<%@meta name="title"%>

by <%@meta name="author"%>, <%=format(as.Date(R.rsp$date), format="%Y-%m-%d")%>

Available on CRAN since 2005 (first version ~2002):

install.packages("R.rsp")

> library("R.rsp")
> rcat("A random number: <%%= sample(1:10, size = 1) %%>")
A random number: 7

<%---------------------------------------------------------------------%> <% slide("Objectives") %> <%---------------------------------------------------------------------%>

• Dynamically generate documents and reports (and web/help pages).
• Quickly turn your favorite static report template into a dynamic one.
• Support all formats, e.g. LaTeX, Markdown, HTML, ... <%-- * Support multiple languages, e.g. R, bash, ... --%>
• Supplement and/or complement Sweave, knitr, ...
• Mix and match code and text however you want.
• Simplify sharing of template and output documents.
• Use for R package vignettes.

Some usage

• PSCBS: PDF reports of copy-number segmentation results
• aroma-project.org: Interactive Chromosome Explorer and Array Explorer

<%---------------------------------------------------------------------%> <% slide("Compiling RSP document into PDF, HTML, ...")%> <%---------------------------------------------------------------------%>

> rfile("http://example.org/vignette.tex.rsp")
RspFileProduct:
Pathname: vignette.pdf
File size: 258.71 kB (264925 bytes)
Content type: application/pdf
Metadata 'title': 'Dynamic document creation using RSP'
Metadata 'keywords': 'Literate programming, HTML, PDF'
Metadata 'author': 'Henrik Bengtsson'

<%---------------------------------------------------------------------%> <% slide("Very simple idea: Translate RSP to R and evaluate")%> <%---------------------------------------------------------------------%>

1. RSP document

Title: Example
Counting:<%% for (i in 1:3) { %%>
 <%%= i %%>
<%% } %%>

2. R script

cat("Title: Example\nCounting:")
for (i in 1:3) {
  cat(" ")
  cat(i)
}

3. RSP output

Title: Example
Counting: 1 2 3

<%---------------------------------------------------------------------%> <% slide("RSP Markup Language")%> <%---------------------------------------------------------------------%>

1. RSP comments (<%%-- ... --%%>)

2. RSP preprocessing directives (<%%@ ... %%>)

3. RSP code expressions (<%% ... %%>)

<%---------------------------------------------------------------------%> <% slide("RSP Markup Language")%> <%---------------------------------------------------------------------%>

1. RSP comments (<%%-- ... --%%>)

<%%-----------------------------
  Compile to PDF:
  R.rsp::rfile("report.tex.rsp")
  ------------------------------%%>
\documentclass{report}
...

RSP comments drop anything within, e.g. private notes, other RSP constructor (nested comments too) and will never be part of the output.

<%---------------------------------------------------------------------%> <% slide("RSP Markup Language")%> <%---------------------------------------------------------------------%>

2. RSP preprocessing directives (<%%@ ... %%>)

Including local and online files

<%%@include file="http://example.org/QC.tex.rsp"%%>

Conditional inclusion

<%%@ifeq version="devel"%%>
  <%%@include file="templates/QA-devel.tex.rsp"%%>
<%%@else%%>
  Quality assessment is still under development.
<%%@endif%%>

Meta data

<%%@meta title="Example"%%>
\hypersetup{pdftitle=<%%@meta name="title"%%>}
\title{<%%@meta name="title"%%>}

RSP preprocessing directives are independent of R, i.e. they would look the same with RSP for Python.

<%---------------------------------------------------------------------%> <% slide("RSP Markup Language")%> <%---------------------------------------------------------------------%>

3. RSP code expressions (<%% ... %%>)

Insert value of evaluated R expressions

<%%= sample(1:100, size = 1) %%>

Code snippets - mixture of RSP and text

<%% for (i in 1:3) { %%>
 Step <%%= i %%>.
<%% } %%>

<%---------------------------------------------------------------------%> <% slide("Looping over mixtures of code and text")%> <%---------------------------------------------------------------------%>

<%% fit <- segmentByPairedPSCBS(data) %%>
\section{Segmentation results}
<%% for (chr in 1:23) { %%>
  \subsection{Chromosome <%%= chr %%>}
  <%% fitT <- extractChromosome(fit, chr) %%>
  PSCBS identified <%%= nbrOfSegments(fitT) %%> segments
  on Chr. <%%= chr %%>.
  ...
<%% } # for (chr ...) %%>

To achieve the same using noweb-style markup (e.g. Sweave and knitr) is tedious.

<%---------------------------------------------------------------------%> <% slide("RSP template functions")%> <%---------------------------------------------------------------------%>

<%%-- RSP TEMPLATES --%%>
<%% chromosomeSummary <- function(chr) { %%>
  <%% fitT <- extractChromosome(fit, chr) %%>
  PSCBS identified <%%= nbrOfSegments(fitT) %%> segments
  on Chr. <%%= chr %%>.
  ...
<%% } %%>
<%%-- DOCUMENT --%%>
...
<%% for (chr in 1:23) { %%>
  \subsection{Chromosome <%%= chr %%>}
  <%% chromosomeSummary(chr) %%>
<%% } # for (chr ...) %%>

<%--- <%---------------------------------------------------------------------%> <% slide("RSP template functions")%> <%---------------------------------------------------------------------%>

<%%-- RSP TEMPLATES --%%>
<%%@include file="http://example.org/chrSum.tex.rsp"%%>
<%%-- DOCUMENT --%%>
...
<%% for (chr in 1:23) { %%>
  \subsection{Chromosome <%%=chr%%>}
  <%% chromosomeSummary(chr) %%>
<%% } # for (chr ...) %%>

---%>

<%---------------------------------------------------------------------%> <% slide("R.rsp package - RSP engine for R")%> <%---------------------------------------------------------------------%>

rcat() - RSP version of cat()

> rcat("A random integer in [1,100]:
        <%%=sample(1:100, size = 1)%%>\n")
A random integer in [1,100]: 77

rsource() - RSP version of source()

Consider RSP file 'count.rsp' (think 'count.R'):

Counting:<%% for (i in 1:10) { %%>
  <%% Sys.sleep(0.3) %%><%%= i %%>
<%% } %%>.

Running this RSP script gives:

> rsource("count.rsp")
Counting: 1 2 3 4 5 6 7 8 9 10.

<%---------------------------------------------------------------------%> <% slide("rfile() - end-to-end compilation")%> <%---------------------------------------------------------------------%>

> rfile("report.md.rsp", args = list(n = 50, model = "L1"))
RspFileProduct:
Pathname: report.html
File size: 42.54 kB (43564 bytes)
Content type: text/html

> rfile("http://example.org/vignette.tex.rsp")
RspFileProduct:
Pathname: vignette.pdf
File size: 258.71 kB (264925 bytes)
Content type: application/pdf
Metadata 'title': 'Dynamic document creation using RSP'
Metadata 'keywords': 'Literate programming, HTML, PDF'
Metadata 'author': 'Henrik Bengtsson'

<%---------------------------------------------------------------------%> <% slide("Including graphics (R.devices package)") %> <%---------------------------------------------------------------------%> RSP-embedded LaTeX

\includegraphics{<%%= toPDF("MyFigure,yeah,cool", {
  curve(dnorm, from = -5, to = +5)
}) %%>}

generates the image file and outputs

\includegraphics{MyFigure,yeah,cool}

which appears as

" width=480>

<%---------------------------------------------------------------------%> <% slide("Appendix") %> <%---------------------------------------------------------------------%> Session info:

<% print(sessionInfo()) %>

These slides were generated using R.rsp::rfile() in <%= dt <- round(Sys.time()-t0, digits = 2) %> <%= attr(dt, "units") %>.