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)

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> x <- array(list(1,1,'T',0,0,'T',0,0,'T',0,0,'T',0,0,'T',0,2,'T',0,0,'T',1,0,'T',0,0,'T',0,1,'T',1,1,'T',0,0,'T',0,2,'T',1,1,'T',0,2,'T',1,2,'T',1,4,'T',1,1,'T',0,0,'T',1,3,'T',0,2,'T',0,3,'T',0,1,'T',0,2,'T',1,1,'T',0,2,'T',0,1,'T',0,1,'T',0,0,'T',0,1,'T',0,0,'T',0,1,'T',0,2,'T',1,0,'T',0,0,'T',0,0,'T',1,3,'T',0,1,'T',0,1,'T',1,1,'T',0,3,'T',0,1,'T',0,2,'T',1,1,'T',0,1,'T',0,1,'T',0,0,'T',0,0,'T',0,1,'T',0,0,'T',1,1,'T',1,4,'T',0,0,'T',0,2,'T',0,0,'T',1,1,'T',0,2,'T',0,0,'T',0,0,'T',1,4,'T',1,1,'T',0,2,'T',0,0,'T',1,1,'T',0,0,'T',0,0,'T',1,3,'T',0,1,'T',0,0,'T',0,1,'T',0,0,'T',0,0,'T',0,1,'T',0,2,'T',0,0,'T',1,1,'T',0,0,'T',0,2,'T',1,2,'T',1,1,'T',0,0,'T',0,2,'T',0,0,'T',0,2,'T',0,1,'T',0,1,'T'),dim=c(3,86),dimnames=list(c('Treatment','Score','T40'),1:86))
>  y <- array(NA,dim=c(3,86),dimnames=list(c('Treatment','Score','T40'),1:86))
>  for (i in 1:dim(x)[1])
+  {
+  	for (j in 1:dim(x)[2])
+  	{
+  		y[i,j] <- as.numeric(x[i,j])
+  	}
+  }
There were 50 or more warnings (use warnings() to see the first 50)
> par4 = 'TRUE'
> par3 = '1'
> par2 = '3'
> par1 = '2'
> ylab = 'Y Variable Name'
> xlab = 'X Variable Name'
> main = 'Title Goes Here'
> cat1 <- as.numeric(par1) #
> cat2<- as.numeric(par2) #
> cat3 <- as.numeric(par3)
> intercept<-as.logical(par4)
> x <- t(x)
> x1<-as.numeric(x[,cat1])
> f1<-as.character(x[,cat2])
> f2 <- as.character(x[,cat3])
> xdf<-data.frame(x1,f1, f2)
> (V1<-dimnames(y)[[1]][cat1])
[1] "Score"
> (V2<-dimnames(y)[[1]][cat2])
[1] "T40"
> (V3 <-dimnames(y)[[1]][cat3])
[1] "Treatment"
> names(xdf)<-c('Response', 'Treatment_A', 'Treatment_B')
> if(intercept == FALSE) (lmxdf<-lm(Response ~ Treatment_A * Treatment_B- 1, data = xdf) ) else (lmxdf<-lm(Response ~ Treatment_A * Treatment_B, data = xdf) )
Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) : 
  contrasts can be applied only to factors with 2 or more levels
Calls: lm ... model.matrix -> model.matrix.default -> contrasts<-
Execution halted