R/setse.R

In rsetse: Strain Elevation Tension Spring Embedding

#' Basic SETSe embedding
#'
#' Embeds/smooths a feature network using the basic SETSe algorithm. generally setse_auto or setse_bicomp is preferred.
#' 
#' @param g An igraph object
#' @param force A character string. This is the node attribute that contains the force the nodes exert on the network.
#' @param distance A character string. The edge attribute that contains the original/horizontal distance between nodes.
#' @param edge_name A character string. This is the edge attribute that contains the edge_name of the edges.
#' @param k A character string. This is k for the moment don't change it.
#' @param tstep A numeric. The time interval used to iterate through the network dynamics.
#' @param mass A numeric. This is the mass constant of the nodes in normalised networks this is set to 1.
#' @param max_iter An integer. The maximum number of iterations before stopping. Larger networks usually need more iterations.
#' @param coef_drag A numeric. 
#' @param tol A numeric. The tolerance factor for early stopping.
#' @param sparse Logical. Whether or not the function should be run using sparse matrices. must match the actual matrix, this could prob be automated
#' @param two_node_solution Logical. The Newton-Raphson algo is used to find the correct angle
#' @param sample Integer. The dynamics will be stored only if the iteration number is a multiple of the sample. 
#'  This can greatly reduce the size of the results file for large numbers of iterations. Must be a multiple of the max_iter
#' @param static_limit Numeric. The maximum value the static force can reach before the algorithm terminates early. This
#' prevents calculation in a diverging system. The value should be set to some multiple greater than one of the force in the system.
#' If left blank the static limit is twice the system absolute mean force.
#' @param noisy_termination Stop the process if the static force does not monotonically decrease.
#' 
#' @details This is the basic SETS embeddings algorithm, it outputs all elements of the embeddings as well as convergence dynamics. It is a
#' wrapper around the core SETS algorithm which requires data preparation and only produces node embeddings and network dynamics. 
#' There is little reason to use this function as \code{\link{setse_auto}} and \code{\link{setse_bicomp}} 
#' are faster and easier to use.
#' @family setse
# @seealso \code{\link{setse_auto}} \code{\link{setse}}
#' @return A list containing 4 dataframes.
#' \enumerate{
#'   \item The network dynamics describing several key figures of the network during the convergence process, this includes the static_force.
#'   \item The node embeddings. Includes all data on the nodes the forces exerted on them position and dynamics at simulation termination.
#'   \item time taken. the amount of time taken per component, includes the number of edges and nodes.
#'   \item The edge embeddings. Includes all data on the edges as well as the strain and tension values.
#' }
#' 
#' @examples
#' set.seed(234) #set the random see for generating the network
#' g <- generate_peels_network(type = "E")
#' embeddings <- g %>%
#' prepare_edges(k = 500, distance = 1) %>%
#' #prepare the network for a binary embedding
#' prepare_categorical_force(., node_names = "name",
#'                      force_var = "class") %>%
#' #embed the network using auto_setse
#'   setse(., force = "class_A")
#' @export

setse <- function(g, 
                  force ="force", 
                  distance = "distance", 
                  edge_name = "edge_name",
                  k ="k",
                  tstep = 0.02, 
                  mass = 1, 
                  max_iter = 20000, 
                  coef_drag = 1, 
                  tol = 1e-6,
                  sparse = FALSE,
                  two_node_solution = TRUE,
                  sample = 1,
                  static_limit = NULL,
                  noisy_termination = TRUE){
  
  #helper function that prepares the data
  Prep <- setse_data_prep(g = g, 
                          force = force, 
                          distance = distance, 
                          mass = mass, 
                          k = k,
                          edge_name = edge_name,
                          sparse = sparse)
  
  #do special case solution 
  if(igraph::ecount(g)==1 & two_node_solution){
  
    Out <- two_node_solution(g, Prep = Prep, auto_setse_mode = FALSE)
    
    #Solves using the iterative method.
  } else{
    
    #The core algorithm
    Out <- setse_core(
      node_embeddings = Prep$node_embeddings, 
      ten_mat = Prep$ten_mat, 
      non_empty_matrix = Prep$non_empty_matrix, 
      kvect = Prep$kvect, 
      dvect = Prep$dvect, 
      mass = mass,
      tstep = tstep, 
      max_iter = max_iter, 
      coef_drag = coef_drag,
      tol = tol, 
      sparse = sparse,
      sample = sample,
      static_limit = static_limit,
      noisy_termination = noisy_termination) 
    
  }
  
  
  #Extract edge tension and strain from the network
  Out$edge_embeddings <- calc_tension_strain(g = g,
                                              Out$node_embeddings,
                                              distance = distance, 
                                              edge_name = edge_name, 
                                              k = k)
  
  
  return(Out)
  
}