R/PN-epiSEIR-network-T.R
spn_T_epiSEIR_network.RdThis 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.
spn_T_epiSEIR_network(node_list, spn_P, params, cube, h_move, m_move)
| 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 |
| params | a named list of parameters (see details) |
| cube | an inheritance cube from the |
| 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 |
a list with two elements: T contains transitions packets as lists,
v is the character vector of transitions (T)
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")