R : Copyright 2005, The R Foundation for Statistical Computing
Version 2.1.1  (2005-06-20), ISBN 3-900051-07-0

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 a HTML browser interface to help.
Type 'q()' to quit R.

> ### * <HEADER>
> ###
> attach(NULL, name = "CheckExEnv")
> assign(".CheckExEnv", as.environment(2), pos = length(search())) # base
> ## add some hooks to label plot pages for base and grid graphics
> setHook("plot.new", ".newplot.hook")
> setHook("persp", ".newplot.hook")
> setHook("grid.newpage", ".gridplot.hook")
> 
> assign("cleanEx",
+        function(env = .GlobalEnv) {
+ 	   rm(list = ls(envir = env, all.names = TRUE), envir = env)
+            RNGkind("default", "default")
+ 	   set.seed(1)
+    	   options(warn = 1)
+ 	   delayedAssign("T", stop("T used instead of TRUE"),
+ 		  assign.env = .CheckExEnv)
+ 	   delayedAssign("F", stop("F used instead of FALSE"),
+ 		  assign.env = .CheckExEnv)
+ 	   sch <- search()
+ 	   newitems <- sch[! sch %in% .oldSearch]
+ 	   for(item in rev(newitems))
+                eval(substitute(detach(item), list(item=item)))
+ 	   missitems <- .oldSearch[! .oldSearch %in% sch]
+ 	   if(length(missitems))
+ 	       warning("items ", paste(missitems, collapse=", "),
+ 		       " have been removed from the search path")
+        },
+        env = .CheckExEnv)
> assign("..nameEx", "__{must remake R-ex/*.R}__", env = .CheckExEnv) # for now
> assign("ptime", proc.time(), env = .CheckExEnv)
> grDevices::postscript("R2HTML-Examples.ps")
> assign("par.postscript", graphics::par(no.readonly = TRUE), env = .CheckExEnv)
> options(contrasts = c(unordered = "contr.treatment", ordered = "contr.poly"))
> options(warn = 1)    
> library('R2HTML')
> 
> assign(".oldSearch", search(), env = .CheckExEnv)
> assign(".oldNS", loadedNamespaces(), env = .CheckExEnv)
> cleanEx(); ..nameEx <- "HTML"
> 
> ### * HTML
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: HTML
> ### Title: Outputs an object to a HTML file
> ### Aliases: HTML HTML.anova HTML.aov HTML.aovlist HTML.array HTML.atomic
> ###   HTML.by HTML.call HTML.character HTML.coefmat HTML.complex
> ###   HTML.connection HTML.default HTML.density HTML.difftime
> ###   HTML.dummy.coef HTML.dummy.coef.list HTML.environment HTML.factor
> ###   HTML.family HTML.formula HTML.ftable HTML.glm HTML.glm.null
> ###   HTML.hsearch HTML.htest HTML.infl HTML.integer HTML.integrate
> ###   HTML.list HTML.listof HTML.lm HTML.lm.null HTML.logical HTML.logLik
> ###   HTML.MethodsFunction HTML.mtable HTML.noquote HTML.numeric
> ###   HTML.octmode HTML.ordered HTML.pairlist HTML.POSIXct HTML.POSIXlt
> ###   HTML.rle HTML.SavedPlots HTML.simple.list HTML.socket
> ###   HTML.summary.aov HTML.summary.aovlist HTML.summary.glm
> ###   HTML.summary.glm.null HTML.summary.lm HTML.summary.lm.null
> ###   HTML.summary.manova HTML.summary.table HTML.table HTML.tables.aov
> ###   HTML.terms HTML.ts HTML.TukeyHSD HTML.xtable HTML.xtabs HTML.abbrev
> ###   HTML.agnes HTML.Anova HTML.anova.loglm HTML.ar HTML.Arima HTML.arima0
> ###   HTML.boot HTML.bootci HTML.bSpline HTML.clara HTML.correspondence
> ###   HTML.cox.zph HTML.coxph.null HTML.date HTML.diana HTML.dissimilarity
> ###   HTML.dist HTML.ecdf HTML.ellipsoid HTML.factanal HTML.fanny
> ###   HTML.fitdistr HTML.fractions HTML.gam HTML.gamma.shape HTML.glm.dose
> ###   HTML.grob HTML.hclust HTML.HoltWinters HTML.lda HTML.libraryIQR
> ###   HTML.loadings HTML.loess HTML.loglm HTML.lqs HTML.mca HTML.medpolish
> ###   HTML.mona HTML.multinom HTML.nls HTML.nnet HTML.pairwise.htest
> ###   HTML.pam HTML.polr HTML.polySpline HTML.power.htest HTML.ppolySpline
> ###   HTML.ppr HTML.prcomp HTML.princomp HTML.qda HTML.ridgelm HTML.rlm
> ###   HTML.rms.curv HTML.rpart HTML.saddle.distn HTML.shingle
> ###   HTML.shingleLevel HTML.simplex HTML.smooth.spline HTML.stepfun
> ###   HTML.stl HTML.StructTS HTML.structure HTML.summary.agnes
> ###   HTML.summary.clara HTML.summary.diana HTML.summary.fanny
> ###   HTML.summary.gam HTML.summary.loess HTML.summary.loglm
> ###   HTML.summary.mona HTML.summary.multinom HTML.summary.negbin
> ###   HTML.summary.nls HTML.summary.nnet HTML.summary.pam HTML.summary.polr
> ###   HTML.summary.ppr HTML.summary.prcomp HTML.summary.princomp
> ###   HTML.summary.rlm HTML.tskernel HTML.tukeyline HTML.tukeysmooth
> ###   HTML.unit HTML.viewport HTML.reStruct HTML.summary.lme
> ###   HTML.summary.pdDiag
> ### Keywords: print IO file
> 
> ### ** Examples
> 
> dir.create(file.path(tempdir(),"R2HTML"))
> target <- HTMLInitFile(file.path(tempdir(),"R2HTML"),filename="sample", BackGroundColor="#BBBBEE")
> HTML("<br>Don't forget to use the CSS file in order to benefit from fixed size police",file=target)
> tmp <- as.data.frame(matrix(rnorm(100),ncol=10))
> HTML(tmp,file=target)
> HTMLEndFile()
> 
> 
> 
> cleanEx(); ..nameEx <- "HTML.cormat"
> 
> ### * HTML.cormat
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: HTML.cormat
> ### Title: Write a correlation matrix with HTML formatting
> ### Aliases: HTML.cormat
> ### Keywords: IO multivariate
> 
> ### ** Examples
> 
>         tmpfic=HTMLInitFile(tempdir(),CSSFile="http://www.stat.ucl.ac.be/R2HTML/Pastel.css")
>         data(iris)
>         HTML(as.title("Fisher Iris dataset / Correlation matrix - normal matrix"),file=tmpfic)
>         HTML(cor(iris[,1:4]), file=tmpfic)
>         HTML(as.title("Fisher Iris dataset / Correlation matrix - traffic highlighting"),file=tmpfic)
>         HTML.cormat(cor(iris[,1:4]), file=tmpfic)
             Sepal.Length Sepal.Width Petal.Length Petal.Width
Sepal.Length         1.00       -0.12         0.87        0.82
Sepal.Width         -0.12        1.00        -0.43       -0.37
Petal.Length         0.87       -0.43         1.00        0.96
Petal.Width          0.82       -0.37         0.96        1.00
> 
>         # File is generated, you can call the browser:
>         ## Not run: browseURL(tmpfic)
>         
> 
> 
> 
> cleanEx(); ..nameEx <- "HTML.data.frame"
> 
> ### * HTML.data.frame
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: HTML.data.frame
> ### Title: Write a data.frame (or matrix) to a HTML output
> ### Aliases: HTML.data.frame HTML.matrix
> ### Keywords: datasets IO
> 
> ### ** Examples
> 
> tmpfic=HTMLInitFile(tempdir(),CSSFile="http://www.stat.ucl.ac.be/R2HTML/R2HTML.css")
> data(iris)
> HTML(as.title("Fisher Iris dataset"),file=tmpfic)
> HTML(iris, file=tmpfic)
> # File is generated, you can call the browser:
> ## Not run: browseURL(tmpfic)
> 
> # Export one line of iris using default decimal separator
> HTML(iris[1,],file="")

<p align= center >
<table cellspacing=0 border=1>
<caption align=bottom class=captiondataframe></caption>
<tr><td>
	<table border=0 class=dataframe>
	<TBODY> 
	<tr class= firstline > 
		<th>&nbsp;  </th>
		<th>Sepal.Length  </th>
		<th>Sepal.Width  </th>
		<th>Petal.Length  </th>
		<th>Petal.Width  </th>
		<th>Species</th> 
	</tr> <tr><td class=firstcolumn>1</td><td class=cellinside>5.1</td><td class=cellinside>3.5</td><td class=cellinside>1.4</td><td class=cellinside>0.2</td><td class=cellinside>setosa</td></tr>
 
	</TBODY>
</table>
 </td></table>
 <br>
> 
> # Seeing default decimal separator:
> getOption("R2HTML.format.decimal.mark")
[1] "."
> 
> # Modifying it:
> options("R2HTML.format.decimal.mark"=",")
> HTML(iris[1,],file="")

<p align= center >
<table cellspacing=0 border=1>
<caption align=bottom class=captiondataframe></caption>
<tr><td>
	<table border=0 class=dataframe>
	<TBODY> 
	<tr class= firstline > 
		<th>&nbsp;  </th>
		<th>Sepal.Length  </th>
		<th>Sepal.Width  </th>
		<th>Petal.Length  </th>
		<th>Petal.Width  </th>
		<th>Species</th> 
	</tr> <tr><td class=firstcolumn>1</td><td class=cellinside>5,1</td><td class=cellinside>3,5</td><td class=cellinside>1,4</td><td class=cellinside>0,2</td><td class=cellinside>setosa</td></tr>
 
	</TBODY>
</table>
 </td></table>
 <br>
> 
> # Bypassing value set in option:
> HTML(iris[1,],file="",decimal.mark="*")

<p align= center >
<table cellspacing=0 border=1>
<caption align=bottom class=captiondataframe></caption>
<tr><td>
	<table border=0 class=dataframe>
	<TBODY> 
	<tr class= firstline > 
		<th>&nbsp;  </th>
		<th>Sepal.Length  </th>
		<th>Sepal.Width  </th>
		<th>Petal.Length  </th>
		<th>Petal.Width  </th>
		<th>Species</th> 
	</tr> <tr><td class=firstcolumn>1</td><td class=cellinside>5*1</td><td class=cellinside>3*5</td><td class=cellinside>1*4</td><td class=cellinside>0*2</td><td class=cellinside>setosa</td></tr>
 
	</TBODY>
</table>
 </td></table>
 <br>
> 
> # Using a vector for formatting options
> HTML(iris[1:2,1:2],nsmall=c(3,1),file="")

<p align= center >
<table cellspacing=0 border=1>
<caption align=bottom class=captiondataframe></caption>
<tr><td>
	<table border=0 class=dataframe>
	<TBODY> 
	<tr class= firstline > 
		<th>&nbsp;  </th>
		<th>Sepal.Length  </th>
		<th>Sepal.Width</th> 
	</tr> <tr><td class=firstcolumn>1</td><td class=cellinside>5,100</td><td class=cellinside>3,500</td></tr>
 <tr><td class=firstcolumn>2</td><td class=cellinside>4,900</td><td class=cellinside>3,000</td></tr>
 
	</TBODY>
</table>
 </td></table>
 <br>
> 
> 
> 
> cleanEx(); ..nameEx <- "HTML.function"
> 
> ### * HTML.function
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: HTML.function
> ### Title: Writes the code of a function to a target HTML file
> ### Aliases: HTML.function
> ### Keywords: print IO file
> 
> ### ** Examples
> 
> 
> ## Define a function and export it's code to the file /test.html.
> ## Target file may be changed when submitting this code...
> 
> myfile <- paste(tempfile(),".html",sep="")
> myfun <- function(x){
+         cat("\n Euclidian norm")
+         return(sqrt(sum(x^2)))
+  }
> HTML(myfun,file=myfile)
> cat("\n Test output written in: ",myfile)

 Test output written in:  /tmp/RtmpI1U9uH/file10d63af1.html> 
> 
> 
> 
> cleanEx(); ..nameEx <- "HTML.latex"
> 
> ### * HTML.latex
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: HTML.latex
> ### Title: Insert a piece of LaTeX into a HTML file
> ### Aliases: HTML.latex as.latex
> ### Keywords: print IO file
> 
> ### ** Examples
> 
>  fic = HTMLInitFile()
>  HTML.title("sample page",1,file=fic)  
>  HTML("First paragraph",file=fic)
>  cat("Some text and then an equation:",file=fic,append=TRUE)
>  HTML(as.latex("\int_{-\infty}^{1}f(x)dx") ,file=fic)
>  cat(". Nice isn't it?",file=fic,append=TRUE)
>  HTML(as.latex("\int_{-\infty}^{1}f(x)dx",inline=FALSE) ,file=fic)   
>  HTML(as.latex("\int_{-\infty}^{1}f(x)dx",inline=FALSE,count=TRUE) ,file=fic)   
>  HTML(as.latex("\int_{-\infty}^{1}f(x)dx",inline=FALSE,label="My equation") ,file=fic)      
>  cat("file:", fic, "is created")
file: /tmp/RtmpI1U9uH/index.html is created> 
>  ## Not run: browseURL(fic)                  
> 
> 
> 
> cleanEx(); ..nameEx <- "HTML.title"
> 
> ### * HTML.title
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: HTML.title
> ### Title: Writes a title in a target HTML output
> ### Aliases: HTML.title as.title
> ### Keywords: print IO file
> 
> ### ** Examples
> 
> ## Write a title in the file /test.html.
> ## Target file may be changed when submitting this code...
> 
> myfile <- paste(tempfile(),".html",sep="")
> 
> tit1 <- as.title("This is method 1")
> 
> HTML(tit1, file=myfile)
> 
> HTML.title("This is method 2",file=myfile, HR=3)
> cat("\n Test output written in: ",myfile)

 Test output written in:  /tmp/RtmpI1U9uH/file60b7acd9.html> 
> 
> 
> 
> cleanEx(); ..nameEx <- "HTMLCSS"
> 
> ### * HTMLCSS
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: HTMLCSS
> ### Title: Insert HTML code to refer to an external CSS file
> ### Aliases: HTMLCSS
> ### Keywords: print IO file
> 
> ### ** Examples
> 
> myfile <- file.path(tempdir(),"tmp.html")
> HTMLCSS(myfile,CSSfile="myownCSS.CSS")
> 
> 
> 
> cleanEx(); ..nameEx <- "HTMLChangeCSS"
> 
> ### * HTMLChangeCSS
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: HTMLChangeCSS
> ### Title: Change the current CSS file for dynamic use of package
> ### Aliases: HTMLChangeCSS
> ### Keywords: IO file
> 
> ### ** Examples
> 
> ## Not run: 
> ##D         HTMLStart()
> ##D         (x=diag(3))
> ##D         HTMLChangeCSS("Pastel")
> ##D         # refresh the browser
> ## End(Not run)
> 
> 
> 
> cleanEx(); ..nameEx <- "HTMLInitFile"
> 
> ### * HTMLInitFile
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: HTMLInitFile
> ### Title: Begins / Ends a new HTML report output
> ### Aliases: HTMLInitFile HTMLEndFile
> ### Keywords: print IO file
> 
> ### ** Examples
> 
>         # Store in target the name of a output file
>         dir.create(file.path(tempdir(),"R2HTML"))
Warning: '/tmp/RtmpI1U9uH/R2HTML' already exists
>         target <- HTMLInitFile(file.path(tempdir(),"R2HTML"),"index", BackGroundColor="#BBBBEE")
>         # Use target to write a dataframe
>         HTML(as.title("Here is the data frame"),file=target)
>         HTML("<br>Don't forget to use the CSS file in order to benefit from fixed size police",file=target)
>         tmp <- as.data.frame(matrix(rnorm(100),ncol=10))
>         HTML(tmp,file=target)
>         HTMLEndFile()
> 
> 
> 
> cleanEx(); ..nameEx <- "HTMLInsertGraph"
> 
> ### * HTMLInsertGraph
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: HTMLInsertGraph
> ### Title: Insert a graph in a HTML report
> ### Aliases: HTMLInsertGraph
> ### Keywords: print IO file
> 
> ### ** Examples
> 
> 
>         directory=getwd()
>         HTMLoutput=file.path(directory,"output.html")
>         graph1="graph1.png"
>         # Write graph to a file
>         png(file.path(directory,graph1))
>         plot(table(rpois(100,5)), type = "h", col = "red", lwd=10,main="rpois(100,lambda=5)")
>         dev.off()
postscript 
         2 
>         # Insert graph to the HTML output
>         HTMLInsertGraph(graph1,file=HTMLoutput,caption="Sample discrete distribution plot")
[1] TRUE
> 
> 
> 
> cleanEx(); ..nameEx <- "HTMLStart"
> 
> ### * HTMLStart
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: HTMLStart
> ### Title: Start / Stop the automatic redirection of output to HTML files
> ### Aliases: HTMLStart HTMLStop
> ### Keywords: print IO file
> 
> ### ** Examples
> 
> 
> # Perform's one's own direct report
> 
> dir.create(file.path(tempdir(),"R2HTML"))
Warning: '/tmp/RtmpI1U9uH/R2HTML' already exists
> HTMLStart(file.path(tempdir(),"R2HTML"),HTMLframe=FALSE, Title="My report",autobrowse=FALSE)

 *** Output redirected to directory:  /tmp/RtmpI1U9uH/R2HTML
 *** Use HTMLStop() to end redirection.[1] TRUE
HTML> as.title("This is my first title")
[1] "This is my first title"
attr(,"class")
[1] "title"
HTML> x <- 1
HTML> y<- 2
HTML> x+y
[1] 3
HTML> HTMLStop()
[1] "/tmp/RtmpI1U9uH/R2HTML/index.html"
> 
> ## Use for interactive teaching course
> if (interactive()){
+         dir.create(file.path(tempdir(),"R2HTML"))
+         HTMLStart(file.path(tempdir(),"R2HTML"),echo=TRUE)
+         as.title("Manipulation vectors")
+         1:10
+         sum(1:10)
+         c(1:10,rep(3,4))
+         HTMLStop()
+ }
> 
> 
> 
> cleanEx(); ..nameEx <- "HTMLbr"
> 
> ### * HTMLbr
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: HTMLbr
> ### Title: Facility functions to write HTML code
> ### Aliases: HTMLbr HTMLhr HTMLli
> ### Keywords: print IO file
> 
> ### ** Examples
> 
> 
> ## Insert a line to a HTML file
> ## Change the path/name of the file to redirect to your test file
> 
> myfile <- paste(tempfile(),".html",sep="")
> HTMLhr(file=myfile)
> cat("\n Test output written in: ",myfile)

 Test output written in:  /tmp/RtmpI1U9uH/file3ab50c2a.html> 
> 
> 
> 
> cleanEx(); ..nameEx <- "HTMLgrid"
> 
> ### * HTMLgrid
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: HTMLgrid
> ### Title: Creates a HTML grid using ActiveWidget grid -
> ###   www.activewidgets.com
> ### Aliases: HTMLgrid HTMLgrid_inline HTMLgrid_references HTMLgrid_summary
> ### Keywords: datasets IO
> 
> ### ** Examples
> 
>     data(iris)
>     fic <- HTMLInitFile(useGrid=TRUE,useLaTeX=FALSE)
>     fic <- HTMLgrid_inline(iris,file=fic)
>     cat("\n Browse file 'fic':",fic)

 Browse file 'fic': /tmp/RtmpI1U9uH/index.html>     ## Not run: browseURL(fic)
> 
> 
> 
> cleanEx(); ..nameEx <- "HTMLplot"
> 
> ### * HTMLplot
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: HTMLplot
> ### Title: Insert a graphic into an HTML output
> ### Aliases: HTMLplot
> ### Keywords: print IO file
> 
> ### ** Examples
> 
> 
> ## Plots a graphic and insert it into the file /test.html.
> ## Target file and also graph directory should be changed when submitting this code...
> 
> myfile <- paste(tempfile(),".html",sep="")
> plot(sin, -pi, 2*pi,main="Sinus")
> # HTMLplot(file=myfile,GraphDirectory="/",Caption="Look at this curve!")
> 
> 
> 
> cleanEx(); ..nameEx <- "HTMLstem"
> 
> ### * HTMLstem
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: HTMLstem
> ### Title: Insert a stem-and-leaf plot in the HTML output
> ### Aliases: HTMLstem
> ### Keywords: IO univar
> 
> ### ** Examples
> 
>         data(islands)
>         tmpfic=paste(tempfile(),"html",sep=".")
>         HTMLstem(log10(islands),tmpfic)
>         cat("\n stem-and-leaf writen to:", tmpfic,"\n")

 stem-and-leaf writen to: /tmp/RtmpI1U9uH/file56f32f43.html 
> 
> 
> 
> cleanEx(); ..nameEx <- "R2HTML-internal"
> 
> ### * R2HTML-internal
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: HTLMReplaceNA
> ### Title: Internal R2HTML functions
> ### Aliases: HTMLReplaceNA HTMLCommand HTMLcode
> ### Keywords: misc
> 
> ### ** Examples
> 
> 
> 
> 
> 
> cleanEx(); ..nameEx <- "RweaveHTML"
> 
> ### * RweaveHTML
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: RweaveHTML
> ### Title: A driver to parse HTML noweb files with Sweave tool
> ### Aliases: RweaveHTML RweaveHTMLOptions RweaveHTMLFinish
> ###   RweaveHTMLWritedoc RweaveHTMLSetup RweaveHTMLRuncode SweaveSyntaxHTML
> ### Keywords: IO file
> 
> ### ** Examples
> 
> 
> ## Not run: 
> ##D library(tools)
> ##D Sweave("file.snw",driver=RweaveHTML)
> ## End(Not run)
> 
> 
> 
> ### * <FOOTER>
> ###
> cat("Time elapsed: ", proc.time() - get("ptime", env = .CheckExEnv),"\n")
Time elapsed:  0.72 0.17 1.13 0 0.03 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')