From: Uwe Stöhr Date: Mon, 13 Feb 2012 00:36:57 +0000 (+0000) Subject: sweave.lyx: completely revised example file by Yihui Xie X-Git-Tag: 2.1.0beta1~2057 X-Git-Url: https://git.lyx.org/gitweb/?a=commitdiff_plain;h=e0436370b65c754bc67710afd2c67685a095e2c8;p=features.git sweave.lyx: completely revised example file by Yihui Xie git-svn-id: svn://svn.lyx.org/lyx/lyx-devel/trunk@40744 a592a061-630c-0410-9148-cb99ea01b6c8 --- diff --git a/lib/examples/sweave.lyx b/lib/examples/sweave.lyx index b4af67e123..b668753e01 100644 --- a/lib/examples/sweave.lyx +++ b/lib/examples/sweave.lyx @@ -260,7 +260,7 @@ PATH \family sans PATH \family default - under Windows, you may use the R script + under Windows, you may either use the R script \family sans add-R-path-win.R \family default @@ -275,15 +275,64 @@ https://github.com/yihui/lyx \end_inset - to change it automatically (we recommend you to learn + to change it automatically (not recommended; you should learn \family sans PATH \family default - anyway). + 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 -If +\begin_inset ERT +status open + +\begin_layout Plain Layout + +<>= +\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 LyX by +\family sans +Tools\SpecialChar \menuseparator +Reconfigure +\family default +. + If \family typewriter Rscript \family default @@ -739,14 +788,12 @@ name "tab:xtable-demo" \end_layout \begin_layout Plain Layout +\align center \begin_inset ERT status open \begin_layout Plain Layout - -\backslash -begin{center} \end_layout \begin_layout Plain Layout @@ -775,13 +822,6 @@ print(xtable(sapply(iris[,-5], quantile)), floating=FALSE) @ \end_layout -\begin_layout Plain Layout - - -\backslash -end{center} -\end_layout - \end_inset @@ -854,18 +894,12 @@ sideways false status open \begin_layout Plain Layout +\align center \begin_inset ERT status open \begin_layout Plain Layout - -\backslash -begin{center} -\end_layout - -\begin_layout Plain Layout - <>= \end_layout @@ -879,13 +913,6 @@ pairs(iris, col = iris$Species) @ \end_layout -\begin_layout Plain Layout - - -\backslash -end{center} -\end_layout - \end_inset @@ -926,18 +953,12 @@ sideways false status open \begin_layout Plain Layout +\align center \begin_inset ERT status open \begin_layout Plain Layout - -\backslash -begin{center} -\end_layout - -\begin_layout Plain Layout - <>= \end_layout @@ -956,13 +977,6 @@ boxplot(Sepal.Length~Species,data=iris,horizontal=TRUE,xlab='Sepal.Length') @ \end_layout -\begin_layout Plain Layout - - -\backslash -end{center} -\end_layout - \end_inset @@ -1347,6 +1361,79 @@ label= 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 LyX (using +\family sans +Paragraph settings +\family default +), because 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{}<>= +\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 @@ -1516,29 +1603,16 @@ lyxsweave.R \end_layout \begin_layout Standard -Beside the support for the official Sweave in R, we have a few customized - R scripts to unofficially support other R packages under -\begin_inset Flex URL -status collapsed - -\begin_layout Plain Layout - -https://github.com/yihui/lyx -\end_layout - -\end_inset - -, e.g., the -\series bold -pgfSweave -\series default - and the +Beside the support for the official Sweave in R, the \series bold knitr \series default - package. - The former supports cache and tikz graphics in R, and the latter is an - alternative literate programming engine to Sweave which has even more features. + 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