_rate
#> [1] 0.15
#>
#> $a_schools_rate
#> [1] 0.07
#>
#> $a_workplace_rate
#> [1] 0.07
#>
#> $illness_distribution
#> [1] 1
#>
#> $illness_mean
#> [1] 15
#>
#> $illness_sigma
#> [1] 1
#>
#> $incubation_distribution
#> [1] 1
#>
#> $incubation_mean
#> [1] 5
#>
#> $incubation_sigma
#> [1] 0.44
#>
#> $p_asympto
#> [1] 0.48
#>
#> $p_critical
#> [1] 0.02
#>
#> $p_death
#> [1] 0.01
#>
#> $p_visit_major_event
#> [1] 0.01923077
#>
#> $q_household
#> [1] 0.05
#>
#> $q_major_event
#> [1] 2e-04
#>
#> $q_places
#> [1] 0.002
#>
#> $q_school
#> [1] 0.0003333333
#>
#> $q_school_grade
#> [1] 0.002
#>
#> $q_supermarket
#> [1] 0.002
#>
#> $q_workplace
#> [1] 0.2
#>
#> $resistance_threshold
#> [1] 0.4
#> Using policy parameters:
#> $school_lockdown_triggers_exist
#> [1] TRUE
#>
#> $tests_by_state_was_null
#> [1] TRUE
#>
#> $yday_start
#> [1] 0
#>
#> $supermarkets_open
#> [1] FALSE
#>
#> $schools_open
#> [1] FALSE
#>
#> $only_Year12
#> [1] FALSE
#>
#> $school_days_per_wk
#> $school_days_per_wk$AUS
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$NSW
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$VIC
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$QLD
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$SA
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$WA
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$TAS
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$NT
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$ACT
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$OTH
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$week15combns
#> $school_days_per_wk$week15combns[[1]]
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 1 2 3 4 5
#>
#> $school_days_per_wk$week15combns[[2]]
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
#> [1,] 1 1 1 1 2 2 2 3 3 4
#> [2,] 2 3 4 5 3 4 5 4 5 5
#>
#> $school_days_per_wk$week15combns[[3]]
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
#> [1,] 1 1 1 1 1 1 2 2 2 3
#> [2,] 2 2 2 3 3 4 3 3 4 4
#> [3,] 3 4 5 4 5 5 4 5 5 5
#>
#> $school_days_per_wk$week15combns[[4]]
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 1 1 1 1 2
#> [2,] 2 2 2 3 3
#> [3,] 3 3 4 4 4
#> [4,] 4 5 5 5 5
#>
#> $school_days_per_wk$week15combns[[5]]
#> [,1]
#> [1,] 1
#> [2,] 2
#> [3,] 3
#> [4,] 4
#> [5,] 5
#>
#>
#> $school_days_per_wk$all_full_time
#> [1] TRUE
#>
#>
#> $do_contact_tracing
#> [1] TRUE
#>
#> $contact_tracing_days_before_test
#> [1] 0
#>
#> $contact_tracing_days_until_result
#> [1] 3
#>
#> $contact_tracing_only_sympto
#> [1] TRUE
#>
#> $contact_tracing_success
#> [1] 0.9
#>
#> $tests_by_state
#> [1] 30178 9962 12392 1897 2076 2420 906 220 305 0
#>
#> $max_persons_per_event
#> [1] 5
#>
#> $n_major_events_weekday
#> [1] 28
#>
#> $n_major_events_weekend
#> [1] 56
#>
#> $max_persons_per_supermarket
#> [1] 200
#>
#> $cafes_open
#> [1] TRUE
#>
#> $age_based_lockdown
#> [1] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#> [38] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#> [75] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#>
#> $workplaces_open
#> [1] 1
#>
#> $workplace_size_max
#> [1] 2000
#>
#> $workplace_size_beta
#> [1] 13
#>
#> $workplace_size_lmu
#> [1] -1
#>
#> $workplace_size_lsi
#> [1] -1
#>
#> $travel_outside_sa2
#> [1] FALSE
#>
#> $lockdown_triggers__schools
#> $lockdown_triggers__schools$AUS
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$NSW
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$VIC
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$QLD
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$SA
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$WA
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$TAS
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$NT
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$ACT
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$OTH
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#>
#> attr(,"original_call")
#> set_policypars(supermarkets_open = FALSE, workplaces_open = 1,
#> workplace_size_max = 2000)
#> Joining, by = c("day", "state")
#> Joining, by = c("day", "state")
#> Joining, by = c("day", "state")
#> Joining, by = c("day", "state")
#> Joining, by = c("day", "state")
loose_closed_workplaces <-
repeat_simulation("loose_closed_workplaces",
EpiPars = set_epipars(
q_workplace = 0.2,
),
PolicyPars = set_policypars(
supermarkets_open = FALSE,
workplaces_open = .5,
workplace_size_max = 5
)
)
#> Using epi parameters:
#> $CHECKED
#> [1] TRUE
#>
#> $a_household_rate
#> [1] 0.15
#>
#> $a_schools_rate
#> [1] 0.07
#>
#> $a_workplace_rate
#> [1] 0.07
#>
#> $illness_distribution
#> [1] 1
#>
#> $illness_mean
#> [1] 15
#>
#> $illness_sigma
#> [1] 1
#>
#> $incubation_distribution
#> [1] 1
#>
#> $incubation_mean
#> [1] 5
#>
#> $incubation_sigma
#> [1] 0.44
#>
#> $p_asympto
#> [1] 0.48
#>
#> $p_critical
#> [1] 0.02
#>
#> $p_death
#> [1] 0.01
#>
#> $p_visit_major_event
#> [1] 0.01923077
#>
#> $q_household
#> [1] 0.05
#>
#> $q_major_event
#> [1] 2e-04
#>
#> $q_places
#> [1] 0.002
#>
#> $q_school
#> [1] 0.0003333333
#>
#> $q_school_grade
#> [1] 0.002
#>
#> $q_supermarket
#> [1] 0.002
#>
#> $q_workplace
#> [1] 0.2
#>
#> $resistance_threshold
#> [1] 0.4
#> Using policy parameters:
#> $school_lockdown_triggers_exist
#> [1] TRUE
#>
#> $tests_by_state_was_null
#> [1] TRUE
#>
#> $yday_start
#> [1] 0
#>
#> $supermarkets_open
#> [1] FALSE
#>
#> $schools_open
#> [1] FALSE
#>
#> $only_Year12
#> [1] FALSE
#>
#> $school_days_per_wk
#> $school_days_per_wk$AUS
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$NSW
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$VIC
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$QLD
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$SA
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$WA
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$TAS
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$NT
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$ACT
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$OTH
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$week15combns
#> $school_days_per_wk$week15combns[[1]]
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 1 2 3 4 5
#>
#> $school_days_per_wk$week15combns[[2]]
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
#> [1,] 1 1 1 1 2 2 2 3 3 4
#> [2,] 2 3 4 5 3 4 5 4 5 5
#>
#> $school_days_per_wk$week15combns[[3]]
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
#> [1,] 1 1 1 1 1 1 2 2 2 3
#> [2,] 2 2 2 3 3 4 3 3 4 4
#> [3,] 3 4 5 4 5 5 4 5 5 5
#>
#> $school_days_per_wk$week15combns[[4]]
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 1 1 1 1 2
#> [2,] 2 2 2 3 3
#> [3,] 3 3 4 4 4
#> [4,] 4 5 5 5 5
#>
#> $school_days_per_wk$week15combns[[5]]
#> [,1]
#> [1,] 1
#> [2,] 2
#> [3,] 3
#> [4,] 4
#> [5,] 5
#>
#>
#> $school_days_per_wk$all_full_time
#> [1] TRUE
#>
#>
#> $do_contact_tracing
#> [1] TRUE
#>
#> $contact_tracing_days_before_test
#> [1] 0
#>
#> $contact_tracing_days_until_result
#> [1] 3
#>
#> $contact_tracing_only_sympto
#> [1] TRUE
#>
#> $contact_tracing_success
#> [1] 0.9
#>
#> $tests_by_state
#> [1] 30178 9962 12392 1897 2076 2420 906 220 305 0
#>
#> $max_persons_per_event
#> [1] 5
#>
#> $n_major_events_weekday
#> [1] 28
#>
#> $n_major_events_weekend
#> [1] 56
#>
#> $max_persons_per_supermarket
#> [1] 200
#>
#> $cafes_open
#> [1] TRUE
#>
#> $age_based_lockdown
#> [1] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#> [38] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#> [75] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#>
#> $workplaces_open
#> [1] 0.5
#>
#> $workplace_size_max
#> [1] 5
#>
#> $workplace_size_beta
#> [1] 13
#>
#> $workplace_size_lmu
#> [1] -1
#>
#> $workplace_size_lsi
#> [1] -1
#>
#> $travel_outside_sa2
#> [1] FALSE
#>
#> $lockdown_triggers__schools
#> $lockdown_triggers__schools$AUS
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$NSW
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$VIC
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$QLD
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$SA
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$WA
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$TAS
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$NT
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$ACT
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$OTH
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#>
#> attr(,"original_call")
#> set_policypars(supermarkets_open = FALSE, workplaces_open = 0.5,
#> workplace_size_max = 5)
#> Joining, by = c("day", "state")
#> Joining, by = c("day", "state")
#> Joining, by = c("day", "state")
#> Joining, by = c("day", "state")
#> Joining, by = c("day", "state")
tight_open_workplaces <-
repeat_simulation("tight_open_workplaces",
EpiPars = set_epipars(
q_workplace = 0.001
),
PolicyPars = set_policypars(
supermarkets_open = FALSE,
workplaces_open = 1,
workplace_size_max = 200
)
)
#> Using epi parameters:
#> $CHECKED
#> [1] TRUE
#>
#> $a_household_rate
#> [1] 0.15
#>
#> $a_schools_rate
#> [1] 0.07
#>
#> $a_workplace_rate
#> [1] 0.07
#>
#> $illness_distribution
#> [1] 1
#>
#> $illness_mean
#> [1] 15
#>
#> $illness_sigma
#> [1] 1
#>
#> $incubation_distribution
#> [1] 1
#>
#> $incubation_mean
#> [1] 5
#>
#> $incubation_sigma
#> [1] 0.44
#>
#> $p_asympto
#> [1] 0.48
#>
#> $p_critical
#> [1] 0.02
#>
#> $p_death
#> [1] 0.01
#>
#> $p_visit_major_event
#> [1] 0.01923077
#>
#> $q_household
#> [1] 0.05
#>
#> $q_major_event
#> [1] 2e-04
#>
#> $q_places
#> [1] 0.002
#>
#> $q_school
#> [1] 0.0003333333
#>
#> $q_school_grade
#> [1] 0.002
#>
#> $q_supermarket
#> [1] 0.002
#>
#> $q_workplace
#> [1] 0.001
#>
#> $resistance_threshold
#> [1] 0.4
#> Using policy parameters:
#> $school_lockdown_triggers_exist
#> [1] TRUE
#>
#> $tests_by_state_was_null
#> [1] TRUE
#>
#> $yday_start
#> [1] 0
#>
#> $supermarkets_open
#> [1] FALSE
#>
#> $schools_open
#> [1] FALSE
#>
#> $only_Year12
#> [1] FALSE
#>
#> $school_days_per_wk
#> $school_days_per_wk$AUS
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$NSW
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$VIC
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$QLD
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$SA
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$WA
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$TAS
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$NT
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$ACT
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$OTH
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$week15combns
#> $school_days_per_wk$week15combns[[1]]
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 1 2 3 4 5
#>
#> $school_days_per_wk$week15combns[[2]]
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
#> [1,] 1 1 1 1 2 2 2 3 3 4
#> [2,] 2 3 4 5 3 4 5 4 5 5
#>
#> $school_days_per_wk$week15combns[[3]]
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
#> [1,] 1 1 1 1 1 1 2 2 2 3
#> [2,] 2 2 2 3 3 4 3 3 4 4
#> [3,] 3 4 5 4 5 5 4 5 5 5
#>
#> $school_days_per_wk$week15combns[[4]]
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 1 1 1 1 2
#> [2,] 2 2 2 3 3
#> [3,] 3 3 4 4 4
#> [4,] 4 5 5 5 5
#>
#> $school_days_per_wk$week15combns[[5]]
#> [,1]
#> [1,] 1
#> [2,] 2
#> [3,] 3
#> [4,] 4
#> [5,] 5
#>
#>
#> $school_days_per_wk$all_full_time
#> [1] TRUE
#>
#>
#> $do_contact_tracing
#> [1] TRUE
#>
#> $contact_tracing_days_before_test
#> [1] 0
#>
#> $contact_tracing_days_until_result
#> [1] 3
#>
#> $contact_tracing_only_sympto
#> [1] TRUE
#>
#> $contact_tracing_success
#> [1] 0.9
#>
#> $tests_by_state
#> [1] 30178 9962 12392 1897 2076 2420 906 220 305 0
#>
#> $max_persons_per_event
#> [1] 5
#>
#> $n_major_events_weekday
#> [1] 28
#>
#> $n_major_events_weekend
#> [1] 56
#>
#> $max_persons_per_supermarket
#> [1] 200
#>
#> $cafes_open
#> [1] TRUE
#>
#> $age_based_lockdown
#> [1] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#> [38] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#> [75] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#>
#> $workplaces_open
#> [1] 1
#>
#> $workplace_size_max
#> [1] 200
#>
#> $workplace_size_beta
#> [1] 13
#>
#> $workplace_size_lmu
#> [1] -1
#>
#> $workplace_size_lsi
#> [1] -1
#>
#> $travel_outside_sa2
#> [1] FALSE
#>
#> $lockdown_triggers__schools
#> $lockdown_triggers__schools$AUS
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$NSW
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$VIC
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$QLD
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$SA
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$WA
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$TAS
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$NT
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$ACT
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$OTH
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#>
#> attr(,"original_call")
#> set_policypars(supermarkets_open = FALSE, workplaces_open = 1,
#> workplace_size_max = 200)
#> Joining, by = c("day", "state")
#> Joining, by = c("day", "state")
#> Joining, by = c("day", "state")
#> Joining, by = c("day", "state")
#> Joining, by = c("day", "state")
tight_closed_workplaces <-
repeat_simulation("tight_closed_workplaces",
EpiPars = set_epipars(
q_workplace = 0.001
),
PolicyPars = set_policypars(
supermarkets_open = FALSE,
workplaces_open = .5,
workplace_size_max = 5
)
)
#> Using epi parameters:
#> $CHECKED
#> [1] TRUE
#>
#> $a_household_rate
#> [1] 0.15
#>
#> $a_schools_rate
#> [1] 0.07
#>
#> $a_workplace_rate
#> [1] 0.07
#>
#> $illness_distribution
#> [1] 1
#>
#> $illness_mean
#> [1] 15
#>
#> $illness_sigma
#> [1] 1
#>
#> $incubation_distribution
#> [1] 1
#>
#> $incubation_mean
#> [1] 5
#>
#> $incubation_sigma
#> [1] 0.44
#>
#> $p_asympto
#> [1] 0.48
#>
#> $p_critical
#> [1] 0.02
#>
#> $p_death
#> [1] 0.01
#>
#> $p_visit_major_event
#> [1] 0.01923077
#>
#> $q_household
#> [1] 0.05
#>
#> $q_major_event
#> [1] 2e-04
#>
#> $q_places
#> [1] 0.002
#>
#> $q_school
#> [1] 0.0003333333
#>
#> $q_school_grade
#> [1] 0.002
#>
#> $q_supermarket
#> [1] 0.002
#>
#> $q_workplace
#> [1] 0.001
#>
#> $resistance_threshold
#> [1] 0.4
#> Using policy parameters:
#> $school_lockdown_triggers_exist
#> [1] TRUE
#>
#> $tests_by_state_was_null
#> [1] TRUE
#>
#> $yday_start
#> [1] 0
#>
#> $supermarkets_open
#> [1] FALSE
#>
#> $schools_open
#> [1] FALSE
#>
#> $only_Year12
#> [1] FALSE
#>
#> $school_days_per_wk
#> $school_days_per_wk$AUS
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$NSW
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$VIC
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$QLD
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$SA
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$WA
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$TAS
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$NT
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$ACT
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$OTH
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$week15combns
#> $school_days_per_wk$week15combns[[1]]
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 1 2 3 4 5
#>
#> $school_days_per_wk$week15combns[[2]]
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
#> [1,] 1 1 1 1 2 2 2 3 3 4
#> [2,] 2 3 4 5 3 4 5 4 5 5
#>
#> $school_days_per_wk$week15combns[[3]]
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
#> [1,] 1 1 1 1 1 1 2 2 2 3
#> [2,] 2 2 2 3 3 4 3 3 4 4
#> [3,] 3 4 5 4 5 5 4 5 5 5
#>
#> $school_days_per_wk$week15combns[[4]]
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 1 1 1 1 2
#> [2,] 2 2 2 3 3
#> [3,] 3 3 4 4 4
#> [4,] 4 5 5 5 5
#>
#> $school_days_per_wk$week15combns[[5]]
#> [,1]
#> [1,] 1
#> [2,] 2
#> [3,] 3
#> [4,] 4
#> [5,] 5
#>
#>
#> $school_days_per_wk$all_full_time
#> [1] TRUE
#>
#>
#> $do_contact_tracing
#> [1] TRUE
#>
#> $contact_tracing_days_before_test
#> [1] 0
#>
#> $contact_tracing_days_until_result
#> [1] 3
#>
#> $contact_tracing_only_sympto
#> [1] TRUE
#>
#> $contact_tracing_success
#> [1] 0.9
#>
#> $tests_by_state
#> [1] 30178 9962 12392 1897 2076 2420 906 220 305 0
#>
#> $max_persons_per_event
#> [1] 5
#>
#> $n_major_events_weekday
#> [1] 28
#>
#> $n_major_events_weekend
#> [1] 56
#>
#> $max_persons_per_supermarket
#> [1] 200
#>
#> $cafes_open
#> [1] TRUE
#>
#> $age_based_lockdown
#> [1] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#> [38] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#> [75] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#>
#> $workplaces_open
#> [1] 0.5
#>
#> $workplace_size_max
#> [1] 5
#>
#> $workplace_size_beta
#> [1] 13
#>
#> $workplace_size_lmu
#> [1] -1
#>
#> $workplace_size_lsi
#> [1] -1
#>
#> $travel_outside_sa2
#> [1] FALSE
#>
#> $lockdown_triggers__schools
#> $lockdown_triggers__schools$AUS
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$NSW
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$VIC
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$QLD
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$SA
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$WA
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$TAS
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$NT
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$ACT
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$OTH
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#>
#> attr(,"original_call")
#> set_policypars(supermarkets_open = FALSE, workplaces_open = 0.5,
#> workplace_size_max = 5)
#> Joining, by = c("day", "state")
#> Joining, by = c("day", "state")
#> Joining, by = c("day", "state")
#> Joining, by = c("day", "state")
#> Joining, by = c("day", "state")
workplaces <- bind_rows(loose_open_workplaces,
loose_closed_workplaces,
tight_open_workplaces,
tight_closed_workplaces)
# Plot
workplaces %>%
filter(status >= 1) %>%
group_by(conditions, runid, day) %>%
summarise(active = sum(N)) %>%
ggplot(aes(day, active, group = runid)) +
geom_line() +
facet_wrap(vars(conditions))
# End reprexCreated on 2020-06-04 by the reprex package (v0.3.0)
HughParsonage
commented
4 years ago That looks like just an absence of new cases
wfmackey
commented
4 years ago Closed everything:
rebuild_runs <- TRUE
run_days <- 30
repeat_times <- 5
library(tidyverse)
options(dplyr.summarise.inform = FALSE)
library(purrr)
library(data.table)
#>
#> Attaching package: 'data.table'
#> The following objects are masked from 'package:dplyr':
#>
#> between, first, last
#> The following object is masked from 'package:purrr':
#>
#> transpose
library(covid19.model.sa2)
library(fst)
library(glue)
#>
#> Attaching package: 'glue'
#> The following object is masked from 'package:dplyr':
#>
#> collapse
library(lubridate)
#>
#> Attaching package: 'lubridate'
#> The following objects are masked from 'package:data.table':
#>
#> hour, isoweek, mday, minute, month, quarter, second, wday, week,
#> yday, year
#> The following objects are masked from 'package:base':
#>
#> date, intersect, setdiff, union
library(janitor)
#>
#> Attaching package: 'janitor'
#> The following objects are masked from 'package:stats':
#>
#> chisq.test, fisher.test
library(strayr)
repeat_simulation <- function(.name,
.rebuild = rebuild_runs,
.repeat = repeat_times,
.days = run_days,
EpiPars = set_epipars(),
PolicyPars = set_policypars(),
...) {
file_path <- glue("output/{.name}.fst")
if (!.rebuild & file.exists(file_path)) {
message("Run found; loading")
return(read_fst(file_path))
}
# is true otherwise, so proceed
# Show epi settings
message("Using epi parameters:")
print(EpiPars)
# Show policy settings
message("Using policy parameters:")
print(PolicyPars)
return_simulation <- function(x,
to_return = .to_return,
.PolicyPars = PolicyPars,
.EpiPars = EpiPars,
...) {
rep_each <- function(x, len) {
rep(x, each = len / length(x), length.out = len)
}
d <-
simulate_sa2(days_to_simulate = .days,
returner = 3,
PolicyPars = .PolicyPars,
EpiPars = .EpiPars,
...)
# Status
Status12 <- d[["Status12"]]
DT <- data.table(N = Status12)
DT[, day := rep_each(1:.days, .N)]
DT[, state := rep_each(1:9, .N), by = .(day)]
DT[, status := rep_each(-2:3, .N), by = .(day, state)]
DT[, isolated := rep_len(0:1, .N)]
DT[, runid := x]
# New infections
NewInfectionsByState <- d[["NewInfectionsByState"]]
DT2 <- data.table(new_infections = NewInfectionsByState)
DT2[, day := rep_each(1:.days, .N)]
DT2[, state := rep_each(1:9, .N), by = .(day)]
return(left_join(DT, DT2))
}
d <- map_dfr(1:.repeat, return_simulation) %>%
mutate(state_code = state,
state = strayr(state),
conditions = .name)
if (!dir.exists("output")) dir.create("output")
write_fst(d, file_path)
}
# Run
loose_open_workplaces <-
repeat_simulation("loose_open_workplaces",
EpiPars = set_epipars(
q_workplace = 0.5,
a_workplace_rate = 1,
),
PolicyPars = set_policypars(
supermarkets_open = FALSE,
schools_open = FALSE,
do_contact_tracing = FALSE,
cafes_open = FALSE,
travel_outside_sa2 = FALSE,
workplaces_open = 1,
workplace_size_max = 2000
)
)
#> Using epi parameters:
#> $CHECKED
#> [1] TRUE
#>
#> $a_household_rate
#> [1] 0.15
#>
#> $a_schools_rate
#> [1] 0.07
#>
#> $a_workplace_rate
#> [1] 1
#>
#> $illness_distribution
#> [1] 1
#>
#> $illness_mean
#> [1] 15
#>
#> $illness_sigma
#> [1] 1
#>
#> $incubation_distribution
#> [1] 1
#>
#> $incubation_mean
#> [1] 5
#>
#> $incubation_sigma
#> [1] 0.44
#>
#> $p_asympto
#> [1] 0.48
#>
#> $p_critical
#> [1] 0.02
#>
#> $p_death
#> [1] 0.01
#>
#> $p_visit_major_event
#> [1] 0.01923077
#>
#> $q_household
#> [1] 0.05
#>
#> $q_major_event
#> [1] 2e-04
#>
#> $q_places
#> [1] 0.002
#>
#> $q_school
#> [1] 0.0003333333
#>
#> $q_school_grade
#> [1] 0.002
#>
#> $q_supermarket
#> [1] 0.002
#>
#> $q_workplace
#> [1] 0.5
#>
#> $resistance_threshold
#> [1] 0.4
#> Using policy parameters:
#> $school_lockdown_triggers_exist
#> [1] TRUE
#>
#> $tests_by_state_was_null
#> [1] TRUE
#>
#> $yday_start
#> [1] 0
#>
#> $supermarkets_open
#> [1] FALSE
#>
#> $schools_open
#> [1] FALSE
#>
#> $only_Year12
#> [1] FALSE
#>
#> $school_days_per_wk
#> $school_days_per_wk$AUS
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$NSW
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$VIC
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$QLD
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$SA
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$WA
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$TAS
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$NT
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$ACT
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$OTH
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$week15combns
#> $school_days_per_wk$week15combns[[1]]
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 1 2 3 4 5
#>
#> $school_days_per_wk$week15combns[[2]]
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
#> [1,] 1 1 1 1 2 2 2 3 3 4
#> [2,] 2 3 4 5 3 4 5 4 5 5
#>
#> $school_days_per_wk$week15combns[[3]]
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
#> [1,] 1 1 1 1 1 1 2 2 2 3
#> [2,] 2 2 2 3 3 4 3 3 4 4
#> [3,] 3 4 5 4 5 5 4 5 5 5
#>
#> $school_days_per_wk$week15combns[[4]]
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 1 1 1 1 2
#> [2,] 2 2 2 3 3
#> [3,] 3 3 4 4 4
#> [4,] 4 5 5 5 5
#>
#> $school_days_per_wk$week15combns[[5]]
#> [,1]
#> [1,] 1
#> [2,] 2
#> [3,] 3
#> [4,] 4
#> [5,] 5
#>
#>
#> $school_days_per_wk$all_full_time
#> [1] TRUE
#>
#>
#> $do_contact_tracing
#> [1] FALSE
#>
#> $contact_tracing_days_before_test
#> [1] 0
#>
#> $contact_tracing_days_until_result
#> [1] 3
#>
#> $contact_tracing_only_sympto
#> [1] TRUE
#>
#> $contact_tracing_success
#> [1] 0.9
#>
#> $tests_by_state
#> [1] 30178 9962 12392 1897 2076 2420 906 220 305 0
#>
#> $max_persons_per_event
#> [1] 5
#>
#> $n_major_events_weekday
#> [1] 28
#>
#> $n_major_events_weekend
#> [1] 56
#>
#> $max_persons_per_supermarket
#> [1] 200
#>
#> $cafes_open
#> [1] FALSE
#>
#> $age_based_lockdown
#> [1] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#> [38] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#> [75] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#>
#> $workplaces_open
#> [1] 1
#>
#> $workplace_size_max
#> [1] 2000
#>
#> $workplace_size_beta
#> [1] 13
#>
#> $workplace_size_lmu
#> [1] -1
#>
#> $workplace_size_lsi
#> [1] -1
#>
#> $travel_outside_sa2
#> [1] FALSE
#>
#> $lockdown_triggers__schools
#> $lockdown_triggers__schools$AUS
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$NSW
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$VIC
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$QLD
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$SA
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$WA
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$TAS
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$NT
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$ACT
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$OTH
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#>
#> attr(,"original_call")
#> set_policypars(supermarkets_open = FALSE, schools_open = FALSE,
#> do_contact_tracing = FALSE, cafes_open = FALSE, workplaces_open = 1,
#> workplace_size_max = 2000, travel_outside_sa2 = FALSE)
#> Joining, by = c("day", "state")
#> Joining, by = c("day", "state")
#> Joining, by = c("day", "state")
#> Joining, by = c("day", "state")
#> Joining, by = c("day", "state")
loose_closed_workplaces <-
repeat_simulation("loose_closed_workplaces",
EpiPars = set_epipars(
q_workplace = 0.5,
a_workplace_rate = 1,
),
PolicyPars = set_policypars(
supermarkets_open = FALSE,
schools_open = FALSE,
do_contact_tracing = FALSE,
cafes_open = FALSE,
travel_outside_sa2 = FALSE,
workplaces_open = .5,
workplace_size_max = 5
)
)
#> Using epi parameters:
#> $CHECKED
#> [1] TRUE
#>
#> $a_household_rate
#> [1] 0.15
#>
#> $a_schools_rate
#> [1] 0.07
#>
#> $a_workplace_rate
#> [1] 1
#>
#> $illness_distribution
#> [1] 1
#>
#> $illness_mean
#> [1] 15
#>
#> $illness_sigma
#> [1] 1
#>
#> $incubation_distribution
#> [1] 1
#>
#> $incubation_mean
#> [1] 5
#>
#> $incubation_sigma
#> [1] 0.44
#>
#> $p_asympto
#> [1] 0.48
#>
#> $p_critical
#> [1] 0.02
#>
#> $p_death
#> [1] 0.01
#>
#> $p_visit_major_event
#> [1] 0.01923077
#>
#> $q_household
#> [1] 0.05
#>
#> $q_major_event
#> [1] 2e-04
#>
#> $q_places
#> [1] 0.002
#>
#> $q_school
#> [1] 0.0003333333
#>
#> $q_school_grade
#> [1] 0.002
#>
#> $q_supermarket
#> [1] 0.002
#>
#> $q_workplace
#> [1] 0.5
#>
#> $resistance_threshold
#> [1] 0.4
#> Using policy parameters:
#> $school_lockdown_triggers_exist
#> [1] TRUE
#>
#> $tests_by_state_was_null
#> [1] TRUE
#>
#> $yday_start
#> [1] 0
#>
#> $supermarkets_open
#> [1] FALSE
#>
#> $schools_open
#> [1] FALSE
#>
#> $only_Year12
#> [1] FALSE
#>
#> $school_days_per_wk
#> $school_days_per_wk$AUS
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$NSW
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$VIC
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$QLD
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$SA
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$WA
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$TAS
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$NT
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$ACT
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$OTH
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$week15combns
#> $school_days_per_wk$week15combns[[1]]
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 1 2 3 4 5
#>
#> $school_days_per_wk$week15combns[[2]]
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
#> [1,] 1 1 1 1 2 2 2 3 3 4
#> [2,] 2 3 4 5 3 4 5 4 5 5
#>
#> $school_days_per_wk$week15combns[[3]]
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
#> [1,] 1 1 1 1 1 1 2 2 2 3
#> [2,] 2 2 2 3 3 4 3 3 4 4
#> [3,] 3 4 5 4 5 5 4 5 5 5
#>
#> $school_days_per_wk$week15combns[[4]]
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 1 1 1 1 2
#> [2,] 2 2 2 3 3
#> [3,] 3 3 4 4 4
#> [4,] 4 5 5 5 5
#>
#> $school_days_per_wk$week15combns[[5]]
#> [,1]
#> [1,] 1
#> [2,] 2
#> [3,] 3
#> [4,] 4
#> [5,] 5
#>
#>
#> $school_days_per_wk$all_full_time
#> [1] TRUE
#>
#>
#> $do_contact_tracing
#> [1] FALSE
#>
#> $contact_tracing_days_before_test
#> [1] 0
#>
#> $contact_tracing_days_until_result
#> [1] 3
#>
#> $contact_tracing_only_sympto
#> [1] TRUE
#>
#> $contact_tracing_success
#> [1] 0.9
#>
#> $tests_by_state
#> [1] 30178 9962 12392 1897 2076 2420 906 220 305 0
#>
#> $max_persons_per_event
#> [1] 5
#>
#> $n_major_events_weekday
#> [1] 28
#>
#> $n_major_events_weekend
#> [1] 56
#>
#> $max_persons_per_supermarket
#> [1] 200
#>
#> $cafes_open
#> [1] FALSE
#>
#> $age_based_lockdown
#> [1] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#> [38] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#> [75] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#>
#> $workplaces_open
#> [1] 0.5
#>
#> $workplace_size_max
#> [1] 5
#>
#> $workplace_size_beta
#> [1] 13
#>
#> $workplace_size_lmu
#> [1] -1
#>
#> $workplace_size_lsi
#> [1] -1
#>
#> $travel_outside_sa2
#> [1] FALSE
#>
#> $lockdown_triggers__schools
#> $lockdown_triggers__schools$AUS
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$NSW
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$VIC
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$QLD
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$SA
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$WA
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$TAS
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$NT
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$ACT
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$OTH
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#>
#> attr(,"original_call")
#> set_policypars(supermarkets_open = FALSE, schools_open = FALSE,
#> do_contact_tracing = FALSE, cafes_open = FALSE, workplaces_open = 0.5,
#> workplace_size_max = 5, travel_outside_sa2 = FALSE)
#> Joining, by = c("day", "state")
#> Joining, by = c("day", "state")
#> Joining, by = c("day", "state")
#> Joining, by = c("day", "state")
#> Joining, by = c("day", "state")
tight_open_workplaces <-
repeat_simulation("tight_open_workplaces",
EpiPars = set_epipars(
q_workplace = 0.001,
a_workplace_rate = 0.01,
),
PolicyPars = set_policypars(
supermarkets_open = FALSE,
schools_open = FALSE,
do_contact_tracing = FALSE,
cafes_open = FALSE,
travel_outside_sa2 = FALSE,
workplaces_open = 1,
workplace_size_max = 2000
)
)
#> Using epi parameters:
#> $CHECKED
#> [1] TRUE
#>
#> $a_household_rate
#> [1] 0.15
#>
#> $a_schools_rate
#> [1] 0.07
#>
#> $a_workplace_rate
#> [1] 0.01
#>
#> $illness_distribution
#> [1] 1
#>
#> $illness_mean
#> [1] 15
#>
#> $illness_sigma
#> [1] 1
#>
#> $incubation_distribution
#> [1] 1
#>
#> $incubation_mean
#> [1] 5
#>
#> $incubation_sigma
#> [1] 0.44
#>
#> $p_asympto
#> [1] 0.48
#>
#> $p_critical
#> [1] 0.02
#>
#> $p_death
#> [1] 0.01
#>
#> $p_visit_major_event
#> [1] 0.01923077
#>
#> $q_household
#> [1] 0.05
#>
#> $q_major_event
#> [1] 2e-04
#>
#> $q_places
#> [1] 0.002
#>
#> $q_school
#> [1] 0.0003333333
#>
#> $q_school_grade
#> [1] 0.002
#>
#> $q_supermarket
#> [1] 0.002
#>
#> $q_workplace
#> [1] 0.001
#>
#> $resistance_threshold
#> [1] 0.4
#> Using policy parameters:
#> $school_lockdown_triggers_exist
#> [1] TRUE
#>
#> $tests_by_state_was_null
#> [1] TRUE
#>
#> $yday_start
#> [1] 0
#>
#> $supermarkets_open
#> [1] FALSE
#>
#> $schools_open
#> [1] FALSE
#>
#> $only_Year12
#> [1] FALSE
#>
#> $school_days_per_wk
#> $school_days_per_wk$AUS
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$NSW
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$VIC
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$QLD
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$SA
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$WA
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$TAS
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$NT
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$ACT
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$OTH
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$week15combns
#> $school_days_per_wk$week15combns[[1]]
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 1 2 3 4 5
#>
#> $school_days_per_wk$week15combns[[2]]
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
#> [1,] 1 1 1 1 2 2 2 3 3 4
#> [2,] 2 3 4 5 3 4 5 4 5 5
#>
#> $school_days_per_wk$week15combns[[3]]
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
#> [1,] 1 1 1 1 1 1 2 2 2 3
#> [2,] 2 2 2 3 3 4 3 3 4 4
#> [3,] 3 4 5 4 5 5 4 5 5 5
#>
#> $school_days_per_wk$week15combns[[4]]
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 1 1 1 1 2
#> [2,] 2 2 2 3 3
#> [3,] 3 3 4 4 4
#> [4,] 4 5 5 5 5
#>
#> $school_days_per_wk$week15combns[[5]]
#> [,1]
#> [1,] 1
#> [2,] 2
#> [3,] 3
#> [4,] 4
#> [5,] 5
#>
#>
#> $school_days_per_wk$all_full_time
#> [1] TRUE
#>
#>
#> $do_contact_tracing
#> [1] FALSE
#>
#> $contact_tracing_days_before_test
#> [1] 0
#>
#> $contact_tracing_days_until_result
#> [1] 3
#>
#> $contact_tracing_only_sympto
#> [1] TRUE
#>
#> $contact_tracing_success
#> [1] 0.9
#>
#> $tests_by_state
#> [1] 30178 9962 12392 1897 2076 2420 906 220 305 0
#>
#> $max_persons_per_event
#> [1] 5
#>
#> $n_major_events_weekday
#> [1] 28
#>
#> $n_major_events_weekend
#> [1] 56
#>
#> $max_persons_per_supermarket
#> [1] 200
#>
#> $cafes_open
#> [1] FALSE
#>
#> $age_based_lockdown
#> [1] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#> [38] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#> [75] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#>
#> $workplaces_open
#> [1] 1
#>
#> $workplace_size_max
#> [1] 2000
#>
#> $workplace_size_beta
#> [1] 13
#>
#> $workplace_size_lmu
#> [1] -1
#>
#> $workplace_size_lsi
#> [1] -1
#>
#> $travel_outside_sa2
#> [1] FALSE
#>
#> $lockdown_triggers__schools
#> $lockdown_triggers__schools$AUS
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$NSW
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$VIC
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$QLD
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$SA
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$WA
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$TAS
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$NT
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$ACT
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$OTH
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#>
#> attr(,"original_call")
#> set_policypars(supermarkets_open = FALSE, schools_open = FALSE,
#> do_contact_tracing = FALSE, cafes_open = FALSE, workplaces_open = 1,
#> workplace_size_max = 2000, travel_outside_sa2 = FALSE)
#> Joining, by = c("day", "state")
#> Joining, by = c("day", "state")
#> Joining, by = c("day", "state")
#> Joining, by = c("day", "state")
#> Joining, by = c("day", "state")
tight_closed_workplaces <-
repeat_simulation("tight_closed_workplaces",
EpiPars = set_epipars(
q_workplace = 0.001,
a_workplace_rate = 0.01,
),
PolicyPars = set_policypars(
supermarkets_open = FALSE,
schools_open = FALSE,
do_contact_tracing = FALSE,
cafes_open = FALSE,
travel_outside_sa2 = FALSE,
workplaces_open = .5,
workplace_size_max = 5
)
)
#> Using epi parameters:
#> $CHECKED
#> [1] TRUE
#>
#> $a_household_rate
#> [1] 0.15
#>
#> $a_schools_rate
#> [1] 0.07
#>
#> $a_workplace_rate
#> [1] 0.01
#>
#> $illness_distribution
#> [1] 1
#>
#> $illness_mean
#> [1] 15
#>
#> $illness_sigma
#> [1] 1
#>
#> $incubation_distribution
#> [1] 1
#>
#> $incubation_mean
#> [1] 5
#>
#> $incubation_sigma
#> [1] 0.44
#>
#> $p_asympto
#> [1] 0.48
#>
#> $p_critical
#> [1] 0.02
#>
#> $p_death
#> [1] 0.01
#>
#> $p_visit_major_event
#> [1] 0.01923077
#>
#> $q_household
#> [1] 0.05
#>
#> $q_major_event
#> [1] 2e-04
#>
#> $q_places
#> [1] 0.002
#>
#> $q_school
#> [1] 0.0003333333
#>
#> $q_school_grade
#> [1] 0.002
#>
#> $q_supermarket
#> [1] 0.002
#>
#> $q_workplace
#> [1] 0.001
#>
#> $resistance_threshold
#> [1] 0.4
#> Using policy parameters:
#> $school_lockdown_triggers_exist
#> [1] TRUE
#>
#> $tests_by_state_was_null
#> [1] TRUE
#>
#> $yday_start
#> [1] 0
#>
#> $supermarkets_open
#> [1] FALSE
#>
#> $schools_open
#> [1] FALSE
#>
#> $only_Year12
#> [1] FALSE
#>
#> $school_days_per_wk
#> $school_days_per_wk$AUS
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$NSW
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$VIC
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$QLD
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$SA
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$WA
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$TAS
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$NT
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$ACT
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$OTH
#> [1] 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
#>
#> $school_days_per_wk$week15combns
#> $school_days_per_wk$week15combns[[1]]
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 1 2 3 4 5
#>
#> $school_days_per_wk$week15combns[[2]]
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
#> [1,] 1 1 1 1 2 2 2 3 3 4
#> [2,] 2 3 4 5 3 4 5 4 5 5
#>
#> $school_days_per_wk$week15combns[[3]]
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
#> [1,] 1 1 1 1 1 1 2 2 2 3
#> [2,] 2 2 2 3 3 4 3 3 4 4
#> [3,] 3 4 5 4 5 5 4 5 5 5
#>
#> $school_days_per_wk$week15combns[[4]]
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 1 1 1 1 2
#> [2,] 2 2 2 3 3
#> [3,] 3 3 4 4 4
#> [4,] 4 5 5 5 5
#>
#> $school_days_per_wk$week15combns[[5]]
#> [,1]
#> [1,] 1
#> [2,] 2
#> [3,] 3
#> [4,] 4
#> [5,] 5
#>
#>
#> $school_days_per_wk$all_full_time
#> [1] TRUE
#>
#>
#> $do_contact_tracing
#> [1] FALSE
#>
#> $contact_tracing_days_before_test
#> [1] 0
#>
#> $contact_tracing_days_until_result
#> [1] 3
#>
#> $contact_tracing_only_sympto
#> [1] TRUE
#>
#> $contact_tracing_success
#> [1] 0.9
#>
#> $tests_by_state
#> [1] 30178 9962 12392 1897 2076 2420 906 220 305 0
#>
#> $max_persons_per_event
#> [1] 5
#>
#> $n_major_events_weekday
#> [1] 28
#>
#> $n_major_events_weekend
#> [1] 56
#>
#> $max_persons_per_supermarket
#> [1] 200
#>
#> $cafes_open
#> [1] FALSE
#>
#> $age_based_lockdown
#> [1] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#> [38] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#> [75] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#>
#> $workplaces_open
#> [1] 0.5
#>
#> $workplace_size_max
#> [1] 5
#>
#> $workplace_size_beta
#> [1] 13
#>
#> $workplace_size_lmu
#> [1] -1
#>
#> $workplace_size_lsi
#> [1] -1
#>
#> $travel_outside_sa2
#> [1] FALSE
#>
#> $lockdown_triggers__schools
#> $lockdown_triggers__schools$AUS
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$NSW
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$VIC
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$QLD
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$SA
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$WA
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$TAS
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$NT
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$ACT
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#> $lockdown_triggers__schools$OTH
#> default_schools_with_any_critical
#> 1
#> default_schools_with_any_critical_duration_of_lockdown
#> 91
#> default_schools_with_infections
#> 4
#> default_schools_with_infections_duration_of_lockdown
#> 28
#> default_schools_with_infections_geq
#> 3
#> do_school_lockdown
#> 1
#>
#>
#> attr(,"original_call")
#> set_policypars(supermarkets_open = FALSE, schools_open = FALSE,
#> do_contact_tracing = FALSE, cafes_open = FALSE, workplaces_open = 0.5,
#> workplace_size_max = 5, travel_outside_sa2 = FALSE)
#> Joining, by = c("day", "state")
#> Joining, by = c("day", "state")
#> Joining, by = c("day", "state")
#> Joining, by = c("day", "state")
#> Joining, by = c("day", "state")
workplaces <- bind_rows(loose_open_workplaces,
loose_closed_workplaces,
tight_open_workplaces,
tight_closed_workplaces)
# Plot
workplaces %>%
filter(status >= 1) %>%
group_by(conditions, runid, day) %>%
summarise(active = sum(N)) %>%
ggplot(aes(day, active, group = runid)) +
geom_line() +
facet_wrap(vars(conditions))
# End reprexCreated on 2020-06-04 by the reprex package (v0.3.0)
wfmackey
commented
4 years ago Tweaking some other parameters does give expected results, so I think there is an issue with workplaces specifically:
rebuild_runs <- TRUE
run_days <- 30
repeat_times <- 5
library(tidyverse)
options(dplyr.summarise.inform = FALSE)
library(purrr)
library(data.table)
#>
#> Attaching package: 'data.table'
#> The following objects are masked from 'package:dplyr':
#>
#> between, first, last
#> The following object is masked from 'package:purrr':
#>
#> transpose
library(covid19.model.sa2)
library(fst)
library(glue)
#>
#> Attaching package: 'glue'
#> The following object is masked from 'package:dplyr':
#>
#> collapse
library(lubridate)
#>
#> Attaching package: 'lubridate'
#> The following objects are masked from 'package:data.table':
#>
#> hour, isoweek, mday, minute, month, quarter, second, wday, week,
#> yday, year
#> The following objects are masked from 'package:base':
#>
#> date, intersect, setdiff, union
library(janitor)
#>
#> Attaching package: 'janitor'
#> The following objects are masked from 'package:stats':
#>
#> chisq.test, fisher.test
library(strayr)
repeat_simulation <- function(.name,
.rebuild = rebuild_runs,
.repeat = repeat_times,
.days = run_days,
EpiPars = set_epipars(),
PolicyPars = set_policypars(),
...) {
file_path <- glue("output/{.name}.fst")
if (!.rebuild & file.exists(file_path)) {
message("Run found; loading")
return(read_fst(file_path))
}
# is true otherwise, so proceed
# Show epi settings
# message("Using epi parameters:")
# print(EpiPars)
# Show policy settings
# message("Using policy parameters:")
# print(PolicyPars)
return_simulation <- function(x,
to_return = .to_return,
.PolicyPars = PolicyPars,
.EpiPars = EpiPars,
...) {
rep_each <- function(x, len) {
rep(x, each = len / length(x), length.out = len)
}
d <-
simulate_sa2(days_to_simulate = .days,
returner = 3,
PolicyPars = .PolicyPars,
EpiPars = .EpiPars,
...)
# Status
Status12 <- d[["Status12"]]
DT <- data.table(N = Status12)
DT[, day := rep_each(1:.days, .N)]
DT[, state := rep_each(1:9, .N), by = .(day)]
DT[, status := rep_each(-2:3, .N), by = .(day, state)]
DT[, isolated := rep_len(0:1, .N)]
DT[, runid := x]
# New infections
NewInfectionsByState <- d[["NewInfectionsByState"]]
DT2 <- data.table(new_infections = NewInfectionsByState)
DT2[, day := rep_each(1:.days, .N)]
DT2[, state := rep_each(1:9, .N), by = .(day)]
return(left_join(DT, DT2))
}
d <- map_dfr(1:.repeat, return_simulation) %>%
mutate(state_code = state,
state = strayr(state),
conditions = .name)
if (!dir.exists("output")) dir.create("output")
write_fst(d, file_path)
}
# Run
loose_open_workplaces <-
repeat_simulation("loose_open_workplaces",
.first_day = "2020-03-31",
EpiPars = set_epipars(
q_workplace = 0.5,
a_workplace_rate = 1,
),
PolicyPars = set_policypars(
supermarkets_open = FALSE,
schools_open = FALSE,
do_contact_tracing = FALSE,
cafes_open = FALSE,
travel_outside_sa2 = FALSE,
workplaces_open = 1,
workplace_size_max = 2000
)
)
#> Joining, by = c("day", "state")
#> Joining, by = c("day", "state")
#> Joining, by = c("day", "state")
#> Joining, by = c("day", "state")
#> Joining, by = c("day", "state")
tight_closed_workplaces <-
repeat_simulation("tight_closed_workplaces",
.first_day = "2020-03-31",
EpiPars = set_epipars(
q_workplace = 0.001,
a_workplace_rate = 0.01,
),
PolicyPars = set_policypars(
supermarkets_open = FALSE,
schools_open = FALSE,
do_contact_tracing = FALSE,
cafes_open = FALSE,
travel_outside_sa2 = FALSE,
workplaces_open = .5,
workplace_size_max = 5
)
)
#> Joining, by = c("day", "state")
#> Joining, by = c("day", "state")
#> Joining, by = c("day", "state")
#> Joining, by = c("day", "state")
#> Joining, by = c("day", "state")
open_supermarkets <-
repeat_simulation("open_supermarkets",
.first_day = "2020-03-31",
EpiPars = set_epipars(
q_workplace = 0.001,
a_workplace_rate = 0.01,
q_supermarket = 0.1
),
PolicyPars = set_policypars(
supermarkets_open = TRUE,
schools_open = FALSE,
do_contact_tracing = FALSE,
cafes_open = FALSE,
travel_outside_sa2 = FALSE,
workplaces_open = .5,
workplace_size_max = 5
)
)
#> Joining, by = c("day", "state")
#> Joining, by = c("day", "state")
#> Joining, by = c("day", "state")
#> Joining, by = c("day", "state")
#> Joining, by = c("day", "state")
workplaces <- bind_rows(loose_open_workplaces,
tight_closed_workplaces,
open_supermarkets)
# Plot
workplaces %>%
filter(status >= 1) %>%
group_by(conditions, runid, day) %>%
summarise(active = sum(N)) %>%
ggplot(aes(day, active, group = runid)) +
geom_line() +
facet_wrap(vars(conditions))
# End reprexCreated on 2020-06-04 by the reprex package (v0.3.0)
HughParsonage
commented
4 years ago Nope you're right. int to double roundtrip conversion during a refactor.
In the model's current form, workplace settings --
q_workplace,workplaces_open,workplace_size_max-- make no observable difference in outcomes, even when pushed to extremes.Created on 2020-06-04 by the reprex package (v0.3.0)