R/intensitynetUnd.R

In intensitynet: Intensity Analysis of Spatial Point Patterns on Complex Networks

#' Calculates the mean intensity of the given node (for undirected networks)
#' 
#' @description 
#' Calculates the mean intensity of the given node (intensity of all the edges of the node/number of edges of the node)
#' 
#' @name nodeIntensity.intensitynetUnd
#' 
#' @param obj intensitynetUnd object
#' @param node_id ID of the node
#' 
#' @return mean intensity of the given node
#' 
MeanNodeIntensity.intensitynetUnd = function(obj, node_id){
  g <- obj$graph
  
  # If the intensity is already calculated, return it
  if(!is.null(igraph::vertex_attr(g, 'intensity', index=node_id))){
    if(!is.na(igraph::vertex_attr(g, "intensity", index=node_id))[1]){
      
      message("Warning: Node intensities were already calculated in a previous instance, returning the same intensity.")
      return(igraph::vertex_attr(g, 'intensity', index=node_id))
    } 
  }
  
  if(igraph::degree(g, node_id) > 0){
    neighbors_list <- igraph::neighbors(g, node_id)
    
    ev_mat <- matrix(0, ncol = length(neighbors_list)) 
    colnames(ev_mat) <- as.vector(neighbors_list) 
    rownames(ev_mat) <- node_id
    
    for (neighbor_id in neighbors_list){
      ev_mat[as.character(node_id), as.character(neighbor_id)] <- EdgeIntensity(obj = obj, 
                                                                                node_id1 = igraph::V(g)[node_id]$name, 
                                                                                node_id2 = igraph::V(g)[neighbor_id]$name)
    }
    
    mean_intensity <- Reduce('+', ev_mat) / igraph::degree(g, node_id)
    
    mean_intensity
  }
}


#' Calculates intensity statistics for the given intensitynet object
#' 
#' @description 
#' Calculates edgewise and mean nodewise intensities for Undirected networks and, for each edge, the proportions of
#' all event covariates.
#' 
#' @name RelateEventsToNetwork.intensitynetUnd
#' 
#' @param obj intensitynetUnd object
#' 
#' @return proper intensitynetUnd object with a graph containing the nodewise intensity in the node 
#' attributes and the edgewise intensities and event covariate proportions as edge attributes.
#' 
#' @export
RelateEventsToNetwork.intensitynetUnd = function(obj){
  g <- obj$graph
  counts <- c()
  
  if(length(obj$events) == 0){
    stop("Error: No events, cannot calculate any intensity.")
  }
  
  tmp_obj <- EdgeIntensitiesAndProportions.intensitynet(obj)
  g <- tmp_obj$graph
  
  message("\nCalculating node intensities...")
  pb = utils::txtProgressBar(min = 0, max = igraph::gorder(g), initial = 0, style = 3) 
  
  # check if the intensities was previously calculated, if not, calculate them
  v_count <- 0
  for(node_id in igraph::V(g)){
    
    utils::setTxtProgressBar(pb,node_id)
    
    if(is.null(igraph::vertex_attr(g, 'intensity', node_id))){
      if(igraph::degree(g, node_id) > 0){
        #Adds result of Nodewise mean intensity function to 'counts'
        counts[[node_id]]  <- MeanNodeIntensity(tmp_obj, node_id)
      }else{
        # Counts for isolated nodes or NA values
        counts[[node_id]] <- 0
      }
    }else if(is.na(igraph::vertex_attr(g, 'intensity', node_id))[1]){
      counts[[node_id]] <- 0
    }else{
      v_count <- v_count + 1
      counts[[node_id]] <- igraph::vertex_attr(g, 'intensity', node_id)
    }
  }
  close(pb)
  # If the intensity of all edges is already calculated return the object
  if(v_count == length(igraph::V(g))){
    message("Warning: Intensities were already calculated in a previous instance, returning the same object.")
    return(obj)
  } 
  
  
  #g <- g %>% igraph::set_vertex_attr(name = "intensity", value = as.matrix(counts))
  g <- igraph::set_vertex_attr(g, name = "intensity", value = as.numeric(counts))
  
  intnet <- list(graph = g, 
                 events = obj$events, 
                 graph_type = obj$graph_type, 
                 distances_mtx = obj$distances_mtx,
                 event_correction = obj$event_correction,
                 events_related = TRUE)
  attr(intnet, 'class') <- c("intensitynetUnd", "intensitynet")
  return(intnet)
}