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.

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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(4
+ ,'No'
+ ,'Good'
+ ,4
+ ,'No'
+ ,'Bad'
+ ,4
+ ,'No'
+ ,'Bad'
+ ,4
+ ,'No'
+ ,'Bad'
+ ,4
+ ,'No'
+ ,'Bad'
+ ,4
+ ,'No'
+ ,'Good'
+ ,4
+ ,'No'
+ ,'Bad'
+ ,4
+ ,'No'
+ ,'Bad'
+ ,4
+ ,'No'
+ ,'Good'
+ ,4
+ ,'No'
+ ,'Bad'
+ ,4
+ ,'No'
+ ,'Bad'
+ ,4
+ ,'No'
+ ,'Bad'
+ ,4
+ ,'No'
+ ,'Bad'
+ ,4
+ ,'No'
+ ,'Bad'
+ ,4
+ ,'No'
+ ,'Good'
+ ,4
+ ,'No'
+ ,'Good'
+ ,4
+ ,'Yes'
+ ,'Bad'
+ ,4
+ ,'No'
+ ,'Bad'
+ ,4
+ ,'No'
+ ,'Good'
+ ,4
+ ,'Yes'
+ ,'Good'
+ ,4
+ ,'No'
+ ,'Bad'
+ ,4
+ ,'No'
+ ,'Good'
+ ,4
+ ,'No'
+ ,'Good'
+ ,4
+ ,'No'
+ ,'Good'
+ ,4
+ ,'No'
+ ,'Good'
+ ,4
+ ,'No'
+ ,'Bad'
+ ,4
+ ,'No'
+ ,'Good'
+ ,4
+ ,'No'
+ ,'Bad'
+ ,4
+ ,'No'
+ ,'Good'
+ ,4
+ ,'No'
+ ,'Bad'
+ ,4
+ ,'No'
+ ,'Bad'
+ ,4
+ ,'No'
+ ,'Bad'
+ ,4
+ ,'No'
+ ,'Bad'
+ ,4
+ ,'No'
+ ,'Good'
+ ,4
+ ,'No'
+ ,'Bad'
+ ,4
+ ,'No'
+ ,'Bad'
+ ,4
+ ,'No'
+ ,'Bad'
+ ,4
+ ,'No'
+ ,'Good'
+ ,4
+ ,'No'
+ ,'Good'
+ ,4
+ ,'No'
+ ,'Bad'
+ ,4
+ ,'Yes'
+ ,'Good'
+ ,4
+ ,'No'
+ ,'Good'
+ ,4
+ ,'No'
+ ,'Good'
+ ,4
+ ,'No'
+ ,'Bad'
+ ,4
+ ,'No'
+ ,'Bad'
+ ,4
+ ,'No'
+ ,'Good'
+ ,4
+ ,'No'
+ ,'Bad'
+ ,4
+ ,'No'
+ ,'Good'
+ ,4
+ ,'No'
+ ,'Good'
+ ,4
+ ,'No'
+ ,'Bad'
+ ,4
+ ,'No'
+ ,'Bad'
+ ,4
+ ,'Yes'
+ ,'Bad'
+ ,4
+ ,'No'
+ ,'Good'
+ ,4
+ ,'Yes'
+ ,'Bad'
+ ,4
+ ,'No'
+ ,'Bad'
+ ,4
+ ,'No'
+ ,'Good'
+ ,4
+ ,'No'
+ ,'Good'
+ ,4
+ ,'No'
+ ,'Good'
+ ,4
+ ,'No'
+ ,'Good'
+ ,4
+ ,'Yes'
+ ,'Good'
+ ,4
+ ,'No'
+ ,'Good'
+ ,4
+ ,'No'
+ ,'Bad'
+ ,4
+ ,'No'
+ ,'Bad'
+ ,4
+ ,'No'
+ ,'Good'
+ ,4
+ ,'No'
+ ,'Bad'
+ ,4
+ ,'No'
+ ,'Bad'
+ ,4
+ ,'Yes'
+ ,'Bad'
+ ,4
+ ,'No'
+ ,'Bad'
+ ,4
+ ,'No'
+ ,'Good'
+ ,4
+ ,'No'
+ ,'Bad'
+ ,4
+ ,'No'
+ ,'Bad'
+ ,4
+ ,'No'
+ ,'Good'
+ ,4
+ ,'No'
+ ,'Good'
+ ,4
+ ,'No'
+ ,'Bad'
+ ,4
+ ,'No'
+ ,'Good'
+ ,4
+ ,'No'
+ ,'Good'
+ ,4
+ ,'No'
+ ,'Good'
+ ,4
+ ,'No'
+ ,'Good'
+ ,4
+ ,'Yes'
+ ,'Good'
+ ,4
+ ,'No'
+ ,'Bad'
+ ,4
+ ,'No'
+ ,'Bad'
+ ,4
+ ,'No'
+ ,'Good'
+ ,4
+ ,'No'
+ ,'Bad'
+ ,4
+ ,'Yes'
+ ,'Bad'
+ ,4
+ ,'No'
+ ,'Good'
+ ,4
+ ,'No'
+ ,'Bad'
+ ,2
+ ,'No'
+ ,'Good'
+ ,2
+ ,'No'
+ ,'Good'
+ ,2
+ ,'No'
+ ,'Bad'
+ ,2
+ ,'No'
+ ,'Good'
+ ,2
+ ,'No'
+ ,'Bad'
+ ,2
+ ,'No'
+ ,'Bad'
+ ,2
+ ,'No'
+ ,'Bad'
+ ,2
+ ,'No'
+ ,'Bad'
+ ,2
+ ,'No'
+ ,'Bad'
+ ,2
+ ,'No'
+ ,'Good'
+ ,2
+ ,'No'
+ ,'Bad'
+ ,2
+ ,'No'
+ ,'Bad'
+ ,2
+ ,'No'
+ ,'Bad'
+ ,2
+ ,'No'
+ ,'Good'
+ ,2
+ ,'No'
+ ,'Good'
+ ,2
+ ,'No'
+ ,'Bad'
+ ,2
+ ,'No'
+ ,'Bad'
+ ,2
+ ,'No'
+ ,'Bad'
+ ,2
+ ,'No'
+ ,'Bad'
+ ,2
+ ,'No'
+ ,'Bad'
+ ,2
+ ,'No'
+ ,'Bad'
+ ,2
+ ,'No'
+ ,'Bad'
+ ,2
+ ,'No'
+ ,'Bad'
+ ,2
+ ,'No'
+ ,'Bad'
+ ,2
+ ,'No'
+ ,'Bad'
+ ,2
+ ,'No'
+ ,'Bad'
+ ,2
+ ,'No'
+ ,'Bad'
+ ,2
+ ,'No'
+ ,'Bad'
+ ,2
+ ,'No'
+ ,'Bad'
+ ,2
+ ,'No'
+ ,'Bad'
+ ,2
+ ,'No'
+ ,'Good'
+ ,2
+ ,'No'
+ ,'Bad'
+ ,2
+ ,'No'
+ ,'Bad'
+ ,2
+ ,'No'
+ ,'Good'
+ ,2
+ ,'No'
+ ,'Bad'
+ ,2
+ ,'No'
+ ,'Bad'
+ ,2
+ ,'No'
+ ,'Bad'
+ ,2
+ ,'No'
+ ,'Good'
+ ,2
+ ,'No'
+ ,'Good'
+ ,2
+ ,'No'
+ ,'Bad'
+ ,2
+ ,'No'
+ ,'Bad'
+ ,2
+ ,'No'
+ ,'Good'
+ ,2
+ ,'No'
+ ,'Bad'
+ ,2
+ ,'No'
+ ,'Good'
+ ,2
+ ,'No'
+ ,'Bad'
+ ,2
+ ,'No'
+ ,'Good'
+ ,2
+ ,'No'
+ ,'Bad'
+ ,2
+ ,'No'
+ ,'Bad'
+ ,2
+ ,'No'
+ ,'Bad'
+ ,2
+ ,'No'
+ ,'Bad'
+ ,2
+ ,'No'
+ ,'Good'
+ ,2
+ ,'No'
+ ,'Good'
+ ,2
+ ,'No'
+ ,'Bad'
+ ,2
+ ,'No'
+ ,'Bad'
+ ,2
+ ,'Yes'
+ ,'Good'
+ ,2
+ ,'No'
+ ,'Good'
+ ,2
+ ,'No'
+ ,'Bad'
+ ,2
+ ,'No'
+ ,'Good'
+ ,2
+ ,'No'
+ ,'Bad'
+ ,2
+ ,'No'
+ ,'Good'
+ ,2
+ ,'No'
+ ,'Bad'
+ ,2
+ ,'No'
+ ,'Bad'
+ ,2
+ ,'No'
+ ,'Bad'
+ ,2
+ ,'No'
+ ,'Good'
+ ,2
+ ,'No'
+ ,'Good'
+ ,2
+ ,'Yes'
+ ,'Bad'
+ ,2
+ ,'Yes'
+ ,'Bad'
+ ,2
+ ,'No'
+ ,'Bad')
+ ,dim=c(3
+ ,154)
+ ,dimnames=list(c('week'
+ ,'correct'
+ ,'outcome')
+ ,1:154))
>  y <- array(NA,dim=c(3,154),dimnames=list(c('week','correct','outcome'),1:154))
>  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 = 'FALSE'
> par3 = '3'
> par2 = '2'
> par1 = '1'
> ylab = 'Y Variable Name'
> xlab = 'X Variable Name'
> main = 'Title Goes Here'
> par4 <- 'FALSE'
> par3 <- '3'
> par2 <- '2'
> par1 <- '1'
> #'GNU S' R Code compiled by R2WASP v. 1.2.291 ()
> #Author: aston2
> #To cite this work: Ian E. Holliday, 2012, Two-Way ANOVA (v1.0.3) in Free Statistics Software (v$_version), Office for Research Development and Education, URL http://www.wessa.net/Ian.Holliday/rwasp_Two%20Factor%20ANOVA.wasp/
> #Source of accompanying publication: 
> #
> 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] "week"
> (V2<-dimnames(y)[[1]][cat2])
[1] "correct"
> (V3 <-dimnames(y)[[1]][cat3])
[1] "outcome"
> 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 - 1, data = xdf)

Coefficients:
                 Treatment_ANo                  Treatment_AYes  
                        2.9535                          3.4286  
               Treatment_BGood  Treatment_AYes:Treatment_BGood  
                        0.3322                         -0.1608  

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

Terms:
                Treatment_A Treatment_B Treatment_A:Treatment_B Residuals
Sum of Squares    1498.0141      3.7597                  0.0694  146.1568
Deg. of Freedom           2           1                       1       150

Residual standard error: 0.9871062 
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               2 1498.01  749.01 768.7022 < 2e-16 ***
Treatment_B               1    3.76    3.76   3.8585 0.05134 .  
Treatment_A:Treatment_B   1    0.07    0.07   0.0713 0.78987    
Residuals               150  146.16    0.97                     
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 
> 
> #Note: the /var/wessaorg/rcomp/createtable file can be downloaded at http://www.wessa.net/cretab
> load(file="/var/wessaorg/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$coefficients[i], digits=3),,FALSE)
+ }
> a<-table.row.end(a)
> a<-table.end(a)
> table.save(a,file="/var/wessaorg/rcomp/tmp/15c701356126758.tab") 
> a<-table.start()
> a<-table.row.start(a)
> a<-table.element(a,'ANOVA Statistics', 5+1,TRUE)
> a<-table.row.end(a)
> a<-table.row.start(a)
> a<-table.element(a, ' ',,TRUE)
> a<-table.element(a, 'Df',,FALSE)
> a<-table.element(a, 'Sum Sq',,FALSE)
> a<-table.element(a, 'Mean Sq',,FALSE)
> a<-table.element(a, 'F value',,FALSE)
> a<-table.element(a, 'Pr(>F)',,FALSE)
> a<-table.row.end(a)
> for(i in 1 : length(rownames(anova.xdf))-1){
+ a<-table.row.start(a)
+ a<-table.element(a,rownames(anova.xdf)[i] ,,TRUE)
+ a<-table.element(a, anova.xdf$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$'Mean Sq'[i+1], digits=3),,FALSE)
> a<-table.element(a, ' ',,FALSE)
> a<-table.element(a, ' ',,FALSE)
> a<-table.row.end(a)
> a<-table.end(a)
> table.save(a,file="/var/wessaorg/rcomp/tmp/264tf1356126758.tab") 
> postscript(file="/var/wessaorg/rcomp/tmp/3es801356126758.ps",horizontal=F,onefile=F,pagecentre=F,paper="special",width=8.3333333333333,height=5.5555555555556) 
> boxplot(Response ~ Treatment_A + Treatment_B, data=xdf, xlab=V2, ylab=V1, main='Boxplots of ANOVA Groups')
> dev.off()
null device 
          1 
> postscript(file="/var/wessaorg/rcomp/tmp/40zwp1356126758.ps",horizontal=F,onefile=F,pagecentre=F,paper="special",width=8.3333333333333,height=5.5555555555556) 
> xdf2 <- xdf # to preserve xdf make copy for function
> names(xdf2) <- c(V1, V2, V3)
> plot.design(xdf2, main='Design Plot of Group Means')
> dev.off()
null device 
          1 
> postscript(file="/var/wessaorg/rcomp/tmp/573r01356126758.ps",horizontal=F,onefile=F,pagecentre=F,paper="special",width=8.3333333333333,height=5.5555555555556) 
> interaction.plot(xdf$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/wessaorg/rcomp/tmp/68xr51356126758.ps",horizontal=F,onefile=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()
+ }
> 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/wessaorg/rcomp/tmp/7jc7n1356126758.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/wessaorg/rcomp/tmp/8mvuz1356126758.tab") 
+ }
> library(car)
Loading required package: MASS
Loading required package: nnet
> lt.lmxdf<-levene.test(lmxdf)
Warning message:
'levene.test' is deprecated.
Use 'leveneTest' instead.
See help("Deprecated") and help("car-deprecated"). 
> 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/wessaorg/rcomp/tmp/9u3ki1356126758.tab") 
> 
> try(system("convert tmp/3es801356126758.ps tmp/3es801356126758.png",intern=TRUE))
character(0)
> try(system("convert tmp/40zwp1356126758.ps tmp/40zwp1356126758.png",intern=TRUE))
character(0)
> try(system("convert tmp/573r01356126758.ps tmp/573r01356126758.png",intern=TRUE))
character(0)
> try(system("convert tmp/68xr51356126758.ps tmp/68xr51356126758.png",intern=TRUE))
convert: unable to open image `tmp/68xr51356126758.ps':  @ error/blob.c/OpenBlob/2587.
convert: missing an image filename `tmp/68xr51356126758.png' @ error/convert.c/ConvertImageCommand/3011.
character(0)
attr(,"status")
[1] 1
Warning message:
running command 'convert tmp/68xr51356126758.ps tmp/68xr51356126758.png' had status 1 
> 
> 
> proc.time()
   user  system elapsed 
  2.250   0.445   2.692