SISe3_sp {SimInf} | R Documentation |
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)
u0 |
A |
tspan |
A vector (length >= 2) of increasing time points
where the state of each node is to be returned. Can be either
an |
events |
a |
phi |
A numeric vector with the initial environmental infectious pressure in each node. Will be repeated to the length of nrow(u0). Default is NULL which gives 0 in each node. |
upsilon_1 |
Indirect transmission rate of the environmental infectious pressure in age category 1 |
upsilon_2 |
Indirect transmission rate of the environmental infectious pressure in age category 2 |
upsilon_3 |
Indirect transmission rate of the environmental infectious pressure in age category 3 |
gamma_1 |
The recovery rate from infected to susceptible for age category 1 |
gamma_2 |
The recovery rate from infected to susceptible for age category 2 |
gamma_3 |
The recovery rate from infected to susceptible for age category 3 |
alpha |
Shed rate from infected individuals |
beta_t1 |
The decay of the environmental infectious pressure in interval 1. |
beta_t2 |
The decay of the environmental infectious pressure in interval 2. |
beta_t3 |
The decay of the environmental infectious pressure in interval 3. |
beta_t4 |
The decay of the environmental infectious pressure in interval 4. |
end_t1 |
vector with the non-inclusive day of the year that ends interval 1 in each node. Will be repeated to the length of nrow(u0). |
end_t2 |
vector with the non-inclusive day of the year that ends interval 2 in each node. Will be repeated to the length of nrow(u0). |
end_t3 |
vector with the non-inclusive day of the year that ends interval 3 in each node. Will be repeated to the length of nrow(u0). |
end_t4 |
vector with the non-inclusive day of the year that ends interval 4 in each node. Will be repeated to the length of nrow(u0). |
distance |
The distance matrix between neighboring nodes |
coupling |
The coupling between neighboring nodes |
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
SISe3_sp
The time dependent beta is divided into four intervals of the year
where 0 <= day < 365 Case 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)