R version 2.15.2 (2012-10-26) -- "Trick or Treat"
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: i686-pc-linux-gnu (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> x <- array(list(6.8
+ ,225
+ ,0.442
+ ,0.672
+ ,9.2
+ ,6.3
+ ,180
+ ,0.435
+ ,0.797
+ ,11.7
+ ,6.4
+ ,190
+ ,0.456
+ ,0.761
+ ,15.8
+ ,6.2
+ ,180
+ ,0.416
+ ,0.651
+ ,8.6
+ ,6.9
+ ,205
+ ,0.449
+ ,0.9
+ ,23.2
+ ,6.4
+ ,225
+ ,0.431
+ ,0.78
+ ,27.4
+ ,6.3
+ ,185
+ ,0.487
+ ,0.771
+ ,9.3
+ ,6.8
+ ,235
+ ,0.469
+ ,0.75
+ ,16
+ ,6.9
+ ,235
+ ,0.435
+ ,0.818
+ ,4.7
+ ,6.7
+ ,210
+ ,0.48
+ ,0.825
+ ,12.5
+ ,6.9
+ ,245
+ ,0.516
+ ,0.632
+ ,20.1
+ ,6.9
+ ,245
+ ,0.493
+ ,0.757
+ ,9.1
+ ,6.3
+ ,185
+ ,0.374
+ ,0.709
+ ,8.1
+ ,6.1
+ ,185
+ ,0.424
+ ,0.782
+ ,8.6
+ ,6.2
+ ,180
+ ,0.441
+ ,0.775
+ ,20.3
+ ,6.8
+ ,220
+ ,0.503
+ ,0.88
+ ,25
+ ,6.5
+ ,194
+ ,0.503
+ ,0.833
+ ,19.2
+ ,7.6
+ ,225
+ ,0.425
+ ,0.571
+ ,3.3
+ ,6.3
+ ,210
+ ,0.371
+ ,0.816
+ ,11.2
+ ,7.1
+ ,240
+ ,0.504
+ ,0.714
+ ,10.5
+ ,6.8
+ ,225
+ ,0.4
+ ,0.765
+ ,10.1
+ ,7.3
+ ,263
+ ,0.482
+ ,0.655
+ ,7.2
+ ,6.4
+ ,210
+ ,0.475
+ ,0.244
+ ,13.6
+ ,6.8
+ ,235
+ ,0.428
+ ,0.728
+ ,9
+ ,7.2
+ ,230
+ ,0.559
+ ,0.721
+ ,24.6
+ ,6.4
+ ,190
+ ,0.441
+ ,0.757
+ ,12.6
+ ,6.6
+ ,220
+ ,0.492
+ ,0.747
+ ,5.6
+ ,6.8
+ ,210
+ ,0.402
+ ,0.739
+ ,8.7
+ ,6.1
+ ,180
+ ,0.415
+ ,0.713
+ ,7.7
+ ,6.5
+ ,235
+ ,0.492
+ ,0.742
+ ,24.1
+ ,6.4
+ ,185
+ ,0.484
+ ,0.861
+ ,11.7
+ ,6
+ ,175
+ ,0.387
+ ,0.721
+ ,7.7
+ ,6
+ ,192
+ ,0.436
+ ,0.785
+ ,9.6
+ ,7.3
+ ,263
+ ,0.482
+ ,0.655
+ ,7.2
+ ,6.1
+ ,180
+ ,0.34
+ ,0.821
+ ,12.3
+ ,6.7
+ ,240
+ ,0.516
+ ,0.728
+ ,8.9
+ ,6.4
+ ,210
+ ,0.475
+ ,0.846
+ ,13.6
+ ,5.8
+ ,160
+ ,0.412
+ ,0.813
+ ,11.2
+ ,6.9
+ ,230
+ ,0.411
+ ,0.595
+ ,2.8
+ ,7
+ ,245
+ ,0.407
+ ,0.573
+ ,3.2
+ ,7.3
+ ,228
+ ,0.445
+ ,0.726
+ ,9.4
+ ,5.9
+ ,155
+ ,0.291
+ ,0.707
+ ,11.9
+ ,6.2
+ ,200
+ ,0.449
+ ,0.804
+ ,15.4
+ ,6.8
+ ,235
+ ,0.546
+ ,0.784
+ ,7.4
+ ,7
+ ,235
+ ,0.48
+ ,0.744
+ ,18.9
+ ,5.9
+ ,105
+ ,0.359
+ ,0.839
+ ,7.9
+ ,6.1
+ ,180
+ ,0.528
+ ,0.79
+ ,12.2
+ ,5.7
+ ,185
+ ,0.352
+ ,0.701
+ ,11
+ ,7.1
+ ,245
+ ,0.414
+ ,0.778
+ ,2.8
+ ,5.8
+ ,180
+ ,0.425
+ ,0.872
+ ,11.8
+ ,7.4
+ ,240
+ ,0.599
+ ,0.713
+ ,17.1
+ ,6.8
+ ,225
+ ,0.482
+ ,0.701
+ ,11.6
+ ,6.8
+ ,215
+ ,0.457
+ ,0.734
+ ,5.8
+ ,7
+ ,230
+ ,0.435
+ ,0.764
+ ,8.3)
+ ,dim=c(5
+ ,54)
+ ,dimnames=list(c('X1'
+ ,'X2'
+ ,'X3'
+ ,'X4'
+ ,'X5')
+ ,1:54))
>  y <- array(NA,dim=c(5,54),dimnames=list(c('X1','X2','X3','X4','X5'),1:54))
>  for (i in 1:dim(x)[1])
+  {
+  	for (j in 1:dim(x)[2])
+  	{
+  		y[i,j] <- as.numeric(x[i,j])
+  	}
+  }
> par4 = 'no'
> par3 = '4'
> par2 = 'none'
> par1 = '2'
> library(party)
Loading required package: survival
Loading required package: splines
Loading required package: grid
Loading required package: modeltools
Loading required package: stats4
Loading required package: coin
Loading required package: mvtnorm
Loading required package: zoo

Attaching package: 'zoo'

The following object(s) are masked from 'package:base':

    as.Date, as.Date.numeric

Loading required package: sandwich
Loading required package: strucchange
Loading required package: vcd
Loading required package: MASS
Loading required package: colorspace
> library(Hmisc)
Hmisc library by Frank E Harrell Jr

Type library(help='Hmisc'), ?Overview, or ?Hmisc.Overview')
to see overall documentation.

NOTE:Hmisc no longer redefines [.factor to drop unused levels when
subsetting.  To get the old behavior of Hmisc type dropUnusedLevels().


Attaching package: 'Hmisc'

The following object(s) are masked from 'package:survival':

    untangle.specials

The following object(s) are masked from 'package:base':

    format.pval, round.POSIXt, trunc.POSIXt, units

> par1 <- as.numeric(par1)
> par3 <- as.numeric(par3)
> x <- data.frame(t(y))
> is.data.frame(x)
[1] TRUE
> x <- x[!is.na(x[,par1]),]
> k <- length(x[1,])
> n <- length(x[,1])
> colnames(x)[par1]
[1] "X2"
> x[,par1]
 [1] 225 180 190 180 205 225 185 235 235 210 245 245 185 185 180 220 194 225 210
[20] 240 225 263 210 235 230 190 220 210 180 235 185 175 192 263 180 240 210 160
[39] 230 245 228 155 200 235 235 105 180 185 245 180 240 225 215 230
> if (par2 == 'kmeans') {
+ cl <- kmeans(x[,par1], par3)
+ print(cl)
+ clm <- matrix(cbind(cl$centers,1:par3),ncol=2)
+ clm <- clm[sort.list(clm[,1]),]
+ for (i in 1:par3) {
+ cl$cluster[cl$cluster==clm[i,2]] <- paste('C',i,sep='')
+ }
+ cl$cluster <- as.factor(cl$cluster)
+ print(cl$cluster)
+ x[,par1] <- cl$cluster
+ }
> if (par2 == 'quantiles') {
+ x[,par1] <- cut2(x[,par1],g=par3)
+ }
> if (par2 == 'hclust') {
+ hc <- hclust(dist(x[,par1])^2, 'cen')
+ print(hc)
+ memb <- cutree(hc, k = par3)
+ dum <- c(mean(x[memb==1,par1]))
+ for (i in 2:par3) {
+ dum <- c(dum, mean(x[memb==i,par1]))
+ }
+ hcm <- matrix(cbind(dum,1:par3),ncol=2)
+ hcm <- hcm[sort.list(hcm[,1]),]
+ for (i in 1:par3) {
+ memb[memb==hcm[i,2]] <- paste('C',i,sep='')
+ }
+ memb <- as.factor(memb)
+ print(memb)
+ x[,par1] <- memb
+ }
> if (par2=='equal') {
+ ed <- cut(as.numeric(x[,par1]),par3,labels=paste('C',1:par3,sep=''))
+ x[,par1] <- as.factor(ed)
+ }
> table(x[,par1])

105 155 160 175 180 185 190 192 194 200 205 210 215 220 225 228 230 235 240 245 
  1   1   1   1   7   5   2   1   1   1   1   5   1   2   5   1   3   6   3   4 
263 
  2 
> colnames(x)
[1] "X1" "X2" "X3" "X4" "X5"
> colnames(x)[par1]
[1] "X2"
> x[,par1]
 [1] 225 180 190 180 205 225 185 235 235 210 245 245 185 185 180 220 194 225 210
[20] 240 225 263 210 235 230 190 220 210 180 235 185 175 192 263 180 240 210 160
[39] 230 245 228 155 200 235 235 105 180 185 245 180 240 225 215 230
> if (par2 == 'none') {
+ m <- ctree(as.formula(paste(colnames(x)[par1],' ~ .',sep='')),data = x)
+ }
> 
> #Note: the /var/wessaorg/rcomp/createtable file can be downloaded at http://www.wessa.net/cretab
> load(file="/var/wessaorg/rcomp/createtable")
> 
> if (par2 != 'none') {
+ m <- ctree(as.formula(paste('as.factor(',colnames(x)[par1],') ~ .',sep='')),data = x)
+ if (par4=='yes') {
+ a<-table.start()
+ a<-table.row.start(a)
+ a<-table.element(a,'10-Fold Cross Validation',3+2*par3,TRUE)
+ a<-table.row.end(a)
+ a<-table.row.start(a)
+ a<-table.element(a,'',1,TRUE)
+ a<-table.element(a,'Prediction (training)',par3+1,TRUE)
+ a<-table.element(a,'Prediction (testing)',par3+1,TRUE)
+ a<-table.row.end(a)
+ a<-table.row.start(a)
+ a<-table.element(a,'Actual',1,TRUE)
+ for (jjj in 1:par3) a<-table.element(a,paste('C',jjj,sep=''),1,TRUE)
+ a<-table.element(a,'CV',1,TRUE)
+ for (jjj in 1:par3) a<-table.element(a,paste('C',jjj,sep=''),1,TRUE)
+ a<-table.element(a,'CV',1,TRUE)
+ a<-table.row.end(a)
+ for (i in 1:10) {
+ ind <- sample(2, nrow(x), replace=T, prob=c(0.9,0.1))
+ m.ct <- ctree(as.formula(paste('as.factor(',colnames(x)[par1],') ~ .',sep='')),data =x[ind==1,])
+ if (i==1) {
+ m.ct.i.pred <- predict(m.ct, newdata=x[ind==1,])
+ m.ct.i.actu <- x[ind==1,par1]
+ m.ct.x.pred <- predict(m.ct, newdata=x[ind==2,])
+ m.ct.x.actu <- x[ind==2,par1]
+ } else {
+ m.ct.i.pred <- c(m.ct.i.pred,predict(m.ct, newdata=x[ind==1,]))
+ m.ct.i.actu <- c(m.ct.i.actu,x[ind==1,par1])
+ m.ct.x.pred <- c(m.ct.x.pred,predict(m.ct, newdata=x[ind==2,]))
+ m.ct.x.actu <- c(m.ct.x.actu,x[ind==2,par1])
+ }
+ }
+ print(m.ct.i.tab <- table(m.ct.i.actu,m.ct.i.pred))
+ numer <- 0
+ for (i in 1:par3) {
+ print(m.ct.i.tab[i,i] / sum(m.ct.i.tab[i,]))
+ numer <- numer + m.ct.i.tab[i,i]
+ }
+ print(m.ct.i.cp <- numer / sum(m.ct.i.tab))
+ print(m.ct.x.tab <- table(m.ct.x.actu,m.ct.x.pred))
+ numer <- 0
+ for (i in 1:par3) {
+ print(m.ct.x.tab[i,i] / sum(m.ct.x.tab[i,]))
+ numer <- numer + m.ct.x.tab[i,i]
+ }
+ print(m.ct.x.cp <- numer / sum(m.ct.x.tab))
+ for (i in 1:par3) {
+ a<-table.row.start(a)
+ a<-table.element(a,paste('C',i,sep=''),1,TRUE)
+ for (jjj in 1:par3) a<-table.element(a,m.ct.i.tab[i,jjj])
+ a<-table.element(a,round(m.ct.i.tab[i,i]/sum(m.ct.i.tab[i,]),4))
+ for (jjj in 1:par3) a<-table.element(a,m.ct.x.tab[i,jjj])
+ a<-table.element(a,round(m.ct.x.tab[i,i]/sum(m.ct.x.tab[i,]),4))
+ a<-table.row.end(a)
+ }
+ a<-table.row.start(a)
+ a<-table.element(a,'Overall',1,TRUE)
+ for (jjj in 1:par3) a<-table.element(a,'-')
+ a<-table.element(a,round(m.ct.i.cp,4))
+ for (jjj in 1:par3) a<-table.element(a,'-')
+ a<-table.element(a,round(m.ct.x.cp,4))
+ a<-table.row.end(a)
+ a<-table.end(a)
+ table.save(a,file="/var/wessaorg/rcomp/tmp/1whys1355259526.tab") 
+ }
+ }
> m

	 Conditional inference tree with 4 terminal nodes

Response:  X2 
Inputs:  X1, X3, X4, X5 
Number of observations:  54 

1) X1 <= 6.4; criterion = 1, statistic = 36.893
  2) X1 <= 6; criterion = 0.981, statistic = 7.993
    3)*  weights = 7 
  2) X1 > 6
    4)*  weights = 17 
1) X1 > 6.4
  5) X4 <= 0.728; criterion = 0.975, statistic = 7.489
    6)*  weights = 14 
  5) X4 > 0.728
    7)*  weights = 16 
> postscript(file="/var/wessaorg/rcomp/tmp/2ndrk1355259526.ps",horizontal=F,onefile=F,pagecentre=F,paper="special",width=8.3333333333333,height=5.5555555555556) 
> plot(m)
> dev.off()
null device 
          1 
> postscript(file="/var/wessaorg/rcomp/tmp/3wfq11355259526.ps",horizontal=F,onefile=F,pagecentre=F,paper="special",width=8.3333333333333,height=5.5555555555556) 
> plot(x[,par1] ~ as.factor(where(m)),main='Response by Terminal Node',xlab='Terminal Node',ylab='Response')
> dev.off()
null device 
          1 
> if (par2 == 'none') {
+ forec <- predict(m)
+ result <- as.data.frame(cbind(x[,par1],forec,x[,par1]-forec))
+ colnames(result) <- c('Actuals','Forecasts','Residuals')
+ print(result)
+ }
   Actuals Forecasts  Residuals
1      225  238.1429 -13.142857
2      180  191.4706 -11.470588
3      190  191.4706  -1.470588
4      180  191.4706 -11.470588
5      205  224.6250 -19.625000
6      225  191.4706  33.529412
7      185  191.4706  -6.470588
8      235  224.6250  10.375000
9      235  224.6250  10.375000
10     210  224.6250 -14.625000
11     245  238.1429   6.857143
12     245  224.6250  20.375000
13     185  191.4706  -6.470588
14     185  191.4706  -6.470588
15     180  191.4706 -11.470588
16     220  224.6250  -4.625000
17     194  224.6250 -30.625000
18     225  238.1429 -13.142857
19     210  191.4706  18.529412
20     240  238.1429   1.857143
21     225  224.6250   0.375000
22     263  238.1429  24.857143
23     210  191.4706  18.529412
24     235  238.1429  -3.142857
25     230  238.1429  -8.142857
26     190  191.4706  -1.470588
27     220  224.6250  -4.625000
28     210  224.6250 -14.625000
29     180  191.4706 -11.470588
30     235  224.6250  10.375000
31     185  191.4706  -6.470588
32     175  164.5714  10.428571
33     192  164.5714  27.428571
34     263  238.1429  24.857143
35     180  191.4706 -11.470588
36     240  238.1429   1.857143
37     210  191.4706  18.529412
38     160  164.5714  -4.571429
39     230  238.1429  -8.142857
40     245  238.1429   6.857143
41     228  238.1429 -10.142857
42     155  164.5714  -9.571429
43     200  191.4706   8.529412
44     235  224.6250  10.375000
45     235  224.6250  10.375000
46     105  164.5714 -59.571429
47     180  191.4706 -11.470588
48     185  164.5714  20.428571
49     245  224.6250  20.375000
50     180  164.5714  15.428571
51     240  238.1429   1.857143
52     225  238.1429 -13.142857
53     215  224.6250  -9.625000
54     230  224.6250   5.375000
> if (par2 != 'none') {
+ print(cbind(as.factor(x[,par1]),predict(m)))
+ myt <- table(as.factor(x[,par1]),predict(m))
+ print(myt)
+ }
> postscript(file="/var/wessaorg/rcomp/tmp/47yj51355259526.ps",horizontal=F,onefile=F,pagecentre=F,paper="special",width=8.3333333333333,height=5.5555555555556) 
> if(par2=='none') {
+ op <- par(mfrow=c(2,2))
+ plot(density(result$Actuals),main='Kernel Density Plot of Actuals')
+ plot(density(result$Residuals),main='Kernel Density Plot of Residuals')
+ plot(result$Forecasts,result$Actuals,main='Actuals versus Predictions',xlab='Predictions',ylab='Actuals')
+ plot(density(result$Forecasts),main='Kernel Density Plot of Predictions')
+ par(op)
+ }
> if(par2!='none') {
+ plot(myt,main='Confusion Matrix',xlab='Actual',ylab='Predicted')
+ }
> dev.off()
null device 
          1 
> if (par2 == 'none') {
+ detcoef <- cor(result$Forecasts,result$Actuals)
+ a<-table.start()
+ a<-table.row.start(a)
+ a<-table.element(a,'Goodness of Fit',2,TRUE)
+ a<-table.row.end(a)
+ a<-table.row.start(a)
+ a<-table.element(a,'Correlation',1,TRUE)
+ a<-table.element(a,round(detcoef,4))
+ a<-table.row.end(a)
+ a<-table.row.start(a)
+ a<-table.element(a,'R-squared',1,TRUE)
+ a<-table.element(a,round(detcoef*detcoef,4))
+ a<-table.row.end(a)
+ a<-table.row.start(a)
+ a<-table.element(a,'RMSE',1,TRUE)
+ a<-table.element(a,round(sqrt(mean((result$Residuals)^2)),4))
+ a<-table.row.end(a)
+ a<-table.end(a)
+ table.save(a,file="/var/wessaorg/rcomp/tmp/5zul41355259526.tab") 
+ a<-table.start()
+ a<-table.row.start(a)
+ a<-table.element(a,'Actuals, Predictions, and Residuals',4,TRUE)
+ a<-table.row.end(a)
+ a<-table.row.start(a)
+ a<-table.element(a,'#',header=TRUE)
+ a<-table.element(a,'Actuals',header=TRUE)
+ a<-table.element(a,'Forecasts',header=TRUE)
+ a<-table.element(a,'Residuals',header=TRUE)
+ a<-table.row.end(a)
+ for (i in 1:length(result$Actuals)) {
+ a<-table.row.start(a)
+ a<-table.element(a,i,header=TRUE)
+ a<-table.element(a,result$Actuals[i])
+ a<-table.element(a,result$Forecasts[i])
+ a<-table.element(a,result$Residuals[i])
+ a<-table.row.end(a)
+ }
+ a<-table.end(a)
+ table.save(a,file="/var/wessaorg/rcomp/tmp/657lf1355259526.tab") 
+ }
> if (par2 != 'none') {
+ a<-table.start()
+ a<-table.row.start(a)
+ a<-table.element(a,'Confusion Matrix (predicted in columns / actuals in rows)',par3+1,TRUE)
+ a<-table.row.end(a)
+ a<-table.row.start(a)
+ a<-table.element(a,'',1,TRUE)
+ for (i in 1:par3) {
+ a<-table.element(a,paste('C',i,sep=''),1,TRUE)
+ }
+ a<-table.row.end(a)
+ for (i in 1:par3) {
+ a<-table.row.start(a)
+ a<-table.element(a,paste('C',i,sep=''),1,TRUE)
+ for (j in 1:par3) {
+ a<-table.element(a,myt[i,j])
+ }
+ a<-table.row.end(a)
+ }
+ a<-table.end(a)
+ table.save(a,file="/var/wessaorg/rcomp/tmp/7mq7n1355259526.tab") 
+ }
> 
> try(system("convert tmp/2ndrk1355259526.ps tmp/2ndrk1355259526.png",intern=TRUE))
character(0)
> try(system("convert tmp/3wfq11355259526.ps tmp/3wfq11355259526.png",intern=TRUE))
character(0)
> try(system("convert tmp/47yj51355259526.ps tmp/47yj51355259526.png",intern=TRUE))
character(0)
> 
> 
> proc.time()
   user  system elapsed 
  3.804   0.460   4.243