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lyx_mirror/lib/examples/sweave.lyx
Scott Kostyshak 2f4233721d Update docs to latest format for 2.2.0alpha2
2015-11-27 03:23:22 -05:00

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#LyX 2.2 created this file. For more info see http://www.lyx.org/
\lyxformat 503
\begin_document
\begin_header
\origin /systemlyxdir/examples/
\textclass article
\begin_preamble
%% maxwidth is the original width if it's less than linewidth
%% otherwise use linewidth (to make sure the graphics do not exceed the margin)
\def\maxwidth{%
\ifdim\Gin@nat@width>\linewidth
\linewidth
\else
\Gin@nat@width
\fi
}
\end_preamble
\options nogin
\use_default_options true
\begin_modules
sweave
\end_modules
\maintain_unincluded_children false
\language english
\language_package auto
\inputencoding default
\fontencoding global
\font_roman "palatino" "default"
\font_sans "lmss" "default"
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\cite_engine_type default
\biblio_style plain
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\suppress_date false
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\index Index
\shortcut idx
\color #008000
\end_index
\leftmargin 3cm
\topmargin 3cm
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\secnumdepth 3
\tocdepth 3
\paragraph_separation indent
\paragraph_indentation default
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\tracking_changes false
\output_changes false
\html_math_output 0
\html_css_as_file 0
\html_be_strict false
\end_header
\begin_body
\begin_layout Standard
\begin_inset ERT
status open
\begin_layout Plain Layout
%
\backslash
SweaveOpts{prefix=TRUE,prefix.string=sweave-prefix,keep.source=FALSE}
\end_layout
\end_inset
\end_layout
\begin_layout Standard
\begin_inset ERT
status open
\begin_layout Plain Layout
%%
\backslash
maxwidth was defined in the preamble; see document settings
\end_layout
\begin_layout Plain Layout
\backslash
setkeys{Gin}{width=
\backslash
maxwidth}
\end_layout
\end_inset
\end_layout
\begin_layout Title
Using Sweave with \SpecialCharNoPassThru LyX
\end_layout
\begin_layout Author
Yihui Xie
\begin_inset Foot
status collapsed
\begin_layout Plain Layout
Department of Statistics, Iowa State University.
Email:
\begin_inset CommandInset href
LatexCommand href
name "xie@yihui.name"
target "xie@yihui.name"
type "mailto:"
\end_inset
\end_layout
\end_inset
\begin_inset ERT
status collapsed
\begin_layout Plain Layout
\backslash
and
\end_layout
\end_inset
Gregor Gorjanc
\begin_inset ERT
status collapsed
\begin_layout Plain Layout
\backslash
and
\end_layout
\end_inset
Jean-Marc Lasgouttes
\end_layout
\begin_layout Standard
Sweave is a tool in the R language (
\begin_inset Flex URL
status collapsed
\begin_layout Plain Layout
http://www.r-project.org
\end_layout
\end_inset
) for dynamic report generation using the ideas of literate programming.
R code can be mixed into a \SpecialCharNoPassThru LaTeX
document, and will be executed in R when
the document is compiled; the results are written into the \SpecialCharNoPassThru TeX
output.
\end_layout
\begin_layout Standard
Since \SpecialCharNoPassThru LyX
2.0, Sweave can be used out of the box with any document class
using the
\family sans
Sweave
\family default
module.
We can add the
\family sans
Sweave
\family default
module to a \SpecialCharNoPassThru LyX
document from
\family sans
Document\SpecialChar menuseparator
Settings\SpecialChar menuseparator
Modules
\family default
.
In this manual, we demonstrate some common features of Sweave and explain
how the module works.
A PDF version of this manual can be found at
\begin_inset Flex URL
status collapsed
\begin_layout Plain Layout
https://github.com/downloads/yihui/lyx/sweave.pdf
\end_layout
\end_inset
.
\end_layout
\begin_layout Section
System Requirements
\end_layout
\begin_layout Standard
The
\family sans
Sweave
\family default
module depends on the executable
\family typewriter
Rscript
\family default
, so it has to be in the
\family sans
PATH
\family default
variable of the system.
It is usually not a problem for Linux and Mac OS users, but may be confusing
to Windows users; if you do not understand what is
\family sans
PATH
\family default
under Windows, you may either use the R script
\family sans
add-R-path-win.R
\family default
in the repository
\begin_inset Flex URL
status collapsed
\begin_layout Plain Layout
https://github.com/yihui/lyx
\end_layout
\end_inset
to change it automatically (not recommended; you should learn
\family sans
PATH
\family default
anyway), or go to
\family sans
Tools\SpecialChar menuseparator
Preferences\SpecialChar menuseparator
Paths\SpecialChar menuseparator
PATH prefix
\family default
to add the bin path of R (recommended), which is often like
\family sans
C:
\backslash
Program Files
\backslash
R
\backslash
R-x.x.x
\backslash
bin
\family default
and you can find it in R:
\end_layout
\begin_layout Standard
\begin_inset ERT
status open
\begin_layout Plain Layout
<<where-is-R-bin,eval=FALSE>>=
\end_layout
\begin_layout Plain Layout
R.home('bin')
\end_layout
\begin_layout Plain Layout
@
\end_layout
\end_inset
\end_layout
\begin_layout Standard
After you have done these changes, you need to reconfigure \SpecialCharNoPassThru LyX
by
\family sans
Tools\SpecialChar menuseparator
Reconfigure
\family default
.
If
\family typewriter
Rscript
\family default
is not present in
\family sans
PATH
\family default
, the
\family sans
Sweave
\family default
module will be unavailable.
It is recommended to use the latest version of R, since Sweave is still
being updated.
Another dependency is introduced by the \SpecialCharNoPassThru LaTeX
style file
\family sans
Sweave.sty
\family default
which is shipped with R under this path (it is not on CTAN):
\end_layout
\begin_layout Standard
\begin_inset ERT
status open
\begin_layout Plain Layout
<<sweave-sty,eval=FALSE>>=
\end_layout
\begin_layout Plain Layout
file.path(R.home('share'), 'texmf', 'tex', 'latex')
\end_layout
\begin_layout Plain Layout
@
\end_layout
\end_inset
\end_layout
\begin_layout Standard
Mik\SpecialCharNoPassThru TeX
users may add the texmf directory to the list of root directories
in Mik\SpecialCharNoPassThru TeX
through Mik\SpecialCharNoPassThru TeX
settings.
Further note that
\family sans
Sweave.sty
\family default
depends on the
\series bold
fancyvrb
\series default
package and
\emph on
may
\emph default
depend on
\series bold
ae
\series default
.
If \SpecialCharNoPassThru LyX
cannot find
\family sans
Sweave.sty
\family default
, it will directly copy from R, so the Sweave module works even if you do
not know where is this style file.
\end_layout
\begin_layout Section
Sweave Examples
\end_layout
\begin_layout Standard
Before we write an Sweave document, we can set some Sweave options; the
command is
\family typewriter
\backslash
SweaveOpts{}
\family default
in Sweave and it can be inserted in a \SpecialCharNoPassThru LyX
document by
\family sans
Insert\SpecialChar menuseparator
Custom Insets\SpecialChar menuseparator
Sweave Options
\family default
, or just use \SpecialCharNoPassThru TeX
code to write it (
\family sans
Insert\SpecialChar menuseparator
\SpecialCharNoPassThru TeX
Code
\family default
).
For example, we can set a global option
\family typewriter
echo=FALSE
\family default
in the beginning of a document to suppress all R code (by default, both
R code and its output will show up in the \SpecialCharNoPassThru LaTeX
document).
\end_layout
\begin_layout Standard
To write R code in \SpecialCharNoPassThru LyX
, you can first switch to the
\family typewriter
Chunk
\family default
environment in the layout styles list (droplist in the top-left corner
in the toolbar), or you can simply open a \SpecialCharNoPassThru TeX
code environment and write
Sweave code chunks in it.
The latter approach is recommended since it is more stable.
\end_layout
\begin_layout Standard
Some R options can be useful to the Sweave output as well, e.g.
\family typewriter
width
\family default
and
\family typewriter
useFancyQuotes
\family default
.
The former option can adjust the width of the output, and the latter can
avoid a common problem with quotes.
Users are encouraged to read the Sweave manual in R for more details.
\end_layout
\begin_layout Standard
\begin_inset ERT
status open
\begin_layout Plain Layout
<<setup, keep.source=TRUE>>=
\end_layout
\begin_layout Plain Layout
## the option 'digits' can set the (approximate) number of digits
\end_layout
\begin_layout Plain Layout
options(width = 70, useFancyQuotes = FALSE, digits = 4)
\end_layout
\begin_layout Plain Layout
@
\end_layout
\begin_layout Plain Layout
<<sweave-manual, eval=FALSE, keep.source=TRUE>>=
\end_layout
\begin_layout Plain Layout
## view the Sweave vignette (requires R >= 2.13.0)
\end_layout
\begin_layout Plain Layout
vignette("Sweave", package = "utils")
\end_layout
\begin_layout Plain Layout
@
\end_layout
\end_inset
\end_layout
\begin_layout Standard
A simple example that will run in any S engine:
\end_layout
\begin_layout Standard
\begin_inset ERT
status open
\begin_layout Plain Layout
<<print-integers, keep.source=TRUE>>=
\end_layout
\begin_layout Plain Layout
## the integers from 1 to 10 are
\end_layout
\begin_layout Plain Layout
1:10
\end_layout
\begin_layout Plain Layout
@
\end_layout
\begin_layout Plain Layout
<<hide-results, results=hide>>=
\end_layout
\begin_layout Plain Layout
## intentionally hide the output by setting results=hide
\end_layout
\begin_layout Plain Layout
print(1:20)
\end_layout
\begin_layout Plain Layout
@
\end_layout
\end_inset
\end_layout
\begin_layout Standard
We can also emulate a simple calculator:
\end_layout
\begin_layout Standard
\begin_inset ERT
status open
\begin_layout Plain Layout
<<calculator>>=
\end_layout
\begin_layout Plain Layout
1 + pi
\end_layout
\begin_layout Plain Layout
sin(pi/6)
\end_layout
\begin_layout Plain Layout
@
\end_layout
\end_inset
\end_layout
\begin_layout Standard
Now we look at some Gaussian data:
\end_layout
\begin_layout Standard
\begin_inset ERT
status open
\begin_layout Plain Layout
<<rnorm>>=
\end_layout
\begin_layout Plain Layout
set.seed(123) # for reproducibility
\end_layout
\begin_layout Plain Layout
x <- rnorm(20)
\end_layout
\begin_layout Plain Layout
print(x)
\end_layout
\begin_layout Plain Layout
t1 <- t.test(x)
\end_layout
\begin_layout Plain Layout
@
\end_layout
\end_inset
\end_layout
\begin_layout Standard
Note that we can easily integrate some numbers into standard text; this
is done with the command
\family typewriter
\backslash
Sexpr{}
\family default
, and the corresponding \SpecialCharNoPassThru LyX
menu is
\family sans
Insert\SpecialChar menuseparator
Custom Insets\SpecialChar menuseparator
S/R expression
\family default
, or alternatively just use \SpecialCharNoPassThru TeX
code.
For example, the third element of the vector
\family typewriter
x
\family default
is
\begin_inset Flex S/R expression
status collapsed
\begin_layout Plain Layout
x[3]
\end_layout
\end_inset
(i.e.
\family typewriter
x[3]
\family default
) and the
\begin_inset Formula $p$
\end_inset
-value of the test is
\begin_inset Flex S/R expression
status collapsed
\begin_layout Plain Layout
format.pval(t1$p.value)
\end_layout
\end_inset
.
You can round these numbers using functions like
\emph on
round()
\emph default
in R.
\end_layout
\begin_layout Standard
\family roman
\series medium
\shape up
\size normal
\emph off
\bar no
\noun off
\color none
Now we look at a summary of the
\family typewriter
\series default
\shape default
\size default
\emph default
\bar default
\noun default
\color inherit
iris
\family roman
\series medium
\shape up
\size normal
\emph off
\bar no
\noun off
\color none
dataset:
\end_layout
\begin_layout Standard
\begin_inset ERT
status open
\begin_layout Plain Layout
<<iris-summary>>=
\end_layout
\begin_layout Plain Layout
summary(iris[,-5])
\end_layout
\begin_layout Plain Layout
@
\end_layout
\end_inset
\end_layout
\begin_layout Standard
\begin_inset Float table
wide false
sideways false
status open
\begin_layout Plain Layout
\begin_inset Caption Standard
\begin_layout Plain Layout
Quantiles of the first four variables in the
\family typewriter
iris
\family default
data.
\begin_inset CommandInset label
LatexCommand label
name "tab:xtable-demo"
\end_inset
\end_layout
\end_inset
\end_layout
\begin_layout Plain Layout
\align center
\begin_inset ERT
status open
\begin_layout Plain Layout
\end_layout
\begin_layout Plain Layout
<<xtable-demo,results=tex,echo=FALSE>>=
\end_layout
\begin_layout Plain Layout
if (require('xtable')) {
\end_layout
\begin_layout Plain Layout
print(xtable(sapply(iris[,-5], quantile)), floating=FALSE)
\end_layout
\begin_layout Plain Layout
} else cat('the xtable package is not available! please install.packages("xtable"
)')
\end_layout
\begin_layout Plain Layout
@
\end_layout
\end_inset
\end_layout
\end_inset
\end_layout
\begin_layout Standard
Usually people do not like such
\begin_inset Quotes eld
\end_inset
raw
\begin_inset Quotes erd
\end_inset
output, and we can polish these messy numbers with the
\series bold
xtable
\series default
package.
Table
\begin_inset CommandInset ref
LatexCommand ref
reference "tab:xtable-demo"
\end_inset
is an example demonstrating how to use the
\series bold
xtable
\series default
package with Sweave; note the chunk option
\family typewriter
results=tex
\family default
makes sure that the R output is written out as raw \SpecialCharNoPassThru LaTeX
code instead of
being wrapped in a special environment (
\family typewriter
Soutput
\family default
).
\end_layout
\begin_layout Standard
Figure
\begin_inset CommandInset ref
LatexCommand ref
reference "fig:iris-pairs"
\end_inset
and
\begin_inset CommandInset ref
LatexCommand ref
reference "fig:iris-boxplots"
\end_inset
are two simple examples of producing graphics output with Sweave.
\end_layout
\begin_layout Standard
\begin_inset Float figure
wide false
sideways false
status open
\begin_layout Plain Layout
\align center
\begin_inset Note Note
status open
\begin_layout Plain Layout
Both eps and pdf are set to true so that both latex and pdflatex work.
In practice, you would probably just choose one.
\end_layout
\end_inset
\begin_inset ERT
status open
\begin_layout Plain Layout
<<iris-pairs,fig=TRUE,width=4.5,height=4.5,eps=TRUE,pdf=TRUE>>=
\end_layout
\begin_layout Plain Layout
pairs(iris, col = iris$Species)
\end_layout
\begin_layout Plain Layout
@
\end_layout
\end_inset
\end_layout
\begin_layout Plain Layout
\begin_inset Caption Standard
\begin_layout Plain Layout
Scatter plot matrix of the
\family typewriter
iris
\family default
data.
\begin_inset CommandInset label
LatexCommand label
name "fig:iris-pairs"
\end_inset
\end_layout
\end_inset
\end_layout
\end_inset
\end_layout
\begin_layout Standard
\begin_inset Float figure
wide false
sideways false
status open
\begin_layout Plain Layout
\align center
\begin_inset ERT
status open
\begin_layout Plain Layout
<<iris-boxplots,fig=TRUE,width=7,height=2,keep.source=F,eps=T,pdf=T>>=
\end_layout
\begin_layout Plain Layout
par(mar=c(4,5,.1,.3), las=1)
\end_layout
\begin_layout Plain Layout
boxplot(Sepal.Length~Species,data=iris,horizontal=TRUE,xlab='Sepal.Length')
\end_layout
\begin_layout Plain Layout
@
\end_layout
\end_inset
\end_layout
\begin_layout Plain Layout
\begin_inset Caption Standard
\begin_layout Plain Layout
Boxplots of sepal length grouped by species.
\begin_inset CommandInset label
LatexCommand label
name "fig:iris-boxplots"
\end_inset
\end_layout
\end_inset
\end_layout
\end_inset
\end_layout
\begin_layout Standard
We can also export all the R code in an Sweave document as a single R script
(
\family sans
File\SpecialChar menuseparator
Export\SpecialChar menuseparator
R/S code
\family default
), which is done via
\family typewriter
R CMD Stangle
\family default
.
\end_layout
\begin_layout Section
The
\family sans
Sweave
\family default
Module
\end_layout
\begin_layout Standard
The
\family sans
Sweave
\family default
module declares that a \SpecialCharNoPassThru LyX
document contains literate programming components
with R, so that \SpecialCharNoPassThru LyX
will handle such documents according to the specific
converters (see the Customization manual).
The
\family sans
Sweave
\family default
module uses the
\family sans
sweave
\family default
converter, which essentially consists of an R script
\family sans
lyxsweave.R
\family default
under the
\family sans
scripts
\family default
directory of \SpecialCharNoPassThru LyX
.
This script takes an
\family sans
Rnw
\family default
document from \SpecialCharNoPassThru LyX
and call Sweave to process it to a \SpecialCharNoPassThru TeX
document, then
\SpecialCharNoPassThru LyX
takes care of the rest of work.
\end_layout
\begin_layout Standard
The converter from the
\family sans
sweave
\family default
format to \SpecialCharNoPassThru LaTeX
is a call to R via the command line as:
\end_layout
\begin_layout Standard
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
begin{verbatim}
\end_layout
\begin_layout Plain Layout
Rscript --no-save --no-restore $$s/scripts/lyxsweave.R $$p$$i $$p$$o $$e
$$r
\end_layout
\begin_layout Plain Layout
\backslash
end{verbatim}
\end_layout
\end_inset
\end_layout
\begin_layout Standard
The \SpecialCharNoPassThru LyX
library directory
\family typewriter
$$s
\family default
can be found from the menu
\family sans
Help\SpecialChar menuseparator
About \SpecialCharNoPassThru LyX
\family default
.
All the rest of options passed to R are explained in the R script, and
the \SpecialCharNoPassThru LyX
Customization manual also has detailed explanations about
\family typewriter
$$i
\family default
,
\family typewriter
$$o
\family default
,
\family typewriter
$$e
\family default
and
\family typewriter
$$r
\family default
.
General users do not need to know clearly what they mean, but here we need
to explain a few issues in the R code:
\end_layout
\begin_layout Enumerate
the encoding string of the \SpecialCharNoPassThru LyX
document is passed to R as an command line
option; possible values are
\family typewriter
ISO-8859-15
\family default
and
\family typewriter
UTF-8
\family default
, etc.
The encoding is used for R to read the
\family sans
Rnw
\family default
document correctly.
\end_layout
\begin_layout Enumerate
the R code chunks in the Sweave document are executed under the directory
of the \SpecialCharNoPassThru LyX
document (if you are not sure, put
\family typewriter
getwd()
\family default
in a code chunk to see what is the current working directory).
In this case, you can put data files under the same directory and use relative
paths in R to guarantee reproducibility, i.e.
we do not need to write hard-coded paths which may not exist in other systems.
\end_layout
\begin_layout Enumerate
if \SpecialCharNoPassThru LaTeX
cannot find
\family sans
Sweave.sty
\family default
, this R script will copy it to the temporary directory automatically where
the \SpecialCharNoPassThru LaTeX
compilation takes place.
\end_layout
\begin_layout Enumerate
Sweave will use the filename of the Rnw file as the prefix string for the
graphics output by default; one known issue (
\begin_inset CommandInset href
LatexCommand href
name "#7551"
target "http://www.lyx.org/trac/ticket/7551"
\end_inset
) is that if the filename (without extension) contains dots, \SpecialCharNoPassThru LaTeX
can fail
to deal with such files in
\family typewriter
\backslash
includegraphics{}
\family default
.
Therefore, we have set the default value of the prefix to be the filename
with all the dots being replaced by
\begin_inset Quotes eld
\end_inset
-
\begin_inset Quotes erd
\end_inset
.
We can also solve this problem in Sweave directly: set the Sweave option
\family typewriter
prefix.string
\family default
to be a character string without dots, and this option will override the
default value.
\end_layout
\begin_layout Standard
We have pre-specified an option
\family typewriter
noae
\family default
for the Sweave package.
This option stops Sweave from loading these two packages:
\end_layout
\begin_layout Standard
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
begin{verbatim}
\end_layout
\begin_layout Plain Layout
\backslash
RequirePackage[T1]{fontenc}
\end_layout
\begin_layout Plain Layout
\backslash
RequirePackage{ae}
\end_layout
\begin_layout Plain Layout
\backslash
end{verbatim}
\end_layout
\end_inset
\end_layout
\begin_layout Standard
\SpecialCharNoPassThru LyX
can deal with the font encoding by default, so there is no need to ask
Sweave to do this (furthermore, this may bring clashes of package options);
besides, the users can load the
\series bold
ae
\series default
package by themselves in the preamble if needed.
\end_layout
\begin_layout Section
Trouble Shooting
\end_layout
\begin_layout Standard
Since \SpecialCharNoPassThru LyX
2.0, we can see the detailed information during compilation via
\family sans
View\SpecialChar menuseparator
View Messages
\family default
.
This is extremely helpful for trouble shooting \twohyphens
the process of R will
be shown in the message panel, and we will be able to know which chunk
goes wrong in cases of errors.
For example, when you compile this document, you can see messages like
below:
\end_layout
\begin_layout Standard
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
begin{verbatim}
\end_layout
\begin_layout Plain Layout
17:58:47.868: Processing code chunks with options ...
\end_layout
\begin_layout Plain Layout
17:58:47.885: 1 : echo keep.source term verbatim (label=setup)
\end_layout
\begin_layout Plain Layout
17:58:47.889: 2 : echo keep.source (label=sweave-manual)
\end_layout
\begin_layout Plain Layout
17:58:47.908: 3 : echo keep.source term verbatim (label=print-integers)
\end_layout
\begin_layout Plain Layout
....
\end_layout
\begin_layout Plain Layout
17:58:47.941: Loading required package: xtable
\end_layout
\begin_layout Plain Layout
17:58:47.976: 9 : echo term verbatim pdf (label=iris-pairs)
\end_layout
\begin_layout Plain Layout
....
\end_layout
\begin_layout Plain Layout
17:58:48.116: You can now run (pdf)latex on 'sweave.tex'
\end_layout
\begin_layout Plain Layout
\backslash
end{verbatim}
\end_layout
\end_inset
\end_layout
\begin_layout Standard
The string after
\family typewriter
label=
\family default
is the chunk label.
If any chunk causes an error in R, you will see the error message here
immediately.
\end_layout
\begin_layout Standard
Another known issue is the Sweave code chunk may fail when we change the
alignment of the chunk paragraph in \SpecialCharNoPassThru LyX
(using
\family sans
Paragraph settings
\family default
), because \SpecialCharNoPassThru LyX
may add a macro like
\family typewriter
\backslash
centering{}
\family default
before the code chunk without adding a new line, which will lead to a code
chunk like this:
\end_layout
\begin_layout Standard
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
begin{verbatim}
\end_layout
\begin_layout Plain Layout
\backslash
centering{}<<xtable-demo,results=tex,echo=FALSE>>=
\end_layout
\begin_layout Plain Layout
\backslash
end{verbatim}
\end_layout
\end_inset
\end_layout
\begin_layout Standard
This is not a legitimate Sweave code chunk, since
\family typewriter
<<>>=
\family default
must start in a new line with nothing before it.
Therefore we recommend you to double check the real source code via
\family sans
View\SpecialChar menuseparator
View Source
\family default
when changing the alignment of a chunk paragraph, and make sure
\family typewriter
<<>>=
\family default
appears in a new line.
This explains why we manually added an empty line in the code chunk in
Table
\begin_inset CommandInset ref
LatexCommand ref
reference "tab:xtable-demo"
\end_inset
.
\end_layout
\begin_layout Section
Resources
\end_layout
\begin_layout Standard
The homepage of Sweave is at
\begin_inset Flex URL
status collapsed
\begin_layout Plain Layout
http://www.stat.uni-muenchen.de/~leisch/Sweave/
\end_layout
\end_inset
.
The CRAN task view on
\begin_inset Quotes eld
\end_inset
Reproducible Research
\begin_inset Quotes erd
\end_inset
has a list of Sweave-related packages which can be potentially useful;
see
\begin_inset Flex URL
status collapsed
\begin_layout Plain Layout
http://cran.r-project.org/web/views/ReproducibleResearch.html
\end_layout
\end_inset
.
Questions about \SpecialCharNoPassThru LyX
and Sweave can be posted to the \SpecialCharNoPassThru LyX
mailing list (
\begin_inset Flex URL
status collapsed
\begin_layout Plain Layout
http://www.lyx.org/MailingLists
\end_layout
\end_inset
).
More \SpecialCharNoPassThru LyX
examples are provided at
\begin_inset Flex URL
status collapsed
\begin_layout Plain Layout
https://github.com/yihui/lyx
\end_layout
\end_inset
.
\end_layout
\begin_layout Section
FAQ
\end_layout
\begin_layout Subsection
How to use Sweave with beamer?
\end_layout
\begin_layout Standard
You will end up with \SpecialCharNoPassThru LaTeX
errors if you use Sweave in normal beamer slides
in \SpecialCharNoPassThru LyX
; the reason is the beamer frame that contains verbatim R code.
The solution is to use a
\emph on
FragileFrame
\emph default
instead of a normal
\emph on
Frame
\emph default
, or to pass the option
\family typewriter
fragile
\family default
to the frame title via
\family sans
Insert\SpecialChar menuseparator
Frame Options
\family default
.
\end_layout
\begin_layout Subsection
Can I define my own R script to compile the Rnw document?
\end_layout
\begin_layout Standard
Yes, of course.
First you need to understand how the R script
\family typewriter
$$s
\family sans
/scripts/lyxsweave.R
\family default
works, which was introduced previously, and we recommend you to read the
R source code as well (on how R takes the paths and uses
\emph on
Sweave()
\emph default
to handle the Rnw document).
Then you put your customized
\family sans
lyxsweave.R
\family default
under the
\family sans
scripts
\family default
directory of your
\emph on
user directory
\emph default
(again, see
\family sans
Help\SpecialChar menuseparator
About \SpecialCharNoPassThru LyX
\family default
).
Note \SpecialCharNoPassThru LyX
will check the
\emph on
user directory
\emph default
before going to its own
\emph on
library directory
\emph default
; if an R script
\family sans
lyxsweave.R
\family default
is found in the user directory, it will be used.
It is not recommended to hack the script under the \SpecialCharNoPassThru LyX
library directory
directly, since updating \SpecialCharNoPassThru LyX
will override you modified script (the user
directory will not be affected).
\end_layout
\begin_layout Standard
Beside the support for the official Sweave in R, the
\series bold
knitr
\series default
package is also supported, which is an alternative tool to Sweave; the
corresponding module is named
\family sans
Rnw (knitr)
\family default
.
\end_layout
\end_body
\end_document
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