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Create a SimInf_model

Source: R/SimInf_model.R
SimInf_model.Rd

Create a SimInf_model

Usage

SimInf_model(
  G,
  S,
  tspan,
  events = NULL,
  ldata = NULL,
  gdata = NULL,
  U = NULL,
  u0 = NULL,
  v0 = NULL,
  V = NULL,
  E = NULL,
  N = NULL,
  C_code = NULL
)

Arguments

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

tspan

A vector (length >= 1) 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.

events

A data.frame with the scheduled events.

ldata

local data for the nodes. Can either be specified as a data.frame with one row per node. Or as a matrix where each 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.

U

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

u0

The initial state vector. Either a matrix (\(N_c \times N_n\)) or a a data.frame with the number of individuals in each compartment in every node.

v0

The initial continuous state vector in every node. (dim(ldata)[1] \(\times N_N\)). The continuous state vector is updated by the specific model during the simulation in the post time step function.

V

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

E

Sparse matrix to handle scheduled events, see SimInf_events.

N

Sparse matrix to handle scheduled events, see SimInf_events.

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.

Value

SimInf_model