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Set the shift matrix for a SimInf_model object

Source: R/SimInf_events.R
shift_matrix-set.Rd

Utility function to set events@N in a SimInf_model object, see SimInf_events.

Usage

shift_matrix(model) <- value

# S4 method for class 'SimInf_model'
shift_matrix(model) <- value

Arguments

model

The SimInf_model object to set the shift matrix for.

value

The new value for N in the model. N is a matrix to handle scheduled events, see SimInf_events. Each row in N corresponds to one compartment in the model. The values in a column define how to move sampled individuals before adding them to the destination. Let q <- shift, then each non-zero entry in N[, q] defines the number of rows to move sampled individuals from that compartment i.e., sampled individuals from compartment p are moved to compartment N[p, q] + p, where 1 <= N[p, q] + p <= N_compartments. This matrix is used for enter, internal transfer and external transfer events. The shift matrix N can either be specified as a matrix, or as a data.frame. When N is specified as a data.frame, it must have one column named compartment that defines which compartment is referred to, and one column shift that defines the column in N. In addition, the data.frame must contain a column named value with the integer value in N.

Value

SimInf_model object

Examples

## Create an SIR model
model <- SIR(u0 = data.frame(S = 99, I = 1, R = 0),
             tspan = 1:5, beta = 0.16, gamma = 0.077)

## Set the shift matrix.
shift_matrix(model) <- matrix(c(2, 1, 0), nrow = 3)

## Extract the shift matrix from the model.
shift_matrix(model)
#>   1
#> S 2
#> I 1
#> R 0

## Set the shift matrix using a data.frame instead.
shift_matrix(model) <- data.frame(
    compartment = c("S", "I", "R"),
    shift = c(1, 1, 1),
    value = c(2, 1, 0))

## Extract the shift matrix from the model.
shift_matrix(model)
#>   1
#> S 2
#> I 1
#> R 0