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. R is a collaborative project with many contributors. 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(0 + ,0 + ,'E' + ,0 + ,1 + ,0 + ,1 + ,'F' + ,1 + ,0 + ,0 + ,0 + ,'F' + ,0 + ,1 + ,0 + ,0 + ,'H' + ,0 + ,1 + ,0 + ,0 + ,'H' + ,0 + ,1 + ,0 + ,0 + ,'H' + ,0 + ,1 + ,0 + ,1 + ,'E' + ,1 + ,1 + ,0 + ,1 + ,'F' + ,1 + ,1 + ,0 + ,0 + ,'E' + ,0 + ,1 + ,0 + ,1 + ,'F' + ,1 + ,0 + ,0 + ,0 + ,'H' + ,0 + ,0 + ,0 + ,0 + ,'E' + ,0 + ,0 + ,0 + ,1 + ,'F' + ,1 + ,1 + ,0 + ,0 + ,'H' + ,0 + ,0 + ,0 + ,1 + ,'E' + ,1 + ,0 + ,0 + ,0 + ,'H' + ,0 + ,0 + ,0 + ,0 + ,'E' + ,0 + ,1 + ,0 + ,0 + ,'F' + ,0 + ,1 + ,0 + ,0 + ,'H' + ,0 + ,0 + ,0 + ,1 + ,'F' + ,1 + ,0 + ,0 + ,0 + ,'H' + ,0 + ,0 + ,0 + ,0 + ,'H' + ,0 + ,1 + ,0 + ,0 + ,'H' + ,0 + ,0 + ,0 + ,0 + ,'E' + ,0 + ,0 + ,0 + ,1 + ,'F' + ,1 + ,0 + ,0 + ,1 + ,'E' + ,1 + ,0 + ,0 + ,1 + ,'E' + ,1 + ,0 + ,1 + ,1 + ,'F' + ,0 + ,1 + ,0 + ,0 + ,'F' + ,0 + ,0 + ,0 + ,0 + ,'H' + ,0 + ,0 + ,0 + ,0 + ,'E' + ,0 + ,1 + ,0 + ,1 + ,'E' + ,1 + ,1 + ,0 + ,0 + ,'H' + ,0 + ,1 + ,0 + ,1 + ,'E' + ,1 + ,1 + ,0 + ,1 + ,'F' + ,1 + ,1 + ,0 + ,0 + ,'E' + ,0 + ,1 + ,0 + ,1 + ,'F' + ,1 + ,0 + ,0 + ,0 + ,'H' + ,0 + ,0 + ,0 + ,1 + ,'E' + ,1 + ,0 + ,0 + ,1 + ,'F' + ,1 + ,0 + ,0 + ,1 + ,'F' + ,1 + ,0 + ,0 + ,0 + ,'F' + ,0 + ,0 + ,0 + ,1 + ,'F' + ,1 + ,0 + ,0 + ,1 + ,'H' + ,1 + ,1 + ,0 + ,1 + ,'E' + ,1 + ,0 + ,0 + ,0 + ,'E' + ,0 + ,0 + ,0 + ,0 + ,'H' + ,0 + ,0 + ,0 + ,1 + ,'E' + ,1 + ,1 + ,0 + ,0 + ,'F' + ,0 + ,1 + ,0 + ,0 + ,'F' + ,0 + ,0 + ,0 + ,0 + ,'H' + ,0 + ,0 + ,0 + ,0 + ,'E' + ,0 + ,1 + ,0 + ,1 + ,'F' + ,1 + ,1 + ,0 + ,1 + ,'E' + ,1 + ,1 + ,0 + ,0 + ,'H' + ,0 + ,1 + ,0 + ,0 + ,'H' + ,0 + ,1 + ,0 + ,0 + ,'H' + ,0 + ,1 + ,0 + ,0 + ,'E' + ,0 + ,1 + ,0 + ,0 + ,'H' + ,0 + ,0 + ,0 + ,1 + ,'E' + ,1 + ,0 + ,0 + ,0 + ,'H' + ,0 + ,1 + ,0 + ,0 + ,'F' + ,0 + ,1 + ,0 + ,0 + ,'H' + ,0 + ,1 + ,0 + ,1 + ,'F' + ,1 + ,0 + ,0 + ,0 + ,'E' + ,0 + ,1 + ,0 + ,1 + ,'E' + ,1 + ,1 + ,0 + ,0 + ,'F' + ,0 + ,0 + ,0 + ,0 + ,'H' + ,0 + ,1 + ,0 + ,0 + ,'F' + ,0 + ,0 + ,0 + ,0 + ,'E' + ,0 + ,1 + ,1 + ,0 + ,'E' + ,-1 + ,1 + ,0 + ,0 + ,'H' + ,0 + ,0 + ,0 + ,0 + ,'H' + ,0 + ,1 + ,0 + ,0 + ,'F' + ,0 + ,1 + ,0 + ,0 + ,'H' + ,0 + ,1 + ,0 + ,1 + ,'E' + ,1 + ,0 + ,0 + ,0 + ,'F' + ,0 + ,1 + ,0 + ,1 + ,'E' + ,1 + ,0 + ,0 + ,0 + ,'E' + ,0 + ,0 + ,0 + ,0 + ,'E' + ,0 + ,0 + ,0 + ,0 + ,'F' + ,0 + ,1 + ,0 + ,0 + ,'E' + ,0 + ,1 + ,0 + ,1 + ,'F' + ,1 + ,1 + ,0 + ,0 + ,'H' + ,0 + ,1 + ,1 + ,1 + ,'H' + ,0 + ,1 + ,0 + ,0 + ,'H' + ,0 + ,1 + ,0 + ,0 + ,'F' + ,0 + ,0 + ,0 + ,0 + ,'H' + ,0 + ,1 + ,0 + ,0 + ,'H' + ,0 + ,1 + ,0 + ,1 + ,'F' + ,1 + ,1 + ,0 + ,1 + ,'F' + ,1 + ,1 + ,0 + ,0 + ,'H' + ,0 + ,0 + ,0 + ,0 + ,'F' + ,0 + ,1 + ,0 + ,0 + ,'H' + ,0 + ,1 + ,0 + ,0 + ,'E' + ,0 + ,0 + ,0 + ,1 + ,'F' + ,1 + ,1 + ,0 + ,0 + ,'E' + ,0 + ,0 + ,0 + ,0 + ,'H' + ,0 + ,1 + ,0 + ,1 + ,'F' + ,1 + ,1 + ,1 + ,1 + ,'F' + ,0 + ,1 + ,0 + ,0 + ,'H' + ,0 + ,1 + ,0 + ,1 + ,'E' + ,1 + ,1 + ,0 + ,0 + ,'F' + ,0 + ,0 + ,0 + ,0 + ,'H' + ,0 + ,1 + ,0 + ,0 + ,'E' + ,0 + ,1 + ,0 + ,0 + ,'F' + ,0 + ,0 + ,0 + ,0 + ,'H' + ,0 + ,0 + ,0 + ,0 + ,'H' + ,0 + ,1 + ,0 + ,1 + ,'F' + ,1 + ,1 + ,0 + ,1 + ,'F' + ,1 + ,1 + ,0 + ,0 + ,'H' + ,0 + ,1 + ,0 + ,0 + ,'E' + ,0 + ,0 + ,0 + ,0 + ,'H' + ,0 + ,1 + ,0 + ,0 + ,'E' + ,0 + ,1 + ,0 + ,0 + ,'E' + ,0 + ,0 + ,0 + ,0 + ,'F' + ,0 + ,1 + ,0 + ,0 + ,'F' + ,0 + ,1) + ,dim=c(5 + ,117) + ,dimnames=list(c('pre' + ,'post' + ,'treat' + ,'diff' + ,'gender') + ,1:117)) > y <- array(NA,dim=c(5,117),dimnames=list(c('pre','post','treat','diff','gender'),1:117)) > 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 = '5' > par2 = '3' > par1 = '4' > 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] "diff" > (V2<-dimnames(y)[[1]][cat2]) [1] "treat" > (V3 <-dimnames(y)[[1]][cat3]) [1] "gender" > 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_AF 0.47059 0.05882 Treatment_AH Treatment_B1 -0.47059 -0.17059 Treatment_AF:Treatment_B1 Treatment_AH:Treatment_B1 0.11944 0.20905 > (aov.xdf<-aov(lmxdf) ) Call: aov(formula = lmxdf) Terms: Treatment_A Treatment_B Treatment_A:Treatment_B Residuals Sum of Squares 4.852212 0.105118 0.201328 21.371257 Deg. of Freedom 2 1 2 111 Residual standard error: 0.4387868 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 4.8522 2.42611 12.6009 1.17e-05 *** Treatment_B 1 0.1051 0.10512 0.5460 0.4615 Treatment_A:Treatment_B 2 0.2013 0.10066 0.5228 0.5943 Residuals 111 21.3713 0.19253 --- 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$coefficients[i], digits=3),,FALSE) + } > a<-table.row.end(a) > a<-table.end(a) > table.save(a,file="/var/fisher/rcomp/tmp/1upl71356242315.tab") > a<-table.start() > a<-table.row.start(a) > a<-table.element(a,'ANOVA Statistics', 5+1,TRUE) > a<-table.row.end(a) > a<-table.row.start(a) > a<-table.element(a, ' ',,TRUE) > a<-table.element(a, 'Df',,FALSE) > a<-table.element(a, 'Sum Sq',,FALSE) > a<-table.element(a, 'Mean Sq',,FALSE) > a<-table.element(a, 'F value',,FALSE) > a<-table.element(a, 'Pr(>F)',,FALSE) > a<-table.row.end(a) > for(i in 1 : length(rownames(anova.xdf))-1){ + a<-table.row.start(a) + a<-table.element(a,rownames(anova.xdf)[i] ,,TRUE) + a<-table.element(a, anova.xdf$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$'Mean Sq'[i+1], digits=3),,FALSE) > a<-table.element(a, ' ',,FALSE) > a<-table.element(a, ' ',,FALSE) > a<-table.row.end(a) > a<-table.end(a) > table.save(a,file="/var/fisher/rcomp/tmp/2z8zt1356242315.tab") > postscript(file="/var/fisher/rcomp/tmp/3b5ta1356242315.ps",horizontal=F,onefile=F,pagecentre=F,paper="special",width=8.3333333333333,height=5.5555555555556) > boxplot(Response ~ Treatment_A + Treatment_B, data=xdf, xlab=V2, ylab=V1, main='Boxplots of ANOVA Groups') > dev.off() null device 1 > postscript(file="/var/fisher/rcomp/tmp/4rvqn1356242315.ps",horizontal=F,onefile=F,pagecentre=F,paper="special",width=8.3333333333333,height=5.5555555555556) > xdf2 <- xdf # to preserve xdf make copy for function > names(xdf2) <- c(V1, V2, V3) > plot.design(xdf2, main='Design Plot of Group Means') > dev.off() null device 1 > postscript(file="/var/fisher/rcomp/tmp/5ykbd1356242315.ps",horizontal=F,onefile=F,pagecentre=F,paper="special",width=8.3333333333333,height=5.5555555555556) > interaction.plot(xdf$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/6foyx1356242315.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/7wbq31356242315.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/8qs3a1356242315.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/9u88o1356242315.tab") > > try(system("convert tmp/3b5ta1356242315.ps tmp/3b5ta1356242315.png",intern=TRUE)) character(0) > try(system("convert tmp/4rvqn1356242315.ps tmp/4rvqn1356242315.png",intern=TRUE)) character(0) > try(system("convert tmp/5ykbd1356242315.ps tmp/5ykbd1356242315.png",intern=TRUE)) character(0) > try(system("convert tmp/6foyx1356242315.ps tmp/6foyx1356242315.png",intern=TRUE)) character(0) > > > proc.time() user system elapsed 2.539 0.826 3.352