R version 2.8.0 (2008-10-20)
Copyright (C) 2008 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

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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(104.37
+ ,1
+ ,1
+ ,167.16
+ ,101.56
+ ,100.93
+ ,104.89
+ ,2
+ ,2
+ ,179.84
+ ,102.13
+ ,101.18
+ ,105.15
+ ,3
+ ,3
+ ,174.44
+ ,102.39
+ ,101.11
+ ,105.72
+ ,4
+ ,4
+ ,180.35
+ ,102.42
+ ,102.42
+ ,106.38
+ ,5
+ ,5
+ ,193.17
+ ,103.87
+ ,102.37
+ ,106.40
+ ,6
+ ,6
+ ,195.16
+ ,104.44
+ ,101.95
+ ,106.47
+ ,7
+ ,7
+ ,202.43
+ ,104.97
+ ,102.20
+ ,106.59
+ ,8
+ ,8
+ ,189.91
+ ,105.17
+ ,103.35
+ ,106.76
+ ,9
+ ,9
+ ,195.98
+ ,105.35
+ ,103.65
+ ,107.35
+ ,10
+ ,10
+ ,212.09
+ ,104.65
+ ,102.06
+ ,107.81
+ ,11
+ ,11
+ ,205.81
+ ,106.62
+ ,102.66
+ ,108.03
+ ,12
+ ,12
+ ,204.31
+ ,107.05
+ ,102.32
+ ,109.08
+ ,1
+ ,13
+ ,196.07
+ ,112.30
+ ,102.21
+ ,109.86
+ ,2
+ ,14
+ ,199.98
+ ,114.70
+ ,102.33
+ ,110.29
+ ,3
+ ,15
+ ,199.1
+ ,115.40
+ ,104.41
+ ,110.34
+ ,4
+ ,16
+ ,198.31
+ ,115.64
+ ,104.33
+ ,110.59
+ ,5
+ ,17
+ ,195.72
+ ,115.66
+ ,105.27
+ ,110.64
+ ,6
+ ,18
+ ,223.04
+ ,114.50
+ ,105.34
+ ,110.83
+ ,7
+ ,19
+ ,238.41
+ ,115.14
+ ,104.88
+ ,111.51
+ ,8
+ ,20
+ ,259.73
+ ,115.41
+ ,105.49
+ ,113.32
+ ,9
+ ,21
+ ,326.54
+ ,119.32
+ ,105.90
+ ,115.89
+ ,10
+ ,22
+ ,335.15
+ ,124.77
+ ,105.39
+ ,116.51
+ ,11
+ ,23
+ ,321.81
+ ,130.96
+ ,104.40
+ ,117.44
+ ,12
+ ,24
+ ,368.62
+ ,141.02
+ ,106.19
+ ,118.25
+ ,1
+ ,25
+ ,369.59
+ ,150.60
+ ,106.54
+ ,118.65
+ ,2
+ ,26
+ ,425
+ ,151.10
+ ,108.26
+ ,118.52
+ ,3
+ ,27
+ ,439.72
+ ,157.19
+ ,106.95
+ ,119.07
+ ,4
+ ,28
+ ,362.23
+ ,157.28
+ ,108.32
+ ,119.12
+ ,5
+ ,29
+ ,328.76
+ ,156.54
+ ,108.35
+ ,119.28
+ ,6
+ ,30
+ ,348.55
+ ,159.62
+ ,109.29
+ ,119.30
+ ,7
+ ,31
+ ,328.18
+ ,163.77
+ ,109.46
+ ,119.44
+ ,8
+ ,32
+ ,329.34
+ ,165.08
+ ,109.50
+ ,119.57
+ ,9
+ ,33
+ ,295.55
+ ,164.75
+ ,109.84
+ ,119.93
+ ,10
+ ,34
+ ,237.38
+ ,163.93
+ ,108.73
+ ,120.03
+ ,11
+ ,35
+ ,226.85
+ ,157.51
+ ,109.38
+ ,119.66
+ ,12
+ ,36
+ ,220.14
+ ,153.36
+ ,109.97
+ ,119.46
+ ,1
+ ,37
+ ,239.36
+ ,156.83
+ ,111.10
+ ,119.48
+ ,2
+ ,38
+ ,224.69
+ ,154.98
+ ,110.53
+ ,119.56
+ ,3
+ ,39
+ ,230.98
+ ,155.02
+ ,110.23
+ ,119.43
+ ,4
+ ,40
+ ,233.47
+ ,153.34
+ ,109.41
+ ,119.57
+ ,5
+ ,41
+ ,256.7
+ ,153.19
+ ,108.94
+ ,119.59
+ ,6
+ ,42
+ ,253.41
+ ,152.80
+ ,109.81
+ ,119.50
+ ,7
+ ,43
+ ,224.95
+ ,152.97
+ ,109.20
+ ,119.54
+ ,8
+ ,44
+ ,210.37
+ ,152.96
+ ,109.45
+ ,119.56
+ ,9
+ ,45
+ ,191.09
+ ,152.35
+ ,110.61
+ ,119.61
+ ,10
+ ,46
+ ,198.85
+ ,151.88
+ ,109.44
+ ,119.64
+ ,11
+ ,47
+ ,211.04
+ ,150.27
+ ,109.77
+ ,119.60
+ ,12
+ ,48
+ ,206.25
+ ,148.80
+ ,108.04
+ ,119.71
+ ,1
+ ,49
+ ,201.19
+ ,149.28
+ ,109.65
+ ,119.72
+ ,2
+ ,50
+ ,194.37
+ ,148.64
+ ,111.69
+ ,119.66
+ ,3
+ ,51
+ ,191.08
+ ,150.36
+ ,111.65
+ ,119.76
+ ,4
+ ,52
+ ,192.87
+ ,149.69
+ ,112.04
+ ,119.80
+ ,5
+ ,53
+ ,181.61
+ ,152.94
+ ,111.42
+ ,119.88
+ ,6
+ ,54
+ ,157.67
+ ,155.18
+ ,112.25
+ ,119.78
+ ,7
+ ,55
+ ,196.14
+ ,156.32
+ ,111.46
+ ,120.08
+ ,8
+ ,56
+ ,246.35
+ ,156.25
+ ,111.62
+ ,120.22
+ ,9
+ ,57
+ ,271.9
+ ,155.52
+ ,111.77)
+ ,dim=c(6
+ ,57)
+ ,dimnames=list(c('Brood'
+ ,'Maand'
+ ,'Trend'
+ ,'Tarwe'
+ ,'Meel'
+ ,'Water')
+ ,1:57))
>  y <- array(NA,dim=c(6,57),dimnames=list(c('Brood','Maand','Trend','Tarwe','Meel','Water'),1:57))
>  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 = ''
> par2 = 'none'
> par1 = '1'
> 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.numeric 

Loading required package: sandwich
Loading required package: strucchange
Loading required package: vcd
Loading required package: MASS
Loading required package: colorspace
> library(Hmisc)

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] "Brood"
> x[,par1]
 [1] 104.37 104.89 105.15 105.72 106.38 106.40 106.47 106.59 106.76 107.35
[11] 107.81 108.03 109.08 109.86 110.29 110.34 110.59 110.64 110.83 111.51
[21] 113.32 115.89 116.51 117.44 118.25 118.65 118.52 119.07 119.12 119.28
[31] 119.30 119.44 119.57 119.93 120.03 119.66 119.46 119.48 119.56 119.43
[41] 119.57 119.59 119.50 119.54 119.56 119.61 119.64 119.60 119.71 119.72
[51] 119.66 119.76 119.80 119.88 119.78 120.08 120.22
> 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])

104.37 104.89 105.15 105.72 106.38  106.4 106.47 106.59 106.76 107.35 107.81 
     1      1      1      1      1      1      1      1      1      1      1 
108.03 109.08 109.86 110.29 110.34 110.59 110.64 110.83 111.51 113.32 115.89 
     1      1      1      1      1      1      1      1      1      1      1 
116.51 117.44 118.25 118.52 118.65 119.07 119.12 119.28  119.3 119.43 119.44 
     1      1      1      1      1      1      1      1      1      1      1 
119.46 119.48  119.5 119.54 119.56 119.57 119.59  119.6 119.61 119.64 119.66 
     1      1      1      1      2      2      1      1      1      1      2 
119.71 119.72 119.76 119.78  119.8 119.88 119.93 120.03 120.08 120.22 
     1      1      1      1      1      1      1      1      1      1 
> colnames(x)
[1] "Brood" "Maand" "Trend" "Tarwe" "Meel"  "Water"
> colnames(x)[par1]
[1] "Brood"
> x[,par1]
 [1] 104.37 104.89 105.15 105.72 106.38 106.40 106.47 106.59 106.76 107.35
[11] 107.81 108.03 109.08 109.86 110.29 110.34 110.59 110.64 110.83 111.51
[21] 113.32 115.89 116.51 117.44 118.25 118.65 118.52 119.07 119.12 119.28
[31] 119.30 119.44 119.57 119.93 120.03 119.66 119.46 119.48 119.56 119.43
[41] 119.57 119.59 119.50 119.54 119.56 119.61 119.64 119.60 119.71 119.72
[51] 119.66 119.76 119.80 119.88 119.78 120.08 120.22
> if (par2 == 'none') {
+ m <- ctree(as.formula(paste(colnames(x)[par1],' ~ .',sep='')),data = x)
+ }
> 
> #Note: the /var/www/html/freestat/rcomp/createtable file can be downloaded at http://www.wessa.net/cretab
> load(file="/var/www/html/freestat/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/www/html/freestat/rcomp/tmp/1krdv1293210371.tab") 
+ }
+ }
> m

	 Conditional inference tree with 6 terminal nodes

Response:  Brood 
Inputs:  Maand, Trend, Tarwe, Meel, Water 
Number of observations:  57 

1) Meel <= 119.32; criterion = 1, statistic = 53.077
  2) Trend <= 12; criterion = 1, statistic = 19.334
    3)*  weights = 12 
  2) Trend > 12
    4)*  weights = 9 
1) Meel > 119.32
  5) Water <= 108.26; criterion = 1, statistic = 24.72
    6)*  weights = 7 
  5) Water > 108.26
    7) Trend <= 47; criterion = 0.999, statistic = 13.827
      8) Tarwe <= 253.41; criterion = 0.985, statistic = 8.767
        9)*  weights = 13 
      8) Tarwe > 253.41
        10)*  weights = 7 
    7) Trend > 47
      11)*  weights = 9 
> postscript(file="/var/www/html/freestat/rcomp/tmp/2krdv1293210371.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/www/html/freestat/rcomp/tmp/3krdv1293210371.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   104.37  106.3267 -1.956666667
2   104.89  106.3267 -1.436666667
3   105.15  106.3267 -1.176666667
4   105.72  106.3267 -0.606666667
5   106.38  106.3267  0.053333333
6   106.40  106.3267  0.073333333
7   106.47  106.3267  0.143333333
8   106.59  106.3267  0.263333333
9   106.76  106.3267  0.433333333
10  107.35  106.3267  1.023333333
11  107.81  106.3267  1.483333333
12  108.03  106.3267  1.703333333
13  109.08  110.7178 -1.637777778
14  109.86  110.7178 -0.857777778
15  110.29  110.7178 -0.427777778
16  110.34  110.7178 -0.377777778
17  110.59  110.7178 -0.127777778
18  110.64  110.7178 -0.077777778
19  110.83  110.7178  0.112222222
20  111.51  110.7178  0.792222222
21  113.32  110.7178  2.602222222
22  115.89  117.8371 -1.947142857
23  116.51  117.8371 -1.327142857
24  117.44  117.8371 -0.397142857
25  118.25  117.8371  0.412857143
26  118.65  117.8371  0.812857143
27  118.52  117.8371  0.682857143
28  119.07  119.3357 -0.265714286
29  119.12  119.3357 -0.215714286
30  119.28  119.3357 -0.055714286
31  119.30  119.3357 -0.035714286
32  119.44  119.3357  0.104285714
33  119.57  119.3357  0.234285714
34  119.93  119.6146  0.315384615
35  120.03  119.6146  0.415384615
36  119.66  119.6146  0.045384615
37  119.46  119.6146 -0.154615385
38  119.48  119.6146 -0.134615385
39  119.56  119.6146 -0.054615385
40  119.43  119.6146 -0.184615385
41  119.57  119.3357  0.234285714
42  119.59  119.6146 -0.024615385
43  119.50  119.6146 -0.114615385
44  119.54  119.6146 -0.074615385
45  119.56  119.6146 -0.054615385
46  119.61  119.6146 -0.004615385
47  119.64  119.6146  0.025384615
48  119.60  117.8371  1.762857143
49  119.71  119.8456 -0.135555556
50  119.72  119.8456 -0.125555556
51  119.66  119.8456 -0.185555556
52  119.76  119.8456 -0.085555556
53  119.80  119.8456 -0.045555556
54  119.88  119.8456  0.034444444
55  119.78  119.8456 -0.065555556
56  120.08  119.8456  0.234444444
57  120.22  119.8456  0.374444444
> if (par2 != 'none') {
+ print(cbind(as.factor(x[,par1]),predict(m)))
+ myt <- table(as.factor(x[,par1]),predict(m))
+ print(myt)
+ }
> postscript(file="/var/www/html/freestat/rcomp/tmp/4didy1293210371.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/www/html/freestat/rcomp/tmp/5rasp1293210371.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/www/html/freestat/rcomp/tmp/6jjaa1293210371.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/www/html/freestat/rcomp/tmp/7n2qy1293210371.tab") 
+ }
> 
> try(system("convert tmp/2krdv1293210371.ps tmp/2krdv1293210371.png",intern=TRUE))
character(0)
> try(system("convert tmp/3krdv1293210371.ps tmp/3krdv1293210371.png",intern=TRUE))
character(0)
> try(system("convert tmp/4didy1293210371.ps tmp/4didy1293210371.png",intern=TRUE))
character(0)
> 
> 
> proc.time()
   user  system elapsed 
  3.988   0.744   4.144