param_seiqhrf.RdSets the epidemic parameters for stochastic individual contact
models simulated with seiqhrf.
All parameters can either be a scalar or a vector of the length of the number of time steps to be simulated.
param_seiqhrf( inf.prob.e = 0.02, act.rate.e = 10, inf.prob.i = 0.05, act.rate.i = 10, inf.prob.q = 0.02, act.rate.q = 2.5, prog.rate = 1/10, quar.rate = 1/30, hosp.rate = 1/100, disch.rate = 1/15, rec.rate = 0.071, arec.rate = 0.05, prog.dist.scale = 5, prog.dist.shape = 1.5, quar.dist.scale = 1, quar.dist.shape = 1, hosp.dist.scale = 1, hosp.dist.shape = 1, disch.dist.scale = 1, disch.dist.shape = 1, rec.dist.scale = 35, rec.dist.shape = 1.5, arec.dist.scale = 35, arec.dist.shape = 1.5, fat.rate.base = 1/50, hosp.cap = 40, fat.rate.overcap = 1/25, fat.tcoeff = 0.5, vital = TRUE, flare.inf.point = NULL, flare.inf.num = NULL, a.rate = (10.5/365)/1000, a.prop.e = 0.01, a.prop.i = 0.001, a.prop.q = 0.01, ds.rate = (7/365)/1000, de.rate = (7/365)/1000, di.rate = (7/365)/1000, dq.rate = (7/365)/1000, dh.rate = (20/365)/1000, dr.rate = (7/365)/1000 )
| inf.prob.e | Probability of passing on infection at each
exposure event for interactions between infectious people in the E
compartment and susceptible in S. Note the default is lower than for
inf.prob.i reflecting the reduced infectivity of infected but
asymptomatic people (the E compartment). Otherwise as for |
|---|---|
| act.rate.e | The number of exposure events (acts) between infectious individuals in the E compartment and susceptible individuals in the S compartment per day. |
| inf.prob.i | Probability of passing on infection at each
exposure event for interactions between infectious people in the I
compartment and susceptible in S. Reducing |
| act.rate.i | The average number of exposure events (acts) between
infectious individuals in the I compartment and susceptible individuals
in the S compartment per day. Note that not every
exposure event results in infection - that is governed by the |
| inf.prob.q | Probability of passing on infection at each
exposure event for interactions between infectious people in the Q
compartment and susceptible in S. Note the default is lower than for
|
| act.rate.q | The number of exposure events (acts) between infectious individuals in the Q compartment (isolated, self or otherwise) and susceptible individuals in the S compartment, per day. Note the much lower rate than for the I and E compartments, reflecting the much greater degree of social isolation for someone in (self-)isolation. The exposure event rate is not zero for this group, just much less. |
| prog.rate | Rate per day at which people who are infected
but asymptomatic (E compartment) progress to becoming symptomatic (or
test-positive), the I compartment.
Only useful if parameter |
| quar.rate | Rate per day at which symptomatic (or tested positive), infected I compartment people enter self-isolation (Q compartment). Asymptomatic E compartment people can't enter self-isolation because they don't yet know they are infected. Default is a low rate reflecting low community awareness or compliance with self-isolation requirements or practices, but this can be tweaked when exploring scenarios. |
| hosp.rate | Rate per day at which symptomatic (or tested
positive), infected I compartment people or self-isolated Q compartment
people enter the state of requiring hospital care -- that is, become
serious cases. A default rate of 1
duration of about 10 days means a bit less than 10
require hospitalisation.
Only useful if parameter |
| disch.rate | Rate per day at which people needing
hospitalisation recover, only useful if parameter |
| rec.rate | Rate per day at which people who are infected and
symptomatic (I compartment) recover, thus entering the R compartment.
Only useful if parameter |
| arec.rate | Rate per day at which people who are exposed but asymptotic
(E compartment) recover, thus entering the R compartment.
Only useful if parameter |
| prog.dist.scale | Scale parameter for Weibull distribution
for progression, only useful if parameter |
| prog.dist.shape | Shape parameter for Weibull distribution
for progression, only useful if parameter |
| quar.dist.scale | Scale parameter for Weibull distribution for
recovery, only useful if parameter |
| quar.dist.shape | Shape parameter for Weibull distribution for
recovery, only useful if parameter |
| hosp.dist.scale | Scale parameter for Weibull distribution for
recovery, only useful if parameter |
| hosp.dist.shape | Shape parameter for Weibull distribution for
recovery, only useful if parameter |
| disch.dist.scale | Scale parameter for Weibull distribution for
recovery, only useful if parameter |
| disch.dist.shape | Shape parameter for Weibull distribution for
recovery, only useful if parameter |
| rec.dist.scale | Scale parameter for Weibull distribution for
recovery, only useful if parameter |
| rec.dist.shape | Shape parameter for Weibull distribution for
recovery, only useful if parameter |
| arec.dist.scale | Scale parameter for Weibull distribution for
recovery, only useful if parameter |
| arec.dist.shape | Shape parameter for Weibull distribution for
recovery, only useful if parameter |
| fat.rate.base | Baseline mortality rate per day for people
needing hospitalisation (deaths due to the virus).
Only useful if parameter |
| hosp.cap | Number of available hospital beds for the modelled
population. See parameter |
| fat.rate.overcap | Mortality rate per day for people needing
hospitalisation but who can't get into hospital due to the hospitals
being full (see parameters |
| fat.tcoeff | Time co-efficient for increasing mortality rate
as time in the H compartment increases for each individual in it.
See parameter |
| vital | Enables demographics, that is, arrivals and departures, to and from the simulated population. |
| flare.inf.point | (Either a vector or a scalar) Time points where there is a sudden arrival of I's. |
| flare.inf.num | (same dimension as flare.inf.point) The number of I's arriving at the specified time points in flare.inf.point. |
| a.rate | Background demographic arrival rate. Currently all arrivals go into the S compartment, the default is approximately the daily birth rate for Australia. Will be extended to cover immigration in future versions. |
| a.prop.e | Arrivals proportion that goes to E (immigration). |
| a.prop.i | Arrivals proportion that goes to I (immigration). |
| a.prop.q | Arrivals proportion that goes to Q (immigration). |
| ds.rate | Background demographic departure (death not due to virus) rates. Defaults based on Australian crude death rates. Can be used to model emigration as well as deaths. |
| de.rate | Background demographic departure (death not due to virus) rates. Defaults based on Australian crude death rates. Can be used to model emigration as well as deaths. |
| di.rate | Background demographic departure (death not due to virus) rates. Defaults based on Australian crude death rates. Can be used to model emigration as well as deaths. |
| dq.rate | Background demographic departure (death not due to virus) rates. Defaults based on Australian crude death rates. Can be used to model emigration as well as deaths. |
| dh.rate | Background demographic departure (death not due to virus) rates. Defaults based on Australian crude death rates. Can be used to model emigration as well as deaths. |
| dr.rate | Background demographic departure (death not due to virus) rates. Defaults based on Australian crude death rates. Can be used to model emigration as well as deaths. |
A param.seiqhrf object with
epidemic parameters for the stochastic individual
contact models simulated with the seiqhrf function.
The model specification will be chosen as a result of
the model parameters entered here and the control settings in
control_seiqhrf.
Use init_seiqhrf to specify the initial conditions and
control_seiqhrf to specify the control settings. Run the
parameterized model with seiqhrf.