[Jboost-cvs] jboost/scripts README,1.1,1.2 atreeplot.R,1.2,1.3

[Aaron A. <aa...@us...>]

Update of /cvsroot/jboost/jboost/scripts
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv28672

Modified Files:
	README atreeplot.R 
Log Message:
Small bug fixes and more documentation

Index: README
===================================================================
RCS file: /cvsroot/jboost/jboost/scripts/README,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** README	31 Jul 2008 22:15:33 -0000	1.1
--- README	15 Aug 2008 21:50:09 -0000	1.2
***************
*** 1,19 ****
! How to use scripts
  -----------------
  
  Requirements:
    * R (version 2.6 or higher)
!   * igraph (R package, can be obtained via install.packages or CRAN)
!   * jboost (R package, can be obtained via install.packages or CRAN)
  
- The best way to use the scripts is to install the jboost package.
- This can be done by using the 'install.packages()' from R or by
- downloading the JBoost package from CRAN and installing via 'R CMD
- INSTALL jboost'.
  
  
  
  
! How to make the package:
  --------------------------
  
--- 1,24 ----
! How to install scripts
  -----------------
  
  Requirements:
+   * Python (tested with version 2.5.2, though lower version may work)
    * R (version 2.6 or higher)
!     * igraph (R package, can be obtained via install.packages() or CRAN)
  
  
+ How to use the visualization scripts
+ --------------------------
+ 
+ source("atreeplot.R")
+ plot.atree(treefile="stem.output.tree", specfile="stem.spec")
+ 
+ source("marginplot.R")
+ plot.margin(infofile="stem.train.boosting.info", specfile="stem.spec", iteration=c(10,50,100))
  
  
  
! 
! How to make the package
  --------------------------
  

Index: atreeplot.R
===================================================================
RCS file: /cvsroot/jboost/jboost/scripts/atreeplot.R,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** atreeplot.R	31 Jul 2008 22:16:52 -0000	1.2
--- atreeplot.R	15 Aug 2008 21:50:11 -0000	1.3
***************
*** 37,41 ****
  
  
! plot.atree <- function(treefile, specfile, flip.labels=F, depth=-1, width=-1, height=-1) {
    labels = parse.labels(specfile)
    num.labels = length(labels);
--- 37,41 ----
  
  
! plot.atree <- function(treefile, specfile, flip.labels=F, depth=-1, plot.width=-1, plot.height=-1) {
    labels = parse.labels(specfile)
    num.labels = length(labels);
***************
*** 79,83 ****
        label = x[4]
        predType = x[4];
!       #show(c(type, iteration, index, label))
        x <- perl.re(predType, ".*MultiPrediction.*")
        y <- perl.re(predType, ".*BinaryPrediction.*=(.*)")
--- 79,83 ----
        label = x[4]
        predType = x[4];
!       show(c(type, iteration, index, label))
        x <- perl.re(predType, ".*MultiPrediction.*")
        y <- perl.re(predType, ".*BinaryPrediction.*=(.*)")
***************
*** 102,105 ****
--- 102,106 ----
        } else if (y[1]=="TRUE") {
          label = y[2]
+         show(sprintf("label is %0.5f", label))
          if(flip.labels) {
            label = as.numeric(label)
***************
*** 107,110 ****
--- 108,114 ----
            label = as.character(label)
          }
+       } else {
+         error(paste("Do not recognize prediction type:", label))
+         return
        }
      }
***************
*** 154,163 ****
          ans <- substr(index,nchar(index), nchar(index))
          if (ans=="0") {
-           E(g)$color[length(E(g))] <- "red"
-           E(g)$label[length(E(g))] <- "False"
-         } else if (ans=="1") {
            E(g)$color[length(E(g))] <- "green"
!           E(g)$label[length(E(g))] <- "True"
!         } else {
            error(paste("The splitter has an invalid return value!\n 1 or 0 expected, recieved", ans))
          }
--- 158,167 ----
          ans <- substr(index,nchar(index), nchar(index))
          if (ans=="0") {
            E(g)$color[length(E(g))] <- "green"
!           E(g)$label[length(E(g))] <- "           Yes"
!         } else if (ans=="1") {
!           E(g)$color[length(E(g))] <- "red"
!           E(g)$label[length(E(g))] <- "No           "
!         } else { 
            error(paste("The splitter has an invalid return value!\n 1 or 0 expected, recieved", ans))
          }
***************
*** 169,176 ****
      }
    
!     w <- warnings()
!     if (length(w)>0) {
!       show(w)
!     }
      i <- i + 1
    }
--- 173,180 ----
      }
    
!     #w <- warnings()
!     #if (length(w)>0) {
!     #  show(w)
!     #}
      i <- i + 1
    }
***************
*** 180,186 ****
    coords[,2] <- max(coords[,2])-coords[,2]
  
    fname <- sprintf("%s.eps", treefile)
    show(sprintf("Writing file to '%s'", fname))
!   postscript(file=sprintf("%s.eps", treefile), fonts=c("serif", "Palatino"), paper="special", width=70, height=40, horizontal=TRUE)
    plot(1, type="n", axes=FALSE, xlab=NA, ylab=NA, xlim=c(-1,1), ylim=c(-1,1))
    sw <- strwidth(paste("", V(g)$label, ""))
--- 184,198 ----
    coords[,2] <- max(coords[,2])-coords[,2]
  
+   if(plot.width<0) {
+     plot.width <- 8
+   }
+   if(plot.height<0) {
+     plot.height <- 9
+   }
+ 
    fname <- sprintf("%s.eps", treefile)
    show(sprintf("Writing file to '%s'", fname))
!   postscript(file=sprintf("%s.eps", treefile), fonts=c("serif", "Palatino"), 
!              paper="special", width=plot.width, height=plot.height, horizontal=TRUE)
    plot(1, type="n", axes=FALSE, xlab=NA, ylab=NA, xlim=c(-1,1), ylim=c(-1,1))
    sw <- strwidth(paste("", V(g)$label, ""))