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Class "SimInf_model"

Source: R/classes.R
SimInf_model-class.Rd

Class to handle data for the SimInf_model.

Slots

G

Dependency graph that indicates the transition rates that need to be updated after a given state transition has occured. A non-zero entry in element G[i, i] indicates that transition rate i needs to be recalculated if the state transition j occurs. Sparse matrix (\(Nt \times Nt\)) of object class dgCMatrix.

S

Each column corresponds to a state transition, and execution of state transition j amounts to adding the S[, j] column to the state vector u[, i] of node i where the transition occurred. Sparse matrix (\(Nc \times Nt\)) of object class dgCMatrix.

U

The result matrix with the number of individuals in each compartment in every node. U[, j] contains the number of individuals in each compartment at tspan[j]. U[1:Nc, j] contains the number of individuals in node 1 at tspan[j]. U[(Nc + 1):(2 * Nc), j] contains the number of individuals in node 2 at tspan[j] etc. Integer matrix (\(N_n N_c \times\) length(tspan)).

U_sparse

If the model was configured to write the solution to a sparse matrix (dgCMatrix) the U_sparse contains the data and U is empty. The layout of the data in U_sparse is identical to U. Please note that U_sparse is numeric and U is integer.

V

The result matrix for the real-valued continuous state. V[, j] contains the real-valued state of the system at tspan[j]. Numeric matrix (\(N_n\)dim(ldata)[1] \(\times\) length(tspan)).

V_sparse

If the model was configured to write the solution to a sparse matrix (dgCMatrix) the V_sparse contains the data and V is empty. The layout of the data in V_sparse is identical to V.

ldata

A matrix with local data for the nodes. The column ldata[, j] contains the local data vector for the node j. The local data vector is passed as an argument to the transition rate functions and the post time step function.

gdata

A numeric vector with global data that is common to all nodes. The global data vector is passed as an argument to the transition rate functions and the post time step function.

tspan

A vector of increasing time points where the state of each node is to be returned.

u0

The initial state vector (\(N_c \times N_n\)) with the number of individuals in each compartment in every node.

v0

The initial value for the real-valued continuous state. Numeric matrix (dim(ldata)[1] \(\times N_n\)).

events

Scheduled events SimInf_events

replicates

Number of replicates of the model.

C_code

Character vector with optional model C code. If non-empty, the C code is written to a temporary C-file when the run method is called. The temporary C-file is compiled and the resulting DLL is dynamically loaded. The DLL is unloaded and the temporary files are removed after running the model.