Usage
PCS_run(interconnection_matrix, initial_state, resting_levels, reset, node_names = NULL, stability_criterion = 10^-6, max_iterations = Inf, convergence_criteria = c(PCS_convergence_McCandR), convergence_names = NULL)
Arguments
interconnection_matrix
A square, matrix representing the link weights
between nodes, such that each entry w_ij represents the link strength
between nodes i and j. Accordingly, for a network of n nodes, the matrix
must be of six n*n. In most applications, the matrix will be symmetric,
meaning that links are bidirectional.
initial_state
Initial node activations before the first iteration is
run. In most cases, this will be a vector of zeros, with the length
corresponding to the number of nodes in the network.
resting_levels
Resting activation level for each node. In most cases,
this will be a vector of zeros, with its length corresponding to the number
of nodes in the network.
reset
Vector denoting nodes with stable activation values. The vector
contains a value for each node; if it is unequal to zero, the node
activation will be reset to this value after each iteration.
node_names
Vector specifying human-readable labels for every node, or
'default', in which case nodes are automatically named.
stability_criterion
Stability theshold for convergence criteria. If
energy changes across iterations fall below this threshold, the model is
considered to have converged.
max_iterations
Maximum number of iterations to run before terminating
the simulation.
convergence_criteria
Array of convergence criteria to apply. This PCS
implementation allows users to define and observe multiple convergence
criteria in one model. Each entry in this array is a convergence criterion,
which is representated as a function that receives the current iteration,
energy, model state history and the stability_criterion defined
above and returns a boolean value representing whether the particular
criterion is met given the model's current state.
convergence_names
Human-readable labels for the convergence criteria,
or 'default', in which case the criteria are numbered automatically,
in which case the criteria are numbered automatically.