R version 2.12.0 (2010-10-15) Copyright (C) 2010 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: i486-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(1 + ,1 + ,'T' + ,0 + ,0 + ,1 + ,1 + ,'T' + ,0 + ,1 + ,0 + ,1 + ,'T' + ,1 + ,1 + ,0 + ,0 + ,'T' + ,0 + ,1 + ,1 + ,1 + ,'T' + ,0 + ,0 + ,1 + ,1 + ,'T' + ,0 + ,1 + ,1 + ,1 + ,'T' + ,0 + ,0 + ,0 + ,1 + ,'T' + ,1 + ,0 + ,0 + ,1 + ,'T' + ,1 + ,1 + ,1 + ,1 + ,'T' + ,0 + ,1 + ,0 + ,0 + ,'T' + ,0 + ,0 + ,0 + ,1 + ,'T' + ,1 + ,0 + ,0 + ,1 + ,'T' + ,1 + ,1 + ,0 + ,1 + ,'T' + ,1 + ,1 + ,0 + ,0 + ,'T' + ,0 + ,0 + ,1 + ,1 + ,'T' + ,0 + ,1 + ,1 + ,1 + ,'T' + ,0 + ,0 + ,1 + ,1 + ,'T' + ,0 + ,1 + ,0 + ,1 + ,'T' + ,1 + ,1 + ,0 + ,0 + ,'T' + ,0 + ,1 + ,1 + ,1 + ,'T' + ,0 + ,1 + ,1 + ,1 + ,'T' + ,0 + ,0 + ,0 + ,0 + ,'T' + ,0 + ,1 + ,1 + ,0 + ,'T' + ,-1 + ,1 + ,1 + ,1 + ,'T' + ,0 + ,0 + ,1 + ,0 + ,'T' + ,-1 + ,1 + ,1 + ,1 + ,'T' + ,0 + ,0 + ,0 + ,0 + ,'T' + ,0 + ,1 + ,0 + ,0 + ,'T' + ,0 + ,1 + ,1 + ,1 + ,'T' + ,0 + ,1 + ,1 + ,0 + ,'T' + ,-1 + ,1 + ,1 + ,1 + ,'T' + ,0 + ,1 + ,0 + ,0 + ,'T' + ,0 + ,0 + ,0 + ,0 + ,'T' + ,0 + ,0 + ,0 + ,0 + ,'T' + ,0 + ,0 + ,1 + ,1 + ,'T' + ,0 + ,1 + ,1 + ,1 + ,'T' + ,0 + ,1 + ,0 + ,1 + ,'E' + ,1 + ,1 + ,0 + ,1 + ,'E' + ,1 + ,0 + ,1 + ,1 + ,'E' + ,0 + ,0 + ,1 + ,1 + ,'E' + ,0 + ,1 + ,1 + ,1 + ,'E' + ,0 + ,0 + ,1 + ,1 + ,'E' + ,0 + ,1 + ,1 + ,1 + ,'E' + ,0 + ,1 + ,0 + ,0 + ,'E' + ,0 + ,1 + ,0 + ,1 + ,'E' + ,1 + ,1 + ,0 + ,1 + ,'E' + ,1 + ,0 + ,1 + ,1 + ,'E' + ,0 + ,0 + ,1 + ,1 + ,'E' + ,0 + ,0 + ,0 + ,0 + ,'E' + ,0 + ,1 + ,0 + ,1 + ,'E' + ,1 + ,1 + ,1 + ,1 + ,'E' + ,0 + ,1 + ,0 + ,1 + ,'E' + ,1 + ,1 + ,0 + ,0 + ,'E' + ,0 + ,1 + ,0 + ,1 + ,'E' + ,1 + ,1 + ,0 + ,1 + ,'E' + ,1 + ,0 + ,0 + ,1 + ,'E' + ,1 + ,0 + ,0 + ,1 + ,'E' + ,1 + ,1 + ,0 + ,0 + ,'E' + ,0 + ,1 + ,0 + ,0 + ,'E' + ,0 + ,1 + ,0 + ,1 + ,'E' + ,1 + ,0 + ,1 + ,1 + ,'E' + ,0 + ,0 + ,1 + ,1 + ,'E' + ,0 + ,0 + ,1 + ,0 + ,'E' + ,-1 + ,1 + ,0 + ,0 + ,'E' + ,0 + ,1 + ,0 + ,1 + ,'E' + ,1 + ,0 + ,0 + ,1 + ,'E' + ,1 + ,1 + ,0 + ,0 + ,'E' + ,0 + ,0 + ,1 + ,1 + ,'E' + ,0 + ,1 + ,1 + ,1 + ,'E' + ,0 + ,0 + ,0 + ,1 + ,'S' + ,1 + ,1 + ,0 + ,1 + ,'S' + ,1 + ,0 + ,0 + ,1 + ,'S' + ,1 + ,1 + ,0 + ,1 + ,'S' + ,1 + ,1 + ,1 + ,1 + ,'S' + ,0 + ,0 + ,1 + ,0 + ,'S' + ,-1 + ,1 + ,0 + ,0 + ,'S' + ,0 + ,1 + ,1 + ,1 + ,'S' + ,0 + ,0 + ,1 + ,0 + ,'S' + ,-1 + ,1 + ,1 + ,1 + ,'S' + ,0 + ,0 + ,0 + ,0 + ,'S' + ,0 + ,0 + ,0 + ,0 + ,'S' + ,0 + ,0 + ,0 + ,0 + ,'S' + ,0 + ,1 + ,1 + ,0 + ,'S' + ,-1 + ,1 + ,0 + ,0 + ,'S' + ,0 + ,0 + ,0 + ,0 + ,'S' + ,0 + ,1 + ,1 + ,0 + ,'S' + ,-1 + ,1 + ,1 + ,1 + ,'S' + ,0 + ,0 + ,0 + ,0 + ,'S' + ,0 + ,1 + ,0 + ,0 + ,'S' + ,0 + ,1 + ,1 + ,1 + ,'S' + ,0 + ,1 + ,1 + ,1 + ,'S' + ,0 + ,1 + ,1 + ,1 + ,'S' + ,0 + ,0 + ,0 + ,1 + ,'S' + ,1 + ,0 + ,1 + ,1 + ,'S' + ,0 + ,1 + ,1 + ,1 + ,'S' + ,0 + ,0 + ,1 + ,1 + ,'S' + ,0 + ,0 + ,1 + ,1 + ,'S' + ,0 + ,1 + ,0 + ,0 + ,'S' + ,0 + ,1 + ,0 + ,0 + ,'S' + ,0 + ,1 + ,1 + ,1 + ,'S' + ,0 + ,0 + ,0 + ,0 + ,'S' + ,0 + ,1 + ,0 + ,0 + ,'S' + ,0 + ,0 + ,0 + ,0 + ,'S' + ,0 + ,0 + ,0 + ,1 + ,'S' + ,1 + ,1) + ,dim=c(5 + ,105) + ,dimnames=list(c('pre' + ,'post1' + ,'treat' + ,'diff1' + ,'gender') + ,1:105)) > y <- array(NA,dim=c(5,105),dimnames=list(c('pre','post1','treat','diff1','gender'),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) > par4 = 'TRUE' > par3 = '5' > par2 = '3' > par1 = '4' > ylab = 'Y Variable Name' > xlab = 'X Variable Name' > main = 'Title Goes Here' > #'GNU S' R Code compiled by R2WASP v. 1.0.44 () > #Author: Dr. Ian E. Holliday > #To cite this work: Ian E. Holliday, 2011, YOUR SOFTWARE TITLE (vNUMBER) in Free Statistics Software (v$_version), Office for Research Development and Education, URL http://www.wessa.net/rwasp_YOURPAGE.wasp/ > #Source of accompanying publication: > #Technical description: > cat1 <- as.numeric(par1) # > cat2<- as.numeric(par2) # > cat3 <- as.numeric(par3) > intercept<-as.logical(par4) > x <- t(x) > x1<-as.numeric(x[,cat1]) > f1<-as.character(x[,cat2]) > f2 <- as.character(x[,cat3]) > xdf<-data.frame(x1,f1, f2) > (V1<-dimnames(y)[[1]][cat1]) [1] "diff1" > (V2<-dimnames(y)[[1]][cat2]) [1] "treat" > (V3 <-dimnames(y)[[1]][cat3]) [1] "gender" > mynames<- c(V1, V2, V3) > xdf2<-xdf > names(xdf2)<-mynames > names(xdf)<-c('R', 'A', 'B') > mynames <- c(V1, V2, V3) > if(intercept == FALSE)eval (substitute(lmout<-lm(xdf$R ~ xdf$A * xdf$B- 1, data = xdf), list(xdf=quote(xdf2),R=mynames[1],A=mynames[2],B=mynames[3]) ))else eval(substitute(lmout<-lm(xdf$R ~ xdf$A * xdf$B, data = xdf), list(xdf=quote(xdf2),R=mynames[1],A=mynames[2],B=mynames[3]) )) > oldnames<-names(lmout$coeff) > newnames<-gsub('xdf2$', '', oldnames) > (names(lmout$coeff)<-newnames) [1] "(Intercept)" "xdf2$treatS" [3] "xdf2$treatT" "xdf2$gender1" [5] "xdf2$treatS:xdf2$gender1" "xdf2$treatT:xdf2$gender1" > (names(lmout$coefficients)<-newnames) [1] "(Intercept)" "xdf2$treatS" [3] "xdf2$treatT" "xdf2$gender1" [5] "xdf2$treatS:xdf2$gender1" "xdf2$treatT:xdf2$gender1" > > #Note: the /var/www/rcomp/createtable file can be downloaded at http://www.wessa.net/cretab > load(file="/var/www/rcomp/createtable") > > a<-table.start() > a<-table.row.start(a) > a<-table.element(a,'ANOVA Model', length(lmout$coefficients)+1,TRUE) > a<-table.row.end(a) > a<-table.row.start(a) > callstr<-gsub('xdf2$', '',as.character(lmout$call$formula)) > callstr<-paste(callstr[2], callstr[1], callstr[3]) > a<-table.element(a,callstr ,length(lmout$coefficients)+1,TRUE) > a<-table.row.end(a) > a<-table.row.start(a) > a<-table.element(a, 'names',,TRUE) > for(i in 1:length(lmout$coefficients)){ + a<-table.element(a, names(lmout$coefficients[i]),,FALSE) + } > a<-table.row.end(a) > a<-table.row.start(a) > a<-table.element(a, 'means',,TRUE) > for(i in 1:length(lmout$coefficients)){ + a<-table.element(a, signif(lmout$coefficients[i], digits=5),,FALSE) + } > a<-table.row.end(a) > a<-table.end(a) > table.save(a,file="/var/www/rcomp/tmp/1z1iu1324648133.tab") > (aov.xdf<-aov(lmout) ) Call: aov(formula = lmout) Terms: xdf2$treat xdf2$gender xdf2$treat:xdf2$gender Residuals Sum of Squares 1.824640 0.254341 0.027764 28.807541 Deg. of Freedom 2 1 2 99 Residual standard error: 0.5394305 Estimated effects may be unbalanced > (anova.xdf<-anova(lmout) ) Analysis of Variance Table Response: xdf2$diff1 Df Sum Sq Mean Sq F value Pr(>F) xdf2$treat 2 1.8246 0.91232 3.1353 0.04784 * xdf2$gender 1 0.2543 0.25434 0.8741 0.35211 xdf2$treat:xdf2$gender 2 0.0278 0.01388 0.0477 0.95343 Residuals 99 28.8075 0.29099 --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 > rownames(anova.xdf)<-gsub('xdf2$','',rownames(anova.xdf)) > 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$Df[1],,FALSE) + a<-table.element(a, signif(anova.xdf$'Sum Sq'[i], digits=5),,FALSE) + a<-table.element(a, signif(anova.xdf$'Mean Sq'[i], digits=5),,FALSE) + a<-table.element(a, signif(anova.xdf$'F value'[i], digits=5),,FALSE) + a<-table.element(a, signif(anova.xdf$'Pr(>F)'[i], digits=5),,FALSE) + a<-table.row.end(a) + } > a<-table.row.start(a) > a<-table.element(a, 'Residuals',,TRUE) > a<-table.element(a, anova.xdf$'Df'[i+1],,FALSE) > a<-table.element(a, signif(anova.xdf$'Sum Sq'[i+1], digits=5),,FALSE) > a<-table.element(a, signif(anova.xdf$'Mean Sq'[i+1], digits=5),,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/rcomp/tmp/2sacq1324648133.tab") > postscript(file="/var/www/rcomp/tmp/3utty1324648133.ps",horizontal=F,onefile=F,pagecentre=F,paper="special",width=8.3333333333333,height=5.5555555555556) > boxplot(R ~ A + B, data=xdf, xlab=V2, ylab=V1, main='Boxplots of ANOVA Groups') > dev.off() null device 1 > postscript(file="/var/www/rcomp/tmp/4ly7l1324648133.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/www/rcomp/tmp/5y8qu1324648133.ps",horizontal=F,onefile=F,pagecentre=F,paper="special",width=8.3333333333333,height=5.5555555555556) > interaction.plot(xdf$A, xdf$B, xdf$R, 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/rcomp/tmp/6seir1324648133.ps",horizontal=F,onefile=F,pagecentre=F,paper="special",width=8.3333333333333,height=5.5555555555556) + layout(matrix(c(0,0,1,2,1,2,0,0,3,3,3,3), 2,6)) + 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,signif(thsd[[nt]][i,j], digits=5), 1, FALSE) + } + a<-table.row.end(a) + } + } # end nt + a<-table.end(a) + table.save(a,file="/var/www/rcomp/tmp/7k4xt1324648133.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/rcomp/tmp/809pz1324648133.tab") + } > library(car) Loading required package: MASS Loading required package: nnet Loading required package: survival Loading required package: splines > lt.lmxdf<-levene.test(lmout) 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,signif(lt.lmxdf[[i]][1], digits=5), 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/rcomp/tmp/9b8u31324648133.tab") > > try(system("convert tmp/3utty1324648133.ps tmp/3utty1324648133.png",intern=TRUE)) character(0) > try(system("convert tmp/4ly7l1324648133.ps tmp/4ly7l1324648133.png",intern=TRUE)) character(0) > try(system("convert tmp/5y8qu1324648133.ps tmp/5y8qu1324648133.png",intern=TRUE)) character(0) > try(system("convert tmp/6seir1324648133.ps tmp/6seir1324648133.png",intern=TRUE)) GPL Ghostscript GPL Ghostscript 8.648.64: : Unrecoverable error, exit code 1 Unrecoverable error, exit code 1 GPL Ghostscript GPL Ghostscript 8.648.64: : Unrecoverable error, exit code 1 Unrecoverable error, exit code 1 convert: Postscript delegate failed `tmp/6seir1324648133.ps': No such file or directory @ coders/ps.c/ReadPSImage/736. convert: missing an image filename `tmp/6seir1324648133.png' @ wand/convert.c/ConvertImageCommand/2710. [1] "Error: /rangecheck in --setdash--" [2] "Operand stack:" [3] " --nostringval-- 0" [4] "Execution stack:" [5] " %interp_exit .runexec2 --nostringval-- --nostringval-- --nostringval-- 2 %stopped_push --nostringval-- --nostringval-- --nostringval-- false 1 %stopped_push 1862 1 3 %oparray_pop 1861 1 3 %oparray_pop --nostringval-- 1845 1 3 %oparray_pop 1739 1 3 %oparray_pop --nostringval-- %errorexec_pop .runexec2 --nostringval-- --nostringval-- --nostringval-- 2 %stopped_push --nostringval-- 1740 2 3 %oparray_pop" [6] "Dictionary stack:" [7] " --dict:1154/1684(ro)(G)-- --dict:0/20(G)-- --dict:97/200(L)--" [8] "Current allocation mode is local" [9] "Current file position is 3311" [10] "Error: /rangecheck in --setdash--" [11] "Operand stack:" [12] " --nostringval-- 0" [13] "Execution stack:" [14] " %interp_exit .runexec2 --nostringval-- --nostringval-- --nostringval-- 2 %stopped_push --nostringval-- --nostringval-- --nostringval-- false 1 %stopped_push 1862 1 3 %oparray_pop 1861 1 3 %oparray_pop --nostringval-- 1845 1 3 %oparray_pop 1739 1 3 %oparray_pop --nostringval-- %errorexec_pop .runexec2 --nostringval-- --nostringval-- --nostringval-- 2 %stopped_push --nostringval-- 1740 2 3 %oparray_pop" [15] "Dictionary stack:" [16] " --dict:1154/1684(ro)(G)-- --dict:0/20(G)-- --dict:97/200(L)--" [17] "Current allocation mode is local" [18] "Current file position is 3311" Warning message: running command 'convert tmp/6seir1324648133.ps tmp/6seir1324648133.png' had status 1 > > > proc.time() user system elapsed 1.630 0.150 1.776