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, ...
• 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

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'

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

RSP Markup Language

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

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

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

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.

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.

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 %>.
<% } %>

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.

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 ...) %>

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.

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'

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

Appendix

Session info:

R version 4.3.2 (2023-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.3 LTS
Matrix products: default
BLAS:   /home/henrik/shared/software/CBI/_ubuntu22_04/R-4.3.2-gcc11/lib/R/lib/libRblas.so 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=C              
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
time zone: America/Los_Angeles
tzcode source: system (glibc)
attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     
other attached packages:
[1] R.devices_2.17.2  R.rsp_0.46.0      R.oo_1.26.0       R.methodsS3_1.8.2
loaded via a namespace (and not attached):
[1] compiler_4.3.2      tools_4.3.2         base64enc_0.1-4    
[4] digest_0.6.34       R.cache_0.16.0      Cairo_1.6-2        
[7] R.utils_2.12.3-9002

These slides were generated using R.rsp::rfile() in 0.06 secs.