R/main.utils.R

   1 #various util functions for the main program
   2
   3 #preliminary: replace NA's by averaging over each serie's values
   4 #TODO: find a better way to handle missing values
   5 replaceNAs = function(M)
   6 {
   7     n = nrow(M)
   8     m = ncol(M)
   9     res = M
  10     for (i in 1:n)
  11     {
  12         avg = mean(M[i,1:(m-2)] [!is.na(M[i,1:(m-2)])])
  13         res[i,1:(m-2)] [is.na(M[i,1:(m-2)])] = avg
  14     }
  15     return (res)
  16 }
  17
  18 #standardize matrix M (remove mean, divide by standard deviation)
  19 standardize = function(M)
  20 {
  21     avgM = colMeans(M, na.rm = TRUE)
  22     stdevs = sqrt( unlist( apply(M, 2, var, na.rm=TRUE) ) )
  23     res = t(M) - avgM
  24     res = t(res / stdevs)
  25     return (list("M"=res,"avg"=avgM,"stv"=stdevs))
  26 }
  27
  28 #opposite of the previous function: get back M from standardized form
  29 destandardize = function(std)
  30 {
  31     M = std$M
  32     M = t(M) * std$stv
  33     M = t(M + std$avg)
  34     return (M)
  35 }
  36
  37 #remap neighbors into some connex component
  38 remapNeighbors = function(NI, indices)
  39 {
  40     revIndices = rep(NA, length(NI))
  41     nc = length(indices)
  42     for (ii in 1:nc)
  43         revIndices[ indices[ii] ] = ii
  44     locNI = list("ix"=as.list(rep(NA,nc)), "ds"=as.list(rep(NA,nc)))
  45     for (ii in 1:nc)
  46     {
  47         locNI$ix[[ii]] = revIndices[ NI$ix[[ indices[ii] ]] ]
  48         locNI$ds[[ii]] = NI$ds[[ indices[ii] ]]
  49     }
  50     return (locNI)
  51 }
  52
  53 #check graph connexity
  54 getConnectedComponents = function(NIix)
  55 {
  56     return (.Call("getConnectedComponents", NIix));
  57 }
  58
  59 #auxiliary function to display clustering information
  60 promptForMapDisplay = function(stage, coordsM, NIix=NULL, clusters=NULL)
  61 {
  62     if (is.null(clusters))
  63         clusters = rep(1, nrow(coordsM))
  64
  65     shouldDisplay = ""
  66     if (stage == "interm")
  67         shouldDisplay = readline(">>> show intermediate map of neighborhoods ? (y/n)\n")
  68     else if (stage == "final")
  69     {
  70         shouldDisplay = readline(
  71 ">>> show final map of clusters ? (y/n) \
  72 NOTE: can be plotted later, see '? drawMapWithSites'\n")
  73     }
  74
  75     if (shouldDisplay == "y")
  76     {
  77         drawMapWithSites(coordsM, clusters)
  78         if (!is.null(NIix))
  79             drawNeighborhoodGraph(coordsM,NIix)
  80         print("Please press 'enter' to continue")
  81         readline()
  82         if (!is.null(dev.list()))
  83             dev.off()
  84     }
  85 }