Implement changes as requested by JNCC

Parses.R

@@ -85,7 +85,7 @@ getInitial <- function(string, letter) {
 }
 
 split <- function(cell) {
-  
+
   params <- unlist(strsplit(cell, ","))
   values <- rep(0, length(states))
 
@@ -126,6 +126,7 @@ buildGraph <- function(model, desc) {
   #inputCode - the top layer of the model
   #outputCodes - all subsequent layers to be included in the model
 
+
   inputNodes <- model$nodes$code[which(startsWith(model$nodes$code, desc$inputCode))]
   inputText <- paste0("[", inputNodes, "]", collapse = "")
 
@@ -151,8 +152,15 @@ buildGraph <- function(model, desc) {
     outDist[[idx]] <- list(coef = coefVal, sd = model$nodes$confidence[nodeRef])
   }
 
-  print("about to build network")
-  print(paste0(inputText, edges))
+  print("Saving model prior to network modelling")
+  modelDefn <- paste0(inputText, edges)
+  save(modelDefn, file="buildGraph.RData")
+
+
+  #print("about to build network")
+  #print(paste0(inputText, edges))
+
+
 
   net <- model2network(paste0(inputText, edges), debug = FALSE)
 
@@ -167,6 +175,8 @@ buildGraph <- function(model, desc) {
   }
 
   allDists <- as.list(setNames(c(inDist, outDist), c(inputNodes, outNodes)))
+
+  #print(allDists)
   cfit <- custom.fit(net, allDists)
 
   cat("about to calculate sample distributions")
@@ -264,6 +274,8 @@ getCode <- function(name, nodeDF) {
 getValidEdges <- function(mapping, nodeDF, prevEdge = NULL, prefix) {
   #utils::str(nodeDF)
 
+  #save(mapping, nodeDF, prevEdge, prefix, file="validEdges.RData")
+
   edgeCols <- c("inputNode", "outputNode", "impact")
   edgeM <- matrix(data = NA, nrow = 0, ncol = length(edgeCols), dimnames = list(NULL, edgeCols))
 
@@ -309,6 +321,8 @@ parseMapping <- function(mapping, prevOutputs, prefix) {
   nodeDF <- getValidNodes(mapping, prevOutputs$nodes, prefix)
   edgeDF <- getValidEdges(mapping, nodeDF, prevEdge = prevOutputs$edges, prefix)
 
+  #save(nodeDF, edgeDF, file="mapping.RData")
+
   return(list(
     #New structure
     nodes = nodeDF,
@@ -329,7 +343,7 @@ parseSheet <- function(fName) {
       sheets <- sort(delNA(match(names, mappings)))
 
       cat("starting sheet parse")
-      print(sheets)
+      #print(sheets)
 
       if (sum(sheets == refs) == length(refs)) {
         #read all mapping tables
@@ -338,12 +352,6 @@ parseSheet <- function(fName) {
         p_op <- parseMapping(readXL(fName,mappings[3], startRow = 1), p_ba, prefix = "op")
         p_es <- parseMapping(readXL(fName,mappings[4], startRow = 1), p_op, prefix = "es")
         legend <- readXL(fName,mappings[5], startRow = 1)
-        
-        #print("building graphs")
-
-        #p_baNet <- buildGraph(p_ba, desc = list(inputCode = "p", outputCodes = "ba"))
-        #p_opNet <- buildGraph(p_op, desc = list(inputCode = "p", outputCodes = c("ba", "op")))
-        #p_esNet <- buildGraph(p_es, desc = list(inputCode = "p", outputCodes = c("ba", "op", "es")))
 
         print("sheet load completed")
         return(