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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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('1'
+ ,'1'
+ ,'3'
+ ,'2'
+ ,'1'
+ ,'1'
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+ ,'2'
+ ,'2'
+ ,'1'
+ ,'1'
+ ,'2'
+ ,'1'
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+ ,'1'
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+ ,'2'
+ ,'2'
+ ,'3'
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+ ,'2'
+ ,'2'
+ ,'1'
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+ ,'4'
+ ,'1'
+ ,'3'
+ ,'3'
+ ,'1'
+ ,'5'
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+ ,'1'
+ ,'1'
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+ ,'3'
+ ,'1'
+ ,'3'
+ ,'4'
+ ,'1'
+ ,'4'
+ ,'4'
+ ,'1'
+ ,'1'
+ ,'3'
+ ,'1'
+ ,'1'
+ ,'4'
+ ,'1'
+ ,'1'
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+ ,'1'
+ ,'3'
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+ ,'1'
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+ ,'1'
+ ,'1'
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+ ,'1'
+ ,'3'
+ ,'3'
+ ,'1'
+ ,'5'
+ ,'4'
+ ,'1'
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+ ,'1'
+ ,'1'
+ ,'4'
+ ,'1'
+ ,'3'
+ ,'4'
+ ,'1'
+ ,'3'
+ ,'4'
+ ,'1'
+ ,'1'
+ ,'4'
+ ,'1'
+ ,'1'
+ ,'4'
+ ,'1'
+ ,'3'
+ ,'4'
+ ,'1'
+ ,'1'
+ ,'3'
+ ,'1'
+ ,'5'
+ ,'4'
+ ,'1'
+ ,'4'
+ ,'4'
+ ,'1'
+ ,'1'
+ ,'3'
+ ,'1'
+ ,'1'
+ ,'4'
+ ,'1'
+ ,'2'
+ ,'4'
+ ,'1'
+ ,'1'
+ ,'4'
+ ,'1'
+ ,'1'
+ ,'4'
+ ,'1'
+ ,'1'
+ ,'4'
+ ,'1'
+ ,'3'
+ ,'4'
+ ,'1'
+ ,'3'
+ ,'4'
+ ,'1'
+ ,'5'
+ ,'4'
+ ,'1'
+ ,'1'
+ ,'4'
+ ,'1'
+ ,'1'
+ ,'4'
+ ,'1'
+ ,'1'
+ ,'4'
+ ,'1'
+ ,'6'
+ ,'3'
+ ,'1'
+ ,'6'
+ ,'3'
+ ,'1'
+ ,'1'
+ ,'4'
+ ,'1'
+ ,'1'
+ ,'4'
+ ,'2'
+ ,'3'
+ ,'3'
+ ,'1'
+ ,'3'
+ ,'4'
+ ,'1'
+ ,'3'
+ ,'4'
+ ,'1'
+ ,'2'
+ ,'4'
+ ,'1'
+ ,'2'
+ ,'3'
+ ,'1'
+ ,'1'
+ ,'3'
+ ,'1'
+ ,'3'
+ ,'3'
+ ,'1'
+ ,'1'
+ ,'4'
+ ,'1'
+ ,'3'
+ ,'4'
+ ,'1'
+ ,'2'
+ ,'4'
+ ,'1'
+ ,'1'
+ ,'4'
+ ,'2'
+ ,'5'
+ ,'4'
+ ,'2'
+ ,'6'
+ ,'4'
+ ,'1'
+ ,'5')
+ ,dim=c(3
+ ,154)
+ ,dimnames=list(c('T/NT2/4'
+ ,'CorrectAnalysis'
+ ,'Uselimit/Used/Useful')
+ ,1:154))
>  y <- array(NA,dim=c(3,154),dimnames=list(c('T/NT2/4','CorrectAnalysis','Uselimit/Used/Useful'),1:154))
>  for (i in 1:dim(x)[1])
+  {
+  	for (j in 1:dim(x)[2])
+  	{
+  		y[i,j] <- as.numeric(x[i,j])
+  	}
+  }
> par4 = 'TRUE'
> par3 = '3'
> par2 = '1'
> par1 = '2'
> ylab = 'Y Variable Name'
> xlab = 'X Variable Name'
> main = 'Title Goes Here'
> par4 <- 'TRUE'
> par3 <- '3'
> par2 <- '1'
> par1 <- '2'
> #'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] "CorrectAnalysis"
> (V2<-dimnames(y)[[1]][cat2])
[1] "T/NT2/4"
> (V3 <-dimnames(y)[[1]][cat3])
[1] "Uselimit/Used/Useful"
> 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_A2  
                1.000e+00                  8.632e-17  
             Treatment_A3               Treatment_A4  
                2.253e-17                  6.415e-17  
             Treatment_B2               Treatment_B3  
                2.214e-17                  9.091e-02  
             Treatment_B4               Treatment_B5  
                6.667e-01                  3.333e-01  
             Treatment_B6  Treatment_A2:Treatment_B2  
                7.500e-01                 -8.907e-17  
Treatment_A3:Treatment_B2  Treatment_A4:Treatment_B2  
                       NA                 -9.033e-17  
Treatment_A2:Treatment_B3  Treatment_A3:Treatment_B3  
                7.576e-02                 -9.091e-02  
Treatment_A4:Treatment_B3  Treatment_A2:Treatment_B4  
               -1.948e-02                 -5.833e-01  
Treatment_A3:Treatment_B4  Treatment_A4:Treatment_B4  
                       NA                 -6.667e-01  
Treatment_A2:Treatment_B5  Treatment_A3:Treatment_B5  
               -3.333e-01                 -3.333e-01  
Treatment_A4:Treatment_B5  Treatment_A2:Treatment_B6  
                       NA                 -7.500e-01  
Treatment_A3:Treatment_B6  Treatment_A4:Treatment_B6  
               -7.500e-01                 -2.500e-01  

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

Terms:
                Treatment_A Treatment_B Treatment_A:Treatment_B Residuals
Sum of Squares     0.949480    1.484810                1.626316  7.004329
Deg. of Freedom           3           5                      12       133

Residual standard error: 0.2294867 
3 out of 24 effects not estimable
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               3 0.9495 0.31649  6.0097 0.0007169 ***
Treatment_B               5 1.4848 0.29696  5.6388 9.529e-05 ***
Treatment_A:Treatment_B  12 1.6263 0.13553  2.5734 0.0042384 ** 
Residuals               133 7.0043 0.05266                      
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 
> 
> #Note: the /var/fisher/rcomp/createtable file can be downloaded at http://www.wessa.net/cretab
> load(file="/var/fisher/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$coefficients[i], digits=3),,FALSE)
+ }
> a<-table.row.end(a)
> a<-table.end(a)
> table.save(a,file="/var/fisher/rcomp/tmp/19xlo1356022697.tab") 
> a<-table.start()
> a<-table.row.start(a)
> a<-table.element(a,'ANOVA Statistics', 5+1,TRUE)
> a<-table.row.end(a)
> a<-table.row.start(a)
> a<-table.element(a, ' ',,TRUE)
> a<-table.element(a, 'Df',,FALSE)
> a<-table.element(a, 'Sum Sq',,FALSE)
> a<-table.element(a, 'Mean Sq',,FALSE)
> a<-table.element(a, 'F value',,FALSE)
> a<-table.element(a, 'Pr(>F)',,FALSE)
> a<-table.row.end(a)
> for(i in 1 : length(rownames(anova.xdf))-1){
+ a<-table.row.start(a)
+ a<-table.element(a,rownames(anova.xdf)[i] ,,TRUE)
+ a<-table.element(a, anova.xdf$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$'Mean Sq'[i+1], digits=3),,FALSE)
> a<-table.element(a, ' ',,FALSE)
> a<-table.element(a, ' ',,FALSE)
> a<-table.row.end(a)
> a<-table.end(a)
> table.save(a,file="/var/fisher/rcomp/tmp/2vh7t1356022697.tab") 
> postscript(file="/var/fisher/rcomp/tmp/3r4c51356022697.ps",horizontal=F,onefile=F,pagecentre=F,paper="special",width=8.3333333333333,height=5.5555555555556) 
> boxplot(Response ~ Treatment_A + Treatment_B, data=xdf, xlab=V2, ylab=V1, main='Boxplots of ANOVA Groups')
> dev.off()
null device 
          1 
> postscript(file="/var/fisher/rcomp/tmp/46gif1356022697.ps",horizontal=F,onefile=F,pagecentre=F,paper="special",width=8.3333333333333,height=5.5555555555556) 
> xdf2 <- xdf # to preserve xdf make copy for function
> names(xdf2) <- c(V1, V2, V3)
> plot.design(xdf2, main='Design Plot of Group Means')
> dev.off()
null device 
          1 
> postscript(file="/var/fisher/rcomp/tmp/5e8lo1356022697.ps",horizontal=F,onefile=F,pagecentre=F,paper="special",width=8.3333333333333,height=5.5555555555556) 
> interaction.plot(xdf$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/fisher/rcomp/tmp/67hp71356022697.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()
+ }
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/fisher/rcomp/tmp/7p7nk1356022697.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/fisher/rcomp/tmp/8yzvy1356022697.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/fisher/rcomp/tmp/9o1es1356022697.tab") 
> 
> try(system("convert tmp/3r4c51356022697.ps tmp/3r4c51356022697.png",intern=TRUE))
character(0)
> try(system("convert tmp/46gif1356022697.ps tmp/46gif1356022697.png",intern=TRUE))
character(0)
> try(system("convert tmp/5e8lo1356022697.ps tmp/5e8lo1356022697.png",intern=TRUE))
character(0)
> try(system("convert tmp/67hp71356022697.ps tmp/67hp71356022697.png",intern=TRUE))
character(0)
> 
> 
> proc.time()
   user  system elapsed 
  4.938   0.854   5.780