Create a SISe3_sp model to be used by the simulation framework.
SISe3_sp(u0, tspan, events = NULL, phi = NULL, upsilon_1 = NULL,
upsilon_2 = NULL, upsilon_3 = NULL, gamma_1 = NULL, gamma_2 = NULL,
gamma_3 = NULL, alpha = NULL, beta_t1 = NULL, beta_t2 = NULL,
beta_t3 = NULL, beta_t4 = NULL, end_t1 = NULL, end_t2 = NULL,
end_t3 = NULL, end_t4 = NULL, distance = NULL, coupling = NULL)A data.frame with the initial state in each
node, see details.
A vector (length >= 2) of increasing time points
where the state of each node is to be returned. Can be either
an integer or a Date vector. A Date
vector is coerced to a numeric vector as days, where
tspan[1] becomes the day of the year of the first year
of tspan. The dates are added as names to the numeric
vector.
a data.frame with the scheduled events, see
SimInf_model.
A numeric vector with the initial environmental infectious pressure in each node. Default NULL which gives 0 in each node.
Indirect transmission rate of the environmental infectious pressure in age category 1
Indirect transmission rate of the environmental infectious pressure in age category 2
Indirect transmission rate of the environmental infectious pressure in age category 3
The recovery rate from infected to susceptible for age category 1
The recovery rate from infected to susceptible for age category 2
The recovery rate from infected to susceptible for age category 3
Shed rate from infected individuals
The decay of the environmental infectious pressure in interval 1.
The decay of the environmental infectious pressure in interval 2.
The decay of the environmental infectious pressure in interval 3.
The decay of the environmental infectious pressure in interval 4.
The non-inclusive day of the year that ends interval 1.
The non-inclusive day of the year that ends interval 2.
The non-inclusive day of the year that ends interval 3.
The non-inclusive day of the year that ends interval 4.
The distance matrix between neighboring nodes
The coupling between neighboring nodes
SISe3_sp
The time dependent beta is divided into four intervals of the year
where 0 <= day < 365Case 1: END_1 < END_2 < END_3 < END_4 INTERVAL_1 INTERVAL_2 INTERVAL_3 INTERVAL_4 INTERVAL_1 [0, END_1) [END_1, END_2) [END_2, END_3) [END_3, END_4) [END_4, 365)
Case 2: END_3 < END_4 < END_1 < END_2 INTERVAL_3 INTERVAL_4 INTERVAL_1 INTERVAL_2 INTERVAL_3 [0, END_3) [END_3, END_4) [END_4, END_1) [END_1, END_2) [END_2, 365)
Case 3: END_4 < END_1 < END_2 < END_3 INTERVAL_4 INTERVAL_1 INTERVAL_2 INTERVAL_3 INTERVAL_4 [0, END_4) [END_4, END_1) [END_1, END_2) [END_2, END_3) [END_3, 365)
The argument u0 must be a data.frame with one row for
each node with the following columns:
The number of sucsceptible in age category 1
The number of infected in age category 1
The number of sucsceptible in age category 2
The number of infected in age category 2
The number of sucsceptible in age category 3
The number of infected in age category 3