Internal R2HTML functions

Description

Internal R2HTML functions

Usage

HTMLReplaceNA(Vec, Replace = " ")
HTMLCommand(x, file = HTMLGetFile(),
Num = "", menu = FALSE, target= "index<-main.html", append = TRUE, ...)
HTMLcode(x,...)

Arguments

Details

These are not to be called by the user.

Wrapper around HTML() to save output to the clipboard

Description

Calls HTML() with appropriate filename and append attributes to write output to clipboard (currently only works on Windows).

Usage

	HTML2clip(x,
	 filename =file("clipboard",
	 ifelse(.Platform$OS == "windows", "w",
	 stop("Writing to clipboard only supported on Windows"))),
	 append = FALSE, ...) 

Arguments

Value

no value returned.

Note

This function was contributed by Gabor Grothendieck.

Author(s)

Eric Lecoutre

See Also

HTML

Examples

if (.Platform$OS == "windows")
	HTML2clip(summary(lm(rating ~., attitude)))

Outputs an object to a HTML file

Description

Generic method equivalent to print that performs HTML output for any R object.

Usage

HTML(x, ...)

Arguments

Details

HTML function acts like cat, with a file argument, which has to be used and a append argument, which is set by default to TRUE. A convenient default value for file argument can be set by calling HTMLInitFile or HTMLSetFile , so that one may begin to set this variable and omit the argument thereafter. Most of the current classes are handled by HTML function. Some specific methods such as HTML.matrix or HTML.data.frame do own a lot of arguments to specify the way the data are exported.

Value

no value returned.

Author(s)

Eric Lecoutre

See Also

HTML.data.frame ,HTML.function , HTMLInitFile , HTMLStart

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-width font",file=target)
tmp <- as.data.frame(matrix(rnorm(100),ncol=10))
HTML(tmp,file=target)
HTMLEndFile()

Write a correlation matrix with HTML formatting

Description

Although the class ‘cormat’ is not defined, the function is called HTML.cormat, to highlight the fact it should be called only with a correlation matrix. It is documented as a regular S3 method for technical reasons. Contrary to the signature shown, below, you will call it as HTML.cormat, explicitly, as shown in the examples.

Usage

## S3 method for class 'cormat'
HTML(x, file = HTMLGetFile(),
digits = 2, append = TRUE, align = "center",
caption = "", captionalign = "bottom",
classcaption = "captiondataframe", classtable = "cormat", useCSS = TRUE, ...)

Arguments

Value

returns (invisibly) the input

Note

“Highlighting traffic” is a simple technique which allows to have a visual representation of data. It is particularly well suited for correlation matrices in order to have at a glance the underlying (linear) structure of data. If your output doesn't rely on CSS styles, you should use useCSS=FALSE option, whihc hard codes grey levels for correlations.

For CSS uses, you can (re)define colours and other attributes for correlations in seq(0,1,length=11)-defined intervals. Some definitions could be equivalent, not showing any difference. You can, by example, redefine CSS so that only correlations greater than 0.9 are showned, and lower the size of cells, which could be usefull for veryu big datasets.

Author(s)

Eric Lecoutre

See Also

HTML

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)
	# File is generated, you can call the browser:
	## Not run: browseURL(tmpfic)
	

Write a data.frame (or matrix) to a HTML output

Description

This function exports a data.frame to a HTML file. Many arguments allow to customize the layout of the HTML table.

Usage

## S3 method for class 'data.frame'
HTML(x, file = HTMLGetFile(),
 Border = 1, innerBorder = 0, classfirstline = "firstline",
 classfirstcolumn = "firstcolumn", classcellinside = "cellinside",
 append = TRUE, align = "center", caption = "", captionalign = "bottom",
 classcaption = "captiondataframe", classtable = "dataframe",
 digits = getOption("R2HTML.format.digits"),
 nsmall = getOption("R2HTML.format.nsmall"),
 big.mark = getOption("R2HTML.format.big.mark"),
 big.interval = getOption("R2HTML.format.big.interval"),
 decimal.mark = getOption("R2HTML.format.decimal.mark"),
 sortableDF = getOption("R2HTML.sortableDF"), row.names = TRUE, ...)

Arguments

Details

For the moment, HTML.matrix and HTML.data.frame do have the same options. Tables are build using two different HTML tables, one beeing encapsulated within the other, which allows to have a table without borders inside but with a border outside. It is nevertheless recommended to rely on CSS to obtain such results...

Now format is called to format numerical values (modif. suggested by Arne Henningsen). The corresponding arguments are: digits, nsmall, big.mark, big.intervall and decimal.mark. For each argument, one can supply either a single value or a vector. In the second case, the size of the vector has to be the number of columns of the data.frame and formatting options will be used element-wise (column by column).

Some options are used to pass default values. You can see those options with (by example): getOption("R2HTML.format.decimal.mark") and options("R2HTML.format.decimal.mark"=",")

Sortable data.frame uses a DHTML behavior. This requires the file ‘tablesort.htc’ which comes with R2HTML to be placed in the same directory than the output. This functionality only works for HTML files located on a web server (not on local computer).

Value

no value returned.

Author(s)

Eric Lecoutre

See Also

HTML

Examples

tmpfic=HTMLInitFile(tempdir(),CSSFile=system.file("samples", "R2HTML.css", package="R2HTML"))
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="")
# Seeing default decimal separator:
getOption("R2HTML.format.decimal.mark")
# Modifying it:
options("R2HTML.format.decimal.mark"=",")
HTML(iris[1,],file="")
# Bypassing value set in option:
HTML(iris[1,],file="",decimal.mark="*")
# Using a vector for formatting options
HTML(iris[1:2,1:2],nsmall=c(3,1),file="")

Writes the code of a function to a target HTML file

Description

Writes the code of a function to a target HTML file

Usage

## S3 method for class 'function'
HTML(x, file = HTMLGetFile(), append=TRUE,...)

Arguments

Details

The code of the function is written in the target HTML file, using HTML <XMP> tag. A CSS class called "function" is used to personalise the output.

Value

no value returned.

Note

For a discussion about .HTML.file default value for file argument, refer to HTMLStart

Author(s)

Eric Lecoutre

See Also

HTML

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)

Insert a piece of LaTeX into a HTML file

Description

This makes use of AsciiMathML javascript functions. Standard LaTeX input will be turned into MathML and displayed through any brower extension that can handle MathML (such as MathPlayer)

Usage

as.latex(x, label=NULL,
inline=ifelse(is.null(label), TRUE, FALSE), count=ifelse(is.null(label), FALSE, TRUE))
## S3 method for class 'latex'
HTML(x, file = HTMLGetFile(), ...)

Arguments

Details

Mathematical notations will be translated in MathML by the AsciiMathML javascript program of Peter Jipsen. Note that his functions allow translating equations with a notation simpler than LaTeX (see his page on AsciiMathML for details). Pieces of LaTeX could be put inline (within text) or on a single line : same opposition that the one between $...$ and $$...$$. In order to work, a reference to the javascipt file has to be present within the HTML file and the HTML body tag has also to include onload="translate()". All the necessary stuff is included in HTMLInitFile .

Value

no value returned.

Author(s)

Eric Lecoutre

References

AsciiMathML: http://www1.chapman.edu/~jipsen/mathml/asciimath.xml

See Also

HTMLInitFile ,HTML

Examples

## Not run: 
	 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")
	 browseURL(fic)
## End(Not run)		 

Writes a title in a target HTML output

Description

A title is a string with the S3 class "title". The function as.title gives this class to an object, so that title method of HTML could apply to it. However, it is also possibly to call this method, explicitly, providing a plain string.

Usage

## S3 method for class 'title'
HTML(x, HR = 2, CSSclass=NULL,
file = HTMLGetFile(), append=TRUE,...)
as.title(x)

Arguments

Value

no value returned.

Note

For a discussion about .HTML.file default value for file argument, refer to HTMLStart

Author(s)

Eric Lecoutre

See Also

HTML

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)

Insert HTML code to refer to an external CSS file

Description

Allow to use CSS file in a report

Usage

HTMLCSS(file = HTMLGetFile(), append = TRUE, CSSfile = "R2HTML.css")

Arguments

Value

no value returned.

Author(s)

Eric Lecoutre

References

For information about CSS, have a look at W3 web site http://www.w3.org/Style/CSS/

Examples

myfile <- file.path(tempdir(),"tmp.html")
HTMLCSS(myfile,CSSfile="myownCSS.CSS")

Change the current CSS file for dynamic use of package

Description

When using in dynamic mode, a call to HTMLStart copy the R2HTML.css file to the specified output directory (temp by default). HTMLChangeCSS copy a new CSS file to this destination (or to working directory). Then, the produced HTML files are now based on this new CSS.

Usage

HTMLChangeCSS(newCSS = "R2HTML", from = NULL)

Arguments

Value

A boolean: wether this has been done or not.

Note

In order to work properly, this assumes you hae used R2HTML.css file (the default one), as this is this file which will be replaced by the new one.

Author(s)

Eric Lecoutre

See Also

HTMLStart

Examples

## Not run: 
	HTMLStart()
	(x=diag(3))
	HTMLChangeCSS("Pastel")
	# refresh the browser
## End(Not run)

Begins / Ends a new HTML report output

Description

HTMLInitFile handles the beginning and HTMLEndFile the ending of a HTML report, by writing the HTML <body><head><title></title></head>...</body> tags and their options. When working manually, the user may need to use it's own functions or to explicitly write to a file using cat("", file=).

HTMLInitFile and HTMLSetFile sets the default file path to be used by HTML functions, and HTMLGetFile retrieves it.

Usage

HTMLInitFile(outdir = tempdir(), filename="index", extension="html",
HTMLframe=FALSE, BackGroundColor = "FFFFFF", BackGroundImg = "",
Title = "R output", CSSFile="R2HTML.css", useLaTeX=TRUE, useGrid=TRUE)
HTMLEndFile(file = HTMLGetFile())
HTMLSetFile(file)
HTMLGetFile()

Arguments

Value

physical path of the main HTML file that will serve for the report.

Author(s)

Eric Lecoutre

See Also

HTML , as.latex , HTMLgrid

Examples

	# Store in target the name of a output file
	dir.create(file.path(tempdir(),"R2HTML"))
	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()

Insert a graph in a HTML report

Description

Write the HTML <img> tag to an output, so that a existant graph could be displayed in the HTML report

Usage

HTMLInsertGraph(GraphFileName="", Caption="", GraphBorder=1,
Align="center", WidthHTML=500, HeightHTML=NULL,
file=HTMLGetFile(), append=TRUE,...)

Arguments

Details

The steps to add a graph to a HTML file are the following: first create the graph, by using a device convenient for web pages, such as GIF, JPEG or PNG. Ensure to write it in the same directory than the HTML file. Then call HTMLInsertGraph.

Value

no value returned.

Author(s)

Eric Lecoutre

See Also

HTMLplot

Examples

	directory=tempdir()
	HTMLoutput=file.path(directory,"output.html")
	graph1="graph1.png"
	# Write graph to a file
	## Not run: png(file.path(directory,graph1))
	## Not run: plot(table(rpois(100,5)), type = "h", col = "red",
	 lwd=10,main="rpois(100,lambda=5)")
## End(Not run)
	## Not run: dev.off()
	# Insert graph to the HTML output
	HTMLInsertGraph(graph1,file=HTMLoutput,caption="Sample discrete distribution plot")

Start / Stop the automatic redirection of output to HTML files

Description

Add the automatic redirection of output to an HTML file. The R session is modified in the following way: a new prompt is proposed (by default HTML>) and each parsed command is also evaluated using HTML generic method, so that the user benefits of both a normal and a HTML output. Please read carefully the details below.

Usage

HTMLStart(outdir = tempdir(), filename = "index", extension = "html",
echo = FALSE, autobrowse = FALSE, HTMLframe = TRUE, withprompt = "HTML> ",
CSSFile = "R2HTML.css", BackGroundColor = "FFFFFF", BackGroundImg = "",
Title = "R output") 
HTMLStop()

Arguments

Details

The user may need to know the following points which describe how R2HTML does work:

- Each parsed command is evaluated and the returned value is passed to the generic function HTML. This evaluation is assured by addTaskCallback function, which is used to add a specific task each time R has to parse an expression.

- A new environment is built, where internal variables such as physical path are stored. This environment is not visible by the user. It is destroyed when calling HTMLStop.

Value

no useful output is returned.

Note

The argument echo is very usefull for teaching purposes.

Author(s)

Eric Lecoutre

See Also

HTML

Examples

# Perform's one's own direct report
dir.create(file.path(tempdir(),"R2HTML"))
HTMLStart(file.path(tempdir(),"R2HTML"),HTMLframe=FALSE, Title="My report",autobrowse=FALSE)
as.title("This is my first title")
x <- 1
y<- 2
x+y
HTMLStop()
## 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()
}

Facility functions to write HTML code

Description

Write <br>, <li> and <hr> tags, which are often used, to an output file.

Usage

HTMLbr(x=1, file = HTMLGetFile(), append=TRUE)
HTMLli(txt="", file = HTMLGetFile(), append=TRUE)
HTMLhr(file = HTMLGetFile(), Width = "100%", Size = "1",
CSSclass=NULL, append=TRUE)

Arguments

Value

no value returned.

Note

For a discussion about .HTML.file default value for file argument, refer to HTMLStart

Author(s)

Eric Lecoutre

See Also

HTML

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)

Creates a HTML grid using ActiveWidget grid - www.activewidgets.com

Description

All HTMLgrid functions do use the component ActiveWidget grid. Basically, we use this component to display data, so the functions export a data.frame. Data could be stored within the HTML file (HTMLgrid_inline) or in an external raw text file which would be required asynchronously (HTMLgrid).

Usage

HTMLgrid(x, file = HTMLGetFile(), append = TRUE,
includeref = FALSE, align = "center", digits = getOption("R2HTML.format.digits"),
nsmall = getOption("R2HTML.format.nsmall"),
big.mark = getOption("R2HTML.format.big.mark"),
big.interval = getOption("R2HTML.format.big.interval"),
decimal.mark = getOption("R2HTML.format.decimal.mark"),
asDF = TRUE, browse = FALSE, classes = NULL, showimages = TRUE)
HTMLgrid_inline(x,file = HTMLGetFile(), append=TRUE,
includeref=FALSE, align="center", digits=getOption("R2HTML.format.digits"),
nsmall = getOption("R2HTML.format.nsmall"),
big.mark = getOption("R2HTML.format.big.mark"),
big.interval = getOption("R2HTML.format.big.interval"),
decimal.mark = getOption("R2HTML.format.decimal.mark"),
asDF=TRUE,browse=FALSE, classes=sapply(x,class), showimages=TRUE)
HTMLgrid_summary(x,file=NULL,append=TRUE, digits=getOption("R2HTML.format.digits"),
nsmall = getOption("R2HTML.format.nsmall"),
big.mark = getOption("R2HTML.format.big.mark"),
big.interval = getOption("R2HTML.format.big.interval"),
decimal.mark = getOption("R2HTML.format.decimal.mark"), browse=FALSE)
HTMLgrid_references(file=)

Arguments

Details

Those exportation methods require severall external files, including the runtime version of ActiveWidgets grid. To include the necessary references, you can use HTMLgrid_references. Be careful: if you intend to put multiple grids on a same output, the references has to be present only once in the output. \ If you set the file argument to NULL, a new temp file will be created.

Value

Note

Presentation relies on pure CSS + Javascript. It may be possible than future upgrade change the presentation of grids created with this version.

Author(s)

Eric Lecoutre

References

ActiveWidgets Grid 1.0 - http://www.activewidgets.com

Examples

 data(iris)
 fic <- HTMLInitFile(useGrid=TRUE,useLaTeX=FALSE)
 fic <- HTMLgrid_inline(iris,file=fic)
 cat("\n Browse file 'fic':",fic)
 ## Not run: browseURL(fic)

Insert a graphic into an HTML output

Description

Exports the active graphic to a JPEG or GIF file and add it to a target HTML output, by writing the <IMG> tag.

Usage

HTMLplot(Caption = "", file = HTMLGetFile(), append = TRUE,
GraphDirectory = ".", GraphFileName = "", GraphSaveAs = "png", GraphBorder = 1,
Align = "center", Width = 500, Height = 500, WidthHTML = NULL, HeightHTML = NULL,
GraphPointSize = 12, GraphBackGround = "white", GraphRes = 72, plotFunction = NULL, ...)

Arguments

Details

Note that this function is coded to work automatically when using automatic exportation with HTMLStart . When using manualy, user should pay attention to the GraphDirectory option, so that graph files are in the same directory as HTML output files. When using to write reports in a non interactive way, first generate the graphic using a device and then use HTMLInsertGraph .

Value

no value returned.

Author(s)

Eric Lecoutre

See Also

HTMLStart , HTMLInsertGraph

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!")

Insert a stem-and-leaf plot in the HTML output

Description

Insert a stem-and-leaf plot in the HTML output.

Usage

HTMLstem(x, file = HTMLGetFile(), append = TRUE, ...)

Arguments

Details

As stem internal function does not return anything but directly print to console, there is no way to automatically export it to the HTML output. Thus, HTMLstem simply captures the output and write it to the HTML file. When using the package in a interactive way, you should call HTMLstem.

Value

no value returned.

Author(s)

Eric Lecoutre

See Also

stem ,HTML

Examples

	data(islands)
	tmpfic=paste(tempfile(),"html",sep=".")
	HTMLstem(log10(islands),tmpfic)
	cat("\n stem-and-leaf writen to:", tmpfic,"\n")

A driver to parse HTML noweb files with Sweave tool

Description

This driver parses HTML files containing R code and replace pieces of code with their output. Graphs are incorporated as png.

Usage

RweaveHTML()

Value

None value is returned. From a .snw noweb file, the corresponding .html is produced (as eventuals png files for graphs).

Note

In order to work properly, noweb codes have to be located at the beginning of a line (no indentation). See samples in the samples directory of the package.

Author(s)

Eric Lecoutre

See Also

Sweave

Examples

## Not run: 
library(tools)
Sweave("file.snw",driver=RweaveHTML)
## End(Not run)