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Create a SimInf_model object

Source: R/SimInf_model.R
SimInf_model.Rd

Construct a low-level SimInf_model object. This function is typically used internally by model constructors (e.g., SIR(), mparse()) or for advanced usage where custom model definitions (e.g., user-provided C code or non-standard matrices) are required.

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. Indicates which transition rates need updating after a state transition. Can be provided as a sparse matrix (class dgCMatrix) or a dense matrix. If a dense matrix is provided, it is automatically converted to a sparse format internally. See SimInf_model for detailed matrix layout.

S

State Transition Matrix. Defines the change in the state vector for each transition. Can be provided as a sparse matrix (class dgCMatrix) or a dense matrix. If a dense matrix is provided, it is automatically converted to a sparse format internally. See SimInf_model for detailed matrix layout.

tspan

Time Span (numeric or Date vector). Increasing time points for output. If Date, converted to days with names, 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

Scheduled Events. A data.frame defining the event schedule (see SimInf_events).

ldata

Local Data. Parameters specific to each node. Can be:

  • A data.frame with one row per node.

  • A matrix where each column ldata[, j] is the data vector for node j.

Passed to transition rate and post-step functions.

gdata

Global Data (numeric vector). Parameters common to all nodes. Passed to transition rate and post-step functions.

U

Result Matrix (integer matrix). Usually empty at creation. See SimInf_model for detailed matrix layout.

u0

Initial State. Initial number of individuals per compartment/node. Can be:

  • A matrix (\(N_c \times N_n\)).

  • A data.frame with columns corresponding to compartments.

  • Any object coercible to a data.frame (e.g., a named numeric vector will be coerced to a one-row data.frame).

v0

Initial Continuous State (numeric matrix). Initial values for continuous states per node.

V

Continuous State Result Matrix (numeric matrix). Usually empty at creation. See SimInf_model for layout.

E

Select Matrix (matrix or data.frame). Defines which compartments are affected by events and their sampling weights.

  • Matrix: Standard sparse matrix.

  • data.frame: Must have columns compartment and select. Optional column value (default 1) sets the weight.

See SimInf_events for usage details.

N

Shift Matrix (matrix or data.frame). Defines how individuals are moved between compartments during events.

  • Matrix: Standard integer matrix.

  • data.frame: Must have columns compartment, shift, and value (integer offset).

See SimInf_events for usage details.

C_code

C Source Code (character vector). Optional C code for custom transition rates. If provided, it is compiled and loaded when run() is called.

Value

A SimInf_model object.

See also

SIR, SEIR, SIS, SISe for examples of compartment model constructors that handle argument validation and matrix setup. mparse for creating custom models using a simple string syntax. SimInf_model for details on the class structure and slots. SimInf_events for details on the event schedule format.