Make Transitions (T) For a Network (SEI Mosquitoes - SEIR Humans)

This function makes the set of transitions (T) for a SPN model of a metapopulation network for simulation of coupled SEI-SEIR dynamics. It is the network version of spn_T_epiSEIR_node.

Usage

spn_T_epiSEIR_network(node_list, spn_P, params, cube, h_move, m_move)

Arguments

node_list: a character vector specifying what type of nodes to create; (m = a node with only mosquitoes, h = a node with only humans, b = a node with both humans and mosquitoes)
spn_P: set of places produced by spn_P_epiSEIR_network
params: a named list of parameters (see details)
cube: an inheritance cube from the MGDrivE package (e.g. cubeMendelian)
h_move: binary adjacency matrix indicating if movement of humans between nodes is possible or not
m_move: binary adjacency matrix indicating if movement of mosquitoes between nodes is possible or not

Value

a list with two elements: T contains transitions packets as lists, v is the character vector of transitions (T)

Details

This function takes the places produced from spn_P_epiSEIR_network and builds all possible transitions between subsets of those places.

The params argument supplies all of the ecological parameters necessary to calculate equilibrium values. This function requires the nE, nL, nP, and nEIP parameters to be specified. For more details, see equilibrium_SEI_SEIR

While this function produces all structural information related to transitions, hazards are produced by a separate function, spn_hazards.

For larger networks, this function may take some time to return, please be patient; the Petri Net modeling formalism trades additional computation time at model initialization for faster sampling of trajectories within a simulation.

Please note, the movement matrices (h_move and m_move) are NOT stochastic matrices, just binary matrices that say if i,j can exchange population. Diagonal elements must be FALSE, and both matrices are checked for validity; the function will stop with errors if the adjacency matrix specifies illegal movement rules (e.g.; mosquito movement from a "h" node to a "b" node)

For examples of using this function, see: vignette("seir-dynamics", package = "MGDrivE2")