run_explicit_SEEIR_model: Run the explicit SEEIR model
In mrc-ide/squire: SEIR transmission model of COVID-19
run_explicit_SEEIR_model R Documentation
Run the explicit SEEIR model
Description
Run the explicit SEEIR model
Usage
run_explicit_SEEIR_model(
country = NULL,
population = NULL,
tt_contact_matrix = 0,
contact_matrix_set = NULL,
R0 = 3,
tt_R0 = 0,
beta_set = NULL,
time_period = 365,
dt = 0.1,
day_return = FALSE,
replicates = 10,
init = NULL,
seed = stats::runif(1, 0, 1e+08),
prob_hosp = NULL,
prob_severe = NULL,
prob_non_severe_death_treatment = NULL,
prob_non_severe_death_no_treatment = NULL,
prob_severe_death_treatment = NULL,
prob_severe_death_no_treatment = NULL,
p_dist = probs$p_dist,
walker_params = FALSE,
dur_E = NULL,
dur_IMild = NULL,
dur_ICase = NULL,
dur_get_ox_survive = NULL,
tt_dur_get_ox_survive = 0,
dur_get_ox_die = NULL,
tt_dur_get_ox_die = 0,
dur_not_get_ox_survive = NULL,
dur_not_get_ox_die = NULL,
dur_get_mv_survive = NULL,
tt_dur_get_mv_survive = 0,
dur_get_mv_die = NULL,
tt_dur_get_mv_die = 0,
dur_not_get_mv_survive = NULL,
dur_not_get_mv_die = NULL,
dur_rec = NULL,
dur_R = NULL,
hosp_bed_capacity = NULL,
ICU_bed_capacity = NULL,
tt_hosp_beds = 0,
tt_ICU_beds = 0,
seeding_cases = NULL
)
Arguments
country
Character for country beign simulated. WIll be used to
generate population and contact_matrix_set if
unprovided. Either country or population and
contact_matrix_set must be provided.
population
Population vector (for each age group). Default = NULL,
which will cause population to be sourced from country
tt_contact_matrix
Time change points for matrix change. Default = 0
contact_matrix_set
Contact matrices used in simulation. Default =
NULL, which will generate this based on the country.
R0
Basic Reproduction Number. Default = 3
tt_R0
Change time points for R0. Default = 0
beta_set
Alternative parameterisation via beta rather than R0.
Default = NULL, which causes beta to be estimated from R0
time_period
Length of simulation. Default = 365
dt
Time Step. Default = 0.1
day_return
Logical, do we want to return outut after each day rather
than each dt. Default = FALSE
replicates
Number of replicates
init
Data.frame of initial conditions. Default = NULL
seed
Random Number Seed.
prob_hosp
Probability of hospitalisation by age.
Default, NULL, will use
c(0.000840764, 0.001182411, 0.001662887, 0.002338607,
0.003288907, 0.004625365, 0.006504897, 0.009148183, 0.012865577,
0.018093546, 0.025445917, 0.035785947, 0.050327683, 0.0707785,
0.099539573, 0.1399878, 0.233470395)
prob_severe
Probability of developing severe symptoms by age.
Default, NULL, will use
c(0.000840764, 0.001182411, 0.001662887, 0.002338607,
0.003288907, 0.004625365, 0.006504897, 0.009148183, 0.012865577,
0.018093546, 0.025445917, 0.035785947, 0.050327683, 0.0707785,
0.099539573, 0.1399878, 0.233470395)
prob_non_severe_death_treatment
Probability of death from non severe
treated infection. Default, NULL, will use
c(0.181354223, 0.181354223, 0.181354223, 0.137454906,
0.121938236, 0.122775613, 0.136057441, 0.160922182, 0.196987378,
0.242011054, 0.289368845, 0.326537862, 0.337229819, 0.309082553,
0.243794865, 0.160480254, 0.057084366)
prob_non_severe_death_no_treatment
Probability of death in non severe
hospital inections that aren't treated. Default, NULL, will use
rep(0.5, 17)
prob_severe_death_treatment
Probability of death from severe infection
that is treated. Default, NULL, will use
c(0.226668959, 0.252420241, 0.281097009, 0.413005389,
0.518451493, 0.573413613, 0.576222065, 0.54253573, 0.493557696,
0.447376527, 0.416666608, 0.411186639, 0.443382594, 0.538718871,
0.570434076, 0.643352843, 0.992620047)
prob_severe_death_no_treatment
Probability of death from severe infection
that is not treated. Default, NULL, will use
rep(0.95, 17)
p_dist
Preferentiality of age group receiving treatment relative to
other age groups when demand exceeds healthcare capacity.
walker_params
Boolean for using parameters in Walker et al. Default = FALSE,
which uses parameter update as of November 2020. For full information see
parameters vignette
dur_E
Mean duration of incubation period (days). Default = 4.6
dur_IMild
Mean duration of mild infection (days). Default = 2.1
dur_ICase
Mean duration from symptom onset to hospitil admission (days).
Default = 4.5
dur_get_ox_survive
Mean duration of oxygen given survive. Default = 9
tt_dur_get_ox_survive
Times at which dur_get_ox_survive changes
(Default = 0 = doesn't change)
dur_get_ox_die
Mean duration of oxygen given death. Default = 9
tt_dur_get_ox_die
Times at which dur_get_ox_die changes
(Default = 0 = doesn't change)
dur_not_get_ox_survive
Mean duration without oxygen given survive.
Default = 4.5
dur_not_get_ox_die
Mean duration without oxygen given death.
Default = 4.5
dur_get_mv_survive
Mean duration of ventilation given survive.
Default = 14.8
tt_dur_get_mv_survive
Times at which dur_get_mv_survive changes
(Default = 0 = doesn't change)
dur_get_mv_die
Mean duration of ventilation given death. Default = 11.1
tt_dur_get_mv_die
Times at which dur_get_mv_die changes
(Default = 0 = doesn't change)
dur_not_get_mv_survive
Mean duration without ventilation given
survive. Default = 7.4
dur_not_get_mv_die
Mean duration without ventilation given
death. Default = 1
dur_rec
Duration of recovery after coming off ventilation. Default = 3
dur_R
Mean duration of immunity (days). Default = Inf
hosp_bed_capacity
General bed capacity. Can be single number or vector if capacity time-varies.
ICU_bed_capacity
ICU bed capacity. Can be single number or vector if capacity time-varies.
tt_hosp_beds
Times at which hospital bed capacity changes (Default = 0 = doesn't change)
tt_ICU_beds
Times at which ICU bed capacity changes (Default = 0 = doesn't change)
seeding_cases
Initial number of cases seeding the epidemic
Details
All durations are in days.
Value
Simulation output
Parameter Updates
Parameters detailing the age-dependent probability of disease
severity and durations of hospital durations have been updated in v0.5.0
of squire to reflect the changing understanding of COVID-19 transmission.
Parameter arguments are by default equal to NULL, which
causes the new updated parameters specified in default_probs
and default_durations to be used. If any provided parameters
are not NULL, these will be used. In order to ease previous fits and
code, function argument walker_params will use the parameters described
in Walker et al. Science. 2020
which can be viewed within the function parse_country_severity
Examples
## Not run:
pop <- get_population("Afghanistan")
m1 <- run_explicit_SEEIR_model(R0 = 2,
population = pop$n, dt = 1,
contact_matrix_set=contact_matrices[[1]])
## End(Not run)
mrc-ide/squire documentation built on Sept. 10, 2022, 1:11 a.m.
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| run_explicit_SEEIR_model | R Documentation |
Run the explicit SEEIR model
Description
Run the explicit SEEIR model
Usage
run_explicit_SEEIR_model( country = NULL, population = NULL, tt_contact_matrix = 0, contact_matrix_set = NULL, R0 = 3, tt_R0 = 0, beta_set = NULL, time_period = 365, dt = 0.1, day_return = FALSE, replicates = 10, init = NULL, seed = stats::runif(1, 0, 1e+08), prob_hosp = NULL, prob_severe = NULL, prob_non_severe_death_treatment = NULL, prob_non_severe_death_no_treatment = NULL, prob_severe_death_treatment = NULL, prob_severe_death_no_treatment = NULL, p_dist = probs$p_dist, walker_params = FALSE, dur_E = NULL, dur_IMild = NULL, dur_ICase = NULL, dur_get_ox_survive = NULL, tt_dur_get_ox_survive = 0, dur_get_ox_die = NULL, tt_dur_get_ox_die = 0, dur_not_get_ox_survive = NULL, dur_not_get_ox_die = NULL, dur_get_mv_survive = NULL, tt_dur_get_mv_survive = 0, dur_get_mv_die = NULL, tt_dur_get_mv_die = 0, dur_not_get_mv_survive = NULL, dur_not_get_mv_die = NULL, dur_rec = NULL, dur_R = NULL, hosp_bed_capacity = NULL, ICU_bed_capacity = NULL, tt_hosp_beds = 0, tt_ICU_beds = 0, seeding_cases = NULL )
Arguments
country |
Character for country beign simulated. WIll be used to
generate |
population |
Population vector (for each age group). Default = NULL,
which will cause population to be sourced from |
tt_contact_matrix |
Time change points for matrix change. Default = 0 |
contact_matrix_set |
Contact matrices used in simulation. Default =
NULL, which will generate this based on the |
R0 |
Basic Reproduction Number. Default = 3 |
tt_R0 |
Change time points for R0. Default = 0 |
beta_set |
Alternative parameterisation via beta rather than R0. Default = NULL, which causes beta to be estimated from R0 |
time_period |
Length of simulation. Default = 365 |
dt |
Time Step. Default = 0.1 |
day_return |
Logical, do we want to return outut after each day rather than each dt. Default = FALSE |
replicates |
Number of replicates |
init |
Data.frame of initial conditions. Default = NULL |
seed |
Random Number Seed. |
prob_hosp |
Probability of hospitalisation by age.
Default, NULL, will use
|
prob_severe |
Probability of developing severe symptoms by age.
Default, NULL, will use
|
prob_non_severe_death_treatment |
Probability of death from non severe
treated infection. Default, NULL, will use
|
prob_non_severe_death_no_treatment |
Probability of death in non severe
hospital inections that aren't treated. Default, NULL, will use
|
prob_severe_death_treatment |
Probability of death from severe infection
that is treated. Default, NULL, will use
|
prob_severe_death_no_treatment |
Probability of death from severe infection
that is not treated. Default, NULL, will use
|
p_dist |
Preferentiality of age group receiving treatment relative to other age groups when demand exceeds healthcare capacity. |
walker_params |
Boolean for using parameters in Walker et al. Default = FALSE, which uses parameter update as of November 2020. For full information see parameters vignette |
dur_E |
Mean duration of incubation period (days). Default = 4.6 |
dur_IMild |
Mean duration of mild infection (days). Default = 2.1 |
dur_ICase |
Mean duration from symptom onset to hospitil admission (days). Default = 4.5 |
dur_get_ox_survive |
Mean duration of oxygen given survive. Default = 9 |
tt_dur_get_ox_survive |
Times at which dur_get_ox_survive changes (Default = 0 = doesn't change) |
dur_get_ox_die |
Mean duration of oxygen given death. Default = 9 |
tt_dur_get_ox_die |
Times at which dur_get_ox_die changes (Default = 0 = doesn't change) |
dur_not_get_ox_survive |
Mean duration without oxygen given survive. Default = 4.5 |
dur_not_get_ox_die |
Mean duration without oxygen given death. Default = 4.5 |
dur_get_mv_survive |
Mean duration of ventilation given survive. Default = 14.8 |
tt_dur_get_mv_survive |
Times at which dur_get_mv_survive changes (Default = 0 = doesn't change) |
dur_get_mv_die |
Mean duration of ventilation given death. Default = 11.1 |
tt_dur_get_mv_die |
Times at which dur_get_mv_die changes (Default = 0 = doesn't change) |
dur_not_get_mv_survive |
Mean duration without ventilation given survive. Default = 7.4 |
dur_not_get_mv_die |
Mean duration without ventilation given death. Default = 1 |
dur_rec |
Duration of recovery after coming off ventilation. Default = 3 |
dur_R |
Mean duration of immunity (days). Default = Inf |
hosp_bed_capacity |
General bed capacity. Can be single number or vector if capacity time-varies. |
ICU_bed_capacity |
ICU bed capacity. Can be single number or vector if capacity time-varies. |
tt_hosp_beds |
Times at which hospital bed capacity changes (Default = 0 = doesn't change) |
tt_ICU_beds |
Times at which ICU bed capacity changes (Default = 0 = doesn't change) |
seeding_cases |
Initial number of cases seeding the epidemic |
Details
All durations are in days.
Value
Simulation output
Parameter Updates
Parameters detailing the age-dependent probability of disease
severity and durations of hospital durations have been updated in v0.5.0
of squire to reflect the changing understanding of COVID-19 transmission.
Parameter arguments are by default equal to NULL, which
causes the new updated parameters specified in default_probs
and default_durations to be used. If any provided parameters
are not NULL, these will be used. In order to ease previous fits and
code, function argument walker_params will use the parameters described
in Walker et al. Science. 2020
which can be viewed within the function parse_country_severity
Examples
## Not run:
pop <- get_population("Afghanistan")
m1 <- run_explicit_SEEIR_model(R0 = 2,
population = pop$n, dt = 1,
contact_matrix_set=contact_matrices[[1]])
## End(Not run)
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