run_explicit_SEEIR_model | R Documentation |
Run the explicit SEEIR model
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 )
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 |
All durations are in days.
Simulation output
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
## 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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