SETSe NOT FLOW DEPENDENT

I have removed the need for flow and edge capacity in all SETSe functions. This is becuase they are only useful on flow networks and not a major component of networks or graphs in general. This is a major update and breaks all previous code using this package.
JonnoB · Apr 21, 2020 · 9b925ab · 9b925ab
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: NetworkSpringEmbedding
 Title: Calculating the Strain Elevation Tension Spring embeddings for a network
-Version: 0.1
+Version: 0.3
 Authors@R: person("Jonathan", "Bourne", email = "jonathan.bourne.15@ucl.ac.uk.com", role = c("aut", "cre"))
 Description: This package is used to calculate the Strain Elevation and Tension embeddings produced by the SETSe algorithm.
 Depends: R (>= 3.4.2)

diff --git a/NAMESPACE b/NAMESPACE
@@ -8,12 +8,13 @@ export(Create_stabilised_blocks)
 export(Create_stabilised_blocks_expanded)
 export(Distance)
 export(ForceV_from_angle)
-export(SETSe)
+export(SETSe2)
 export(SETSe_bicomp)
 export(SETSe_bicomp_expanded)
 export(SETSe_core)
 export(SETSe_core_expanded)
 export(SETSe_data_prep)
+export(SETSe_data_prep_orig)
 export(SETSe_expanded)
 export(angle_from_solved_heights)
 export(auto_SETSe)

diff --git a/R/Create_balanced_blocks.R b/R/Create_balanced_blocks.R
@@ -10,12 +10,11 @@
 #' 
 #' @param g An igraph object. The network for which embeddings will be found
 #' @param force A character vector. The name of the node attribute that is the force exerted by the nodes
-#' @param flow A character vector. The name of the edge attribute that contains the flow over each edge
 #' @return A list containing all the bi connected component where each component is balanced to have a net force of 0.
 #' 
 #' @export
 
-create_balanced_blocks <- function(g, force = "net_generation", flow = "power_flow"){
+create_balanced_blocks <- function(g, force = "force"){
   #This function creates a list of biconnected components or blocks.
   #These blocks are balanced such that the connecting vertices contain all the power of the missing part of the network
   #balancing prevents the network reaching a steady state non-zero velocity.
@@ -69,19 +68,7 @@ create_balanced_blocks <- function(g, force = "net_generation", flow = "power_fl
         left_join(biconnected_component, ., by = "name") %>%
         mutate(temp = ifelse(is.na(AuxPower), !!sym(force), AuxPower)) #
 
-      # This has been commented out as it is unclear what benefits it provides and causes errors when flow
-      # is only a nominal value not a real part of the network
-      # #makes the nodes of the two node 1 edge block have the same power as that which flows between them.
-      # #this forces a balance
-      # #The nodes are by default in alphabetical order so the polarity of the power flow will always be correct
-      # if(nrow(edge_df)==1){
-      #   balanced_component_df <- balanced_component_df %>%
-      #     mutate(temp = edge_df %>%
-      #              pull(., !!sym(flow)) %>% c(., -.) %>% 
-      #              #should this rounding be kept? maybe tiny value aren't a problem? the thing is solved seperately anyway
-      #              round(., 10)) #rounding stops tiny values
-      # }
-
+
       Component_j <- {!(get.vertex.attribute(g, "name") %in% balanced_component_df$name)} %>%
         (1:vcount(g))[.] %>%
         delete.vertices(g,.) 

diff --git a/R/Create_stabilised_blocks .R b/R/Create_stabilised_blocks .R
@@ -9,7 +9,6 @@
 #' @param OriginBlock_number An integer. this is the origin block chosen from the
 #' create_stable_blocks function. Usually this will be the largest block.
 #' @param force A character string. This is the node attribute that contains the force the nodes exert on the network.
-#' @param flow A character string. This is the edge attribute that is the power flow on the edges.
 #' @param edge_name A character string. This is the edge attribute that contains the edge_name of the edges.
 #' @param tstep A numeric. The time interval used to iterate through the network dynamics.
 #' @param coef_drag A numeric. This sets the multiplier of friction. Only use if you want to be annoyed and confused
@@ -27,8 +26,7 @@
 Create_stabilised_blocks <- function(g, 
                                      OriginBlock, 
                                      OriginBlock_number, 
-                                     force ="net_generation", 
-                                     flow = "power_flow", 
+                                     force ="force",
                                      edge_name = "edge_name",  
                                      tstep=0.1, 
                                      coef_drag = coef_drag,
@@ -41,7 +39,7 @@ Create_stabilised_blocks <- function(g,
 
   #Seperate out the graph into balanced blocks
   #This step will have already been done, but it is fast and simplifies the requirements for the function
-  List_of_BiConComps <- create_balanced_blocks(g, force = force, flow = flow)
+  List_of_BiConComps <- create_balanced_blocks(g, force = force)
 
   #remove the Origin block so it doesn't have to be calculated again
   BlockNumbers <-(1:length(List_of_BiConComps))[-OriginBlock_number]
@@ -53,8 +51,7 @@ Create_stabilised_blocks <- function(g,
     map(~{
 
       Out <- SETSe(List_of_BiConComps[[.x]],
-                                  force =force, 
-                                  flow = flow, 
+                                  force =force,
                                   tstep = tstep, 
                                   coef_drag = coef_drag,
                                   tol = tol*sum(abs(get.vertex.attribute(List_of_BiConComps[[.x]], force)))/total_force, #the force has to be scaled to the component 

diff --git a/R/Create_stabilised_blocks_expanded.R b/R/Create_stabilised_blocks_expanded.R
@@ -8,7 +8,6 @@
 #' @param OriginBlock_number An integer. this is the origin block chosen from the
 #' create_stable_blocks function. Usually this will be the largest block.
 #' @param force A character string. This is the node attribute that contains the force the nodes exert on the network.
-#' @param flow A character string. This is the edge attribute that is the power flow on the edges.
 #' @param edge_name A character string. This is the edge attribute that contains the edge_name of the edges.
 #' @param tstep A numeric. The time interval used to iterate through the network dynamics.
 #' @param coef_drag A numeric. This sets the multiplier of friction. Only use if you want to be annoyed and confused
@@ -26,8 +25,7 @@
 Create_stabilised_blocks_expanded <- function(g, 
                                      OriginBlock, 
                                      OriginBlock_number, 
-                                     force ="net_generation", 
-                                     flow = "power_flow", 
+                                     force ="force", 
                                      edge_name = "edge_name",  
                                      tstep=0.1, 
                                      coef_drag = coef_drag,
@@ -40,7 +38,7 @@ Create_stabilised_blocks_expanded <- function(g,
 
   #Seperate out the graph into balanced blocks
   #This step will have already been done, but it is fast and simplifies the requirements for the function
-  List_of_BiConComps <- create_balanced_blocks(g, force = force, flow = flow)
+  List_of_BiConComps <- create_balanced_blocks(g, force = force)
 
   #remove the Origin block so it doesn't have to be calculated again
   BlockNumbers <-(1:length(List_of_BiConComps))[-OriginBlock_number]
@@ -49,8 +47,7 @@ Create_stabilised_blocks_expanded <- function(g,
     map(~{
 
       Out <- SETSe_expanded(List_of_BiConComps[[.x]],
-                                  force =force, 
-                                  flow = flow, 
+                                  force =force,
                                   tstep = tstep, 
                                   coef_drag = coef_drag,
                                   tol = tol, 
@@ -94,7 +91,7 @@ Create_stabilised_blocks_expanded <- function(g,
 
   message("creating adjustment matrices")
   component_adjust_mat <- adjust_components(g, max_iter = max_iter,
-                                            force = force, flow = flow)
+                                            force = force)
 
 
   #print(table(relative_blocks$Iter))

diff --git a/R/SETSe.R b/R/SETSe.R
@@ -2,15 +2,12 @@
 #' 
 #' 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 entwork dynamics.
-#' Flow and capacity are only inlcuded for legacy reasons and an arbitray value should be used for both if it is not applicable.
 #' 
 #' This function is often used in conjunction with \code{Create_stabilised_blocks} and \code{create_balanced_blocks}
 #' 
 #' @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 flow A character string. This is the edge attribute that is the power flow on the edges.
 #' @param distance A character string. The edge attribute that contains the original/horizontal distance between nodes.
-#' @param capacity A character string. This is the edge attribute that is the flow limit of the edges.
 #' @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.
@@ -20,8 +17,6 @@
 #' @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 include_edges Logical. Whether the function will return the edge strain and tension data or just elevation and dynamics. 
-#' Currently default is set to FALSE.
 #' @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
 #'  
@@ -30,31 +25,27 @@
 #' @seealso \code{\link{Create_stabilised_blocks}} \code{\link{create_balanced_blocks}}
 #' @export
 
-SETSe <- function(g, 
-                  force ="net_generation", 
-                  flow = "power_flow", 
-                  distance = "distance", 
-                  capacity = "capacity", 
-                  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,
-                  include_edges = FALSE,
-                  sample = 1){
-
+SETSe2 <- 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){
+
   #helper function that prepares the data
   Prep <- SETSe_data_prep(g = g, 
-                          force = force, 
-                          flow = flow, 
-                          distance = distance, 
-                          mass = mass, 
-                          edge_name = edge_name,
-                          sparse = sparse)
+                           force = force, 
+                           distance = distance, 
+                           mass = mass, 
+                           edge_name = edge_name,
+                           sparse = sparse)
 
   #do special case solution I should change this to a standalone function for ease of reading but it isn't important
   if(nrow(Prep$Link)==1 & two_node_solution){
@@ -93,7 +84,7 @@ SETSe <- function(g,
     )
     #Solves using the iterative method.
   } else{
-
+    
     #The core algorithm
     Out <- SETSe_core(
       node_embeddings = Prep$node_embeddings, 
@@ -111,18 +102,13 @@ SETSe <- function(g,
 
   }
 
-  if(include_edges){
-
-    #Extract edge tension and strain from the network
-    Out$edge_embeddings <- calc_tension_strain(g = g,
-                                               Out$node_embeddings,
-                                               distance = distance, 
-                                               capacity = capacity, 
-                                               flow = flow, 
-                                               edge_name = edge_name, 
-                                               k = k)
-
-  }
+
+  #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)

diff --git a/R/SETSe_bicomp.R b/R/SETSe_bicomp.R
@@ -5,9 +5,7 @@
 #' 
 #' @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 flow A character string. This is the edge attribute that is the power flow on the edges.
 #' @param distance A character string. The edge attribute that contains the original/horizontal distance between nodes.
-#' @param capacity A character string. This is the edge attribute that is the flow limit of the edges.
 #' @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.
@@ -19,12 +17,10 @@
 #' @param sparse Logical. Whether sparse matrices will be used. This becomes valubale for larger networks
 #' 
 #' @return A list containing 3 dataframes, the dataframe of the node embeddings, edge embeddings, and network dynamics
-#'@export
+#' @export
 SETSe_bicomp <- function(g, 
-                          force = "force", 
-                          flow = "flow", 
-                          distance = "distance", 
-                          capacity = "capacity", 
+                          force = "force",
+                          distance = "distance",
                           edge_name = "edge_name",
                           k = "k",
                           tstep,
@@ -37,8 +33,7 @@ SETSe_bicomp <- function(g,
 
   #seperate out the network into blocks
   List_of_BiConComps <- create_balanced_blocks(g, 
-                                               force = force, 
-                                               flow = flow)
+                                               force = force)
 
   #find the largest component and use that as the origin block
   OriginBlock_number <-List_of_BiConComps %>% map_dbl(~vcount(.x)) %>% which.max()
@@ -49,11 +44,9 @@ SETSe_bicomp <- function(g,
   total_force <- sum(abs(get.vertex.attribute(g, force)))
 
   #use the largest block to set the simulation parameters k and m.
-  #k needs to be sufficiently stretched to allow enough topology variation. otherwise all that happens is a 
-  #surface angled in the direct of net power flow. Which is interesting but not that interesting
+  #k needs to be sufficiently stretched to allow enough topology variation.
   OriginBlock <- SETSe(g = List_of_BiConComps[[OriginBlock_number]],
                                       force =force,
-                                      flow = flow,
                                       distance = distance,
                                       edge_name = edge_name,
                                       tstep = tstep,
@@ -71,7 +64,6 @@ SETSe_bicomp <- function(g,
                                                 OriginBlock = OriginBlock,
                                                 OriginBlock_number = OriginBlock_number,
                                                 force = force,
-                                                flow = flow,
                                                 distance = distance,
                                                 edge_name = edge_name,
                                                 tstep = tstep,
@@ -87,9 +79,7 @@ SETSe_bicomp <- function(g,
   #Extract edge tension and strain from the network
   tension_strain_embeddings <- calc_tension_strain(g = g,
                                                    height_embeddings$node_embeddings,
-                                                   distance = distance, 
-                                                   capacity = capacity, 
-                                                   flow = flow, 
+                                                   distance = distance,
                                                    edge_name = edge_name, 
                                                    k = k)
 

diff --git a/R/SETSe_bicomp_expanded.R b/R/SETSe_bicomp_expanded.R
@@ -4,9 +4,7 @@
 #' 
 #' @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 flow A character string. This is the edge attribute that is the power flow on the edges.
 #' @param distance A character string. The edge attribute that contains the original/horizontal distance between nodes.
-#' @param capacity A character string. This is the edge attribute that is the flow limit of the edges.
 #' @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.
@@ -21,7 +19,6 @@
 #'@export
 SETSe_bicomp_expanded <- function(g, 
                           force = "force", 
-                          flow = "flow", 
                           distance = "distance", 
                           capacity = "capacity", 
                           edge_name = "edge_name",
@@ -35,8 +32,7 @@ SETSe_bicomp_expanded <- function(g,
 
   #seperate out the network into blocks
   List_of_BiConComps <- create_balanced_blocks(g, 
-                                               force = force, 
-                                               flow = flow)
+                                               force = force)
 
   #find the largest component and use that as the origin block
   OriginBlock_number <-List_of_BiConComps %>% map_dbl(~vcount(.x)) %>% which.max()
@@ -48,7 +44,6 @@ SETSe_bicomp_expanded <- function(g,
   #surface angled in the direct of net power flow. Which is interesting but not that interesting
   OriginBlock <- SETSe_expanded(g = List_of_BiConComps[[OriginBlock_number]],
                                                force =force,
-                                               flow = flow,
                                                distance = distance,
                                                edge_name = edge_name,
                                                tstep = tstep,
@@ -65,7 +60,6 @@ SETSe_bicomp_expanded <- function(g,
                                                 OriginBlock = OriginBlock,
                                                 OriginBlock_number = OriginBlock_number,
                                                 force = force,
-                                                flow = flow,
                                                 distance = distance,
                                                 edge_name = edge_name,
                                                 tstep = tstep,