R version 3.3.2 (2016-10-31) -- "Sincere Pumpkin Patch"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> source('/home/pw/wessanet/cretab')
> 
> 
> RC.capture <- function (expression, collapse = NULL) {
+     resultConn <- textConnection('RC.resultText', open = 'w', local=TRUE)
+     sink(resultConn)
+     on.exit(function() {
+         sink()
+         close(resultConn)
+     })
+     expression
+     on.exit(NULL)
+     sink()
+     close(resultConn)
+     return(paste(c(RC.resultText, ''), collapse = collapse, sep = ''))
+ }
> RC.texteval <- function (sourceText, collapse = NULL, echo = TRUE) {
+     sourceConn <- textConnection(sourceText, open = 'r')
+     on.exit(close(sourceConn))
+     result <- RC.capture(source(file = sourceConn, local = FALSE, echo = echo, print.eval = TRUE), collapse = collapse)
+     on.exit(NULL)
+     close(sourceConn)
+     res <- ''
+     for(i in 1:length(result)) {
+       if (result[i]!='') res <- paste(res,result[i],'
+ ',sep='')
+     }
+     return(res)
+ }
> 
> 
> myrfcuid = 'r0632432'
> 
> y <- c(3,4,5,4,4,5,5,5,5,5,5,4,4,4,4,5,4,NA,4,5,4,4,4,4,5,5,4,4,5,5,3,5,4,5,4,5,4,4,4,5,4,5,3,5,4,5,5,4,3,NA,5,5,4,3,4,4,4,4,4,4,5,4,4,4,4,4,5,4,4,4,4,4,3,4,4,4,5,4,4,5,5,3,5,4,5,5,5,5,4,4,2,4,5,5,5,4,4,4,5,4,NA,5,4,4,4,5,4,5,4,4,4,3,4,3,5,4,4,5,4,4,4,4,4,4,5,4,4,5,4,4,3,4,4,4,3,4,5,3,4,5,5,4,4,4,3,5,4,5,4,4,3,4,4,4,3,4,5,3,4,5,4,5,4,4,4,4,4,3,4)
> x <- c(4,5,5,3,5,5,5,4,5,5,4,3,4,5,4,5,4,NA,5,5,5,3,4,4,5,3,5,4,4,4,4,5,5,4,5,5,4,5,4,4,4,4,4,5,5,4,4,4,4,4,5,4,4,5,4,4,4,5,4,5,4,4,4,5,5,4,4,4,4,4,4,4,2,5,4,5,5,4,5,5,4,4,4,4,5,4,4,5,5,4,5,4,4,3,4,5,5,4,5,3,5,4,5,3,4,5,5,4,4,4,5,4,5,4,4,4,5,5,5,5,4,5,4,5,5,5,4,4,5,5,4,5,4,5,4,4,3,2,4,4,4,4,5,5,3,4,4,5,4,5,3,5,5,3,5,4,5,5,5,5,4,5,5,4,4,4,4,4,5)
> ylab = 'TVDC3'
> xlab = 'IK1'
> main = 'Scatterplot and histograms'
> #'GNU S' R Code compiled by R2WASP v. 1.2.327 (Thu, 22 Sep 2016 14:19:43 +0200)
> #Author: root
> #To cite this work: Wessa P., (2016), Pearson Correlation (v1.0.12) in Free Statistics Software (v$_version), Office for Research Development and Education, URL http://www.wessa.net/rwasp_correlation.wasp/
> #Source of accompanying publication: Office for Research, Development, and Education
> #
> library(psychometric)
Loading required package: multilevel
Loading required package: nlme
Loading required package: MASS
> x <- x[!is.na(y)]
> y <- y[!is.na(y)]
> y <- y[!is.na(x)]
> x <- x[!is.na(x)]
> postscript(file="/home/pw/wessanet/rcomp/tmp/1i1ph1481049759.ps",horizontal=F,onefile=F,pagecentre=F,paper="special",width=8.3333333333333,height=5.5555555555556) 
> histx <- hist(x, plot=FALSE)
> histy <- hist(y, plot=FALSE)
> maxcounts <- max(c(histx$counts, histx$counts))
> xrange <- c(min(x),max(x))
> yrange <- c(min(y),max(y))
> nf <- layout(matrix(c(2,0,1,3),2,2,byrow=TRUE), c(3,1), c(1,3), TRUE)
> par(mar=c(4,4,1,1))
> plot(x, y, xlim=xrange, ylim=yrange, xlab=xlab, ylab=ylab, sub=main)
> par(mar=c(0,4,1,1))
> barplot(histx$counts, axes=FALSE, ylim=c(0, maxcounts), space=0)
> par(mar=c(4,0,1,1))
> barplot(histy$counts, axes=FALSE, xlim=c(0, maxcounts), space=0, horiz=TRUE)
> dev.off()
null device 
          1 
> lx = length(x)
> makebiased = (lx-1)/lx
> varx = var(x)*makebiased
> vary = var(y)*makebiased
> corxy <- cor.test(x,y,method='pearson', na.rm = T)
> cxy <- as.matrix(corxy$estimate)[1,1]
> 
> a<-table.start()
> a<-table.row.start(a)
> a<-table.element(a,'Pearson Product Moment Correlation - Ungrouped Data',3,TRUE)
> a<-table.row.end(a)
> a<-table.row.start(a)
> a<-table.element(a,'Statistic',1,TRUE)
> a<-table.element(a,'Variable X',1,TRUE)
> a<-table.element(a,'Variable Y',1,TRUE)
> a<-table.row.end(a)
> a<-table.row.start(a)
> a<-table.element(a,'Mean',header=TRUE)
> a<-table.element(a,mean(x))
> a<-table.element(a,mean(y))
> a<-table.row.end(a)
> a<-table.row.start(a)
> a<-table.element(a,'Biased Variance',header=TRUE)
> a<-table.element(a,varx)
> a<-table.element(a,vary)
> a<-table.row.end(a)
> a<-table.row.start(a)
> a<-table.element(a,'Biased Standard Deviation',header=TRUE)
> a<-table.element(a,sqrt(varx))
> a<-table.element(a,sqrt(vary))
> a<-table.row.end(a)
> a<-table.row.start(a)
> a<-table.element(a,'Covariance',header=TRUE)
> a<-table.element(a,cov(x,y),2)
> a<-table.row.end(a)
> a<-table.row.start(a)
> a<-table.element(a,'Correlation',header=TRUE)
> a<-table.element(a,cxy,2)
> a<-table.row.end(a)
> a<-table.row.start(a)
> a<-table.element(a,'Determination',header=TRUE)
> a<-table.element(a,cxy*cxy,2)
> a<-table.row.end(a)
> a<-table.row.start(a)
> a<-table.element(a,'T-Test',header=TRUE)
> a<-table.element(a,as.matrix(corxy$statistic)[1,1],2)
> a<-table.row.end(a)
> a<-table.row.start(a)
> a<-table.element(a,'p-value (2 sided)',header=TRUE)
> a<-table.element(a,(p2 <- as.matrix(corxy$p.value)[1,1]),2)
> a<-table.row.end(a)
> a<-table.row.start(a)
> a<-table.element(a,'p-value (1 sided)',header=TRUE)
> a<-table.element(a,p2/2,2)
> a<-table.row.end(a)
> a<-table.row.start(a)
> a<-table.element(a,'95% CI of Correlation',header=TRUE)
> a<-table.element(a,paste('[',CIr(r=cxy, n = lx, level = .95)[1],', ', CIr(r=cxy, n = lx, level = .95)[2],']',sep=''),2)
> a<-table.row.end(a)
> a<-table.row.start(a)
> a<-table.element(a,'Degrees of Freedom',header=TRUE)
> a<-table.element(a,lx-2,2)
> a<-table.row.end(a)
> a<-table.row.start(a)
> a<-table.element(a,'Number of Observations',header=TRUE)
> a<-table.element(a,lx,2)
> a<-table.row.end(a)
> a<-table.end(a)
> table.save(a,file="/home/pw/wessanet/rcomp/tmp/2bkxu1481049759.tab") 
> library(moments)
> library(nortest)
> jarque.x <- jarque.test(x)
> jarque.y <- jarque.test(y)
> if(lx>7) {
+ ad.x <- ad.test(x)
+ ad.y <- ad.test(y)
+ }
> a<-table.start()
> a<-table.row.start(a)
> a<-table.element(a,'Normality Tests',1,TRUE)
> a<-table.row.end(a)
> a<-table.row.start(a)
> a<-table.element(a,paste('<pre>',RC.texteval('jarque.x'),'</pre>',sep=''))
> a<-table.row.end(a)
> a<-table.row.start(a)
> a<-table.element(a,paste('<pre>',RC.texteval('jarque.y'),'</pre>',sep=''))
> a<-table.row.end(a)
> if(lx>7) {
+ a<-table.row.start(a)
+ a<-table.element(a,paste('<pre>',RC.texteval('ad.x'),'</pre>',sep=''))
+ a<-table.row.end(a)
+ a<-table.row.start(a)
+ a<-table.element(a,paste('<pre>',RC.texteval('ad.y'),'</pre>',sep=''))
+ a<-table.row.end(a)
+ }
> a<-table.end(a)
> table.save(a,file="/home/pw/wessanet/rcomp/tmp/3g4rl1481049759.tab") 
> library(car)
> postscript(file="/home/pw/wessanet/rcomp/tmp/4d3ql1481049759.ps",horizontal=F,onefile=F,pagecentre=F,paper="special",width=8.3333333333333,height=5.5555555555556) 
> qqPlot(x,main='QQplot of variable x')
> dev.off()
null device 
          1 
> postscript(file="/home/pw/wessanet/rcomp/tmp/5f8mw1481049759.ps",horizontal=F,onefile=F,pagecentre=F,paper="special",width=8.3333333333333,height=5.5555555555556) 
> qqPlot(y,main='QQplot of variable y')
> dev.off()
null device 
          1 
> 
> try(system("convert /home/pw/wessanet/rcomp/tmp/1i1ph1481049759.ps /home/pw/wessanet/rcomp/tmp/1i1ph1481049759.png",intern=TRUE))
character(0)
> try(system("convert /home/pw/wessanet/rcomp/tmp/4d3ql1481049759.ps /home/pw/wessanet/rcomp/tmp/4d3ql1481049759.png",intern=TRUE))
character(0)
> try(system("convert /home/pw/wessanet/rcomp/tmp/5f8mw1481049759.ps /home/pw/wessanet/rcomp/tmp/5f8mw1481049759.png",intern=TRUE))
character(0)
> 
> proc.time()
   user  system elapsed 
  3.088   0.196   3.301