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

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> x <- array(list(1,1,'T',1,1,'T',0,1,'T',0,0,'T',1,1,'T',1,1,'T',1,1,'T',0,1,'T',0,1,'T',1,1,'T',0,0,'T',0,1,'T',0,1,'T',0,1,'T',0,0,'T',1,1,'T',1,1,'T',1,1,'T',0,1,'T',0,0,'T',1,1,'T',1,1,'T',0,0,'T',1,0,'T',1,1,'T',1,0,'T',1,1,'T',0,0,'T',0,0,'T',1,1,'T',1,0,'T',1,1,'T',0,0,'T',0,0,'T',0,0,'T',1,1,'T',1,1,'T',0,1,'E',0,1,'E',1,1,'E',1,1,'E',1,1,'E',1,1,'E',1,1,'E',0,0,'E',0,1,'E',0,1,'E',1,1,'E',1,1,'E',0,0,'E',0,1,'E',1,1,'E',0,1,'E',0,0,'E',0,1,'E',0,1,'E',0,1,'E',0,1,'E',0,0,'E',0,0,'E',0,1,'E',1,1,'E',1,1,'E',1,0,'E',0,0,'E',0,1,'E',0,1,'E',0,0,'E',1,1,'E',1,1,'E',0,1,'S',0,1,'S',0,1,'S',0,1,'S',1,1,'S',1,0,'S',0,0,'S',1,1,'S',1,0,'S',1,1,'S',0,0,'S',0,0,'S',0,0,'S',1,0,'S',0,0,'S',0,0,'S',1,0,'S',1,1,'S',0,0,'S',0,0,'S',1,1,'S',1,1,'S',1,1,'S',0,1,'S',1,1,'S',1,1,'S',1,1,'S',1,1,'S',0,0,'S',0,0,'S',1,1,'S',0,0,'S',0,0,'S',0,0,'S',0,1,'S'),dim=c(3,105),dimnames=list(c('Pre','Post','Treatment'),1:105))
>  y <- array(NA,dim=c(3,105),dimnames=list(c('Pre','Post','Treatment'),1:105))
>  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)
> par20 = ''
> par19 = ''
> par18 = ''
> par17 = ''
> par16 = ''
> par15 = ''
> par14 = ''
> par13 = ''
> par12 = ''
> par11 = ''
> par10 = ''
> par9 = ''
> par8 = ''
> par7 = ''
> par6 = ''
> par5 = ''
> par4 = 'TRUE'
> par3 = '3'
> par2 = '2'
> par1 = '1'
> ylab = ''
> xlab = ''
> main = ''
> #'GNU S' R Code compiled by R2WASP v. 1.0.44 ()
> #Author: Dr. Ian E. Holliday
> #To cite this work: Ian E. Holliday, 2009, YOUR SOFTWARE TITLE (vNUMBER) in Free Statistics Software (v$_version), Office for Research Development and Education, URL http://www.wessa.net/rwasp_YOURPAGE.wasp/
> #Source of accompanying publication: 
> #Technical description: 
> 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] "Pre"
> (V2<-dimnames(y)[[1]][cat2])
[1] "Post"
> (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) )

Call:
lm(formula = Response ~ Treatment_A * Treatment_B, data = xdf)

Coefficients:
              (Intercept)               Treatment_A1  
                  0.12500                    0.35500  
             Treatment_BS               Treatment_BT  
                  0.11029                    0.10577  
Treatment_A1:Treatment_BS  Treatment_A1:Treatment_BT  
                  0.07637                    0.12256  

> (aov.xdf<-aov(lmxdf) )
Call:
   aov(formula = lmxdf)

Terms:
                Treatment_A Treatment_B Treatment_A:Treatment_B Residuals
Sum of Squares     3.907096    0.733278                0.053110 21.439849
Deg. of Freedom           1           2                       2        99

Residual standard error: 0.4653645 
Estimated effects may be unbalanced
> (anova.xdf<-anova(lmxdf) )
Analysis of Variance Table

Response: Response
                        Df  Sum Sq Mean Sq F value    Pr(>F)    
Treatment_A              1  3.9071  3.9071 18.0413 4.888e-05 ***
Treatment_B              2  0.7333  0.3666  1.6930    0.1893    
Treatment_A:Treatment_B  2  0.0531  0.0266  0.1226    0.8847    
Residuals               99 21.4398  0.2166                      
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 
> 
> #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")
> 
> a<-table.start()
> a<-table.row.start(a)
> a<-table.element(a,'ANOVA Model', length(lmxdf$coefficients)+1,TRUE)
> a<-table.row.end(a)
> a<-table.row.start(a)
> a<-table.element(a, lmxdf$call['formula'],length(lmxdf$coefficients)+1,TRUE)
> a<-table.row.end(a)
> a<-table.row.start(a)
> a<-table.element(a, 'means',,TRUE)
> for(i in 1:length(lmxdf$coefficients)){
+ a<-table.element(a, round(lmxdf$coefficients[i], digits=3),,FALSE)
+ }
> a<-table.row.end(a)
> a<-table.end(a)
> table.save(a,file="/var/www/html/freestat/rcomp/tmp/16efl1288686729.tab") 
> a<-table.start()
> a<-table.row.start(a)
> a<-table.element(a,'ANOVA Statistics', 5+1,TRUE)
> a<-table.row.end(a)
> a<-table.row.start(a)
> a<-table.element(a, ' ',,TRUE)
> a<-table.element(a, 'Df',,FALSE)
> a<-table.element(a, 'Sum Sq',,FALSE)
> a<-table.element(a, 'Mean Sq',,FALSE)
> a<-table.element(a, 'F value',,FALSE)
> a<-table.element(a, 'Pr(>F)',,FALSE)
> a<-table.row.end(a)
> for(i in 1 : length(rownames(anova.xdf))-1){
+ a<-table.row.start(a)
+ a<-table.element(a,rownames(anova.xdf)[i] ,,TRUE)
+ a<-table.element(a, anova.xdf$Df[1],,FALSE)
+ a<-table.element(a, round(anova.xdf$'Sum Sq'[i], digits=3),,FALSE)
+ a<-table.element(a, round(anova.xdf$'Mean Sq'[i], digits=3),,FALSE)
+ a<-table.element(a, round(anova.xdf$'F value'[i], digits=3),,FALSE)
+ a<-table.element(a, round(anova.xdf$'Pr(>F)'[i], digits=3),,FALSE)
+ a<-table.row.end(a)
+ }
> a<-table.row.start(a)
> a<-table.element(a, 'Residuals',,TRUE)
> a<-table.element(a, anova.xdf$'Df'[i+1],,FALSE)
> a<-table.element(a, round(anova.xdf$'Sum Sq'[i+1], digits=3),,FALSE)
> a<-table.element(a, round(anova.xdf$'Mean Sq'[i+1], digits=3),,FALSE)
> a<-table.element(a, ' ',,FALSE)
> a<-table.element(a, ' ',,FALSE)
> a<-table.row.end(a)
> a<-table.end(a)
> table.save(a,file="/var/www/html/freestat/rcomp/tmp/2k6cb1288686729.tab") 
> postscript(file="/var/www/html/freestat/rcomp/tmp/3k6cb1288686729.ps",horizontal=F,pagecentre=F,paper="special",width=8.3333333333333,height=5.5555555555556) 
> boxplot(Response ~ Treatment_A + Treatment_B, data=xdf, xlab=V2, ylab=V1, main='Boxplots of ANOVA Groups')
> dev.off()
null device 
          1 
> postscript(file="/var/www/html/freestat/rcomp/tmp/4k6cb1288686729.ps",horizontal=F,pagecentre=F,paper="special",width=8.3333333333333,height=5.5555555555556) 
> xdf2 <- xdf # to preserve xdf make copy for function
> names(xdf2) <- c(V1, V2, V3)
> plot.design(xdf2, main='Design Plot of Group Means')
> dev.off()
null device 
          1 
> postscript(file="/var/www/html/freestat/rcomp/tmp/5k6cb1288686729.ps",horizontal=F,pagecentre=F,paper="special",width=8.3333333333333,height=5.5555555555556) 
> interaction.plot(xdf$Treatment_A, xdf$Treatment_B, xdf$Response, xlab=V2, ylab=V1, trace.label=V3, main='Possible Interactions Between Anova Groups')
> dev.off()
null device 
          1 
> if(intercept==TRUE){
+ thsd<-TukeyHSD(aov.xdf)
+ names(thsd) <- c(V2, V3, paste(V2, ':', V3, sep=''))
+ postscript(file="/var/www/html/freestat/rcomp/tmp/6dfuw1288686729.ps",horizontal=F,pagecentre=F,paper="special",width=8.3333333333333,height=5.5555555555556) 
+ layout(matrix(c(1,2,3,3), 2,2))
+ plot(thsd, las=1)
+ dev.off()
+ }
null device 
          1 
> if(intercept==TRUE){
+ ntables<-length(names(thsd))
+ a<-table.start()
+ a<-table.row.start(a)
+ a<-table.element(a,'Tukey Honest Significant Difference Comparisons', 5,TRUE)
+ a<-table.row.end(a)
+ a<-table.row.start(a)
+ a<-table.element(a, ' ', 1, TRUE)
+ for(i in 1:4){
+ a<-table.element(a,colnames(thsd[[1]])[i], 1, TRUE)
+ }
+ a<-table.row.end(a)
+ for(nt in 1:ntables){
+ for(i in 1:length(rownames(thsd[[nt]]))){
+ a<-table.row.start(a)
+ a<-table.element(a,rownames(thsd[[nt]])[i], 1, TRUE)
+ for(j in 1:4){
+ a<-table.element(a,round(thsd[[nt]][i,j], digits=3), 1, FALSE)
+ }
+ a<-table.row.end(a)
+ }
+ } # end nt
+ a<-table.end(a)
+ table.save(a,file="/var/www/html/freestat/rcomp/tmp/7ygak1288686729.tab") 
+ }#end if hsd tables
> if(intercept==FALSE){
+ a<-table.start()
+ a<-table.row.start(a)
+ a<-table.element(a,'TukeyHSD Message', 1,TRUE)
+ a<-table.row.end(a)
+ a<-table.start()
+ a<-table.row.start(a)
+ a<-table.element(a,'Must Include Intercept to use Tukey Test ', 1, FALSE)
+ a<-table.row.end(a)
+ a<-table.end(a)
+ table.save(a,file="/var/www/html/freestat/rcomp/tmp/8rpa51288686729.tab") 
+ }
> library(car)
> lt.lmxdf<-levene.test(lmxdf)
> a<-table.start()
> a<-table.row.start(a)
> a<-table.element(a,'Levenes Test for Homogeneity of Variance', 4,TRUE)
> a<-table.row.end(a)
> a<-table.row.start(a)
> a<-table.element(a,' ', 1, TRUE)
> for (i in 1:3){
+ a<-table.element(a,names(lt.lmxdf)[i], 1, FALSE)
+ }
> a<-table.row.end(a)
> a<-table.row.start(a)
> a<-table.element(a,'Group', 1, TRUE)
> for (i in 1:3){
+ a<-table.element(a,round(lt.lmxdf[[i]][1], digits=3), 1, FALSE)
+ }
> a<-table.row.end(a)
> a<-table.row.start(a)
> a<-table.element(a,' ', 1, TRUE)
> a<-table.element(a,lt.lmxdf[[1]][2], 1, FALSE)
> a<-table.element(a,' ', 1, FALSE)
> a<-table.element(a,' ', 1, FALSE)
> a<-table.row.end(a)
> a<-table.end(a)
> table.save(a,file="/var/www/html/freestat/rcomp/tmp/9c7qb1288686729.tab") 
> try(system("convert tmp/3k6cb1288686729.ps tmp/3k6cb1288686729.png",intern=TRUE))
character(0)
> try(system("convert tmp/4k6cb1288686729.ps tmp/4k6cb1288686729.png",intern=TRUE))
character(0)
> try(system("convert tmp/5k6cb1288686729.ps tmp/5k6cb1288686729.png",intern=TRUE))
character(0)
> try(system("convert tmp/6dfuw1288686729.ps tmp/6dfuw1288686729.png",intern=TRUE))
character(0)
> 
> 
> proc.time()
   user  system elapsed 
  1.434   0.824   1.568