commit d6b1dc4724ddf5f1d203da8224073236400b6623
Author: Guillaume Munch <[email protected]>
Date: Sun Jan 8 19:19:55 2017 +0100
Update Sweave, Knitr manual and showcase the new Navigate menu
Also mention needauth option
---
lib/examples/knitr.lyx | 90 +++++++++-
lib/examples/sweave.lyx | 470 ++++++++++++++++++++++++++++++++++++++--------
2 files changed, 476 insertions(+), 84 deletions(-)
diff --git a/lib/examples/knitr.lyx b/lib/examples/knitr.lyx
index cf6ee09..6e96b2e 100644
--- a/lib/examples/knitr.lyx
+++ b/lib/examples/knitr.lyx
@@ -1,4 +1,4 @@
-#LyX 2.2 created this file. For more info see http://www.lyx.org/
+#LyX 2.3 created this file. For more info see http://www.lyx.org/
\lyxformat 508
\begin_document
\begin_header
@@ -69,11 +69,12 @@ knitr
\papercolumns 1
\papersides 1
\paperpagestyle default
-\tracking_changes false
+\tracking_changes true
\output_changes false
\html_math_output 0
\html_css_as_file 0
\html_be_strict false
+\author 2047637253 "Guillaume Munch"
\end_header
\begin_body
@@ -203,6 +204,31 @@ knitr
\series default
; many of the examples have links to the \SpecialChar LyX
source documents.
+\change_inserted 2047637253 1483899260
+
+\end_layout
+
+\begin_layout Standard
+
+\change_inserted 2047637253 1483899275
+Since \SpecialChar LyX
+ 2.3, it is necessary to enable the use of
+\emph on
+needauth
+\emph default
+ converters in
+\family sans
+ Preferences\SpecialChar menuseparator
+File Handling\SpecialChar menuseparator
+Converters
+\family default
+ in order to compile with
+\series bold
+knitr
+\series default
+.
+\change_unchanged
+
\end_layout
\begin_layout Standard
@@ -216,6 +242,64 @@ knitr
\end_layout
\begin_layout Standard
+
+\change_inserted 2047637253 1483899195
+\begin_inset Flex Chunk
+status open
+
+\begin_layout Plain Layout
+
+\change_inserted 2047637253 1483899204
+
+\begin_inset Argument 1
+status open
+
+\begin_layout Plain Layout
+
+\change_inserted 2047637253 1483899200
+show-off
+\change_unchanged
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Plain Layout
+
+\change_inserted 2047637253 1483899204
+
+rnorm(5)
+\end_layout
+
+\begin_layout Plain Layout
+
+\change_inserted 2047637253 1483899204
+
+df=data.frame(y=rnorm(100), x=1:100)
+\end_layout
+
+\begin_layout Plain Layout
+
+\change_inserted 2047637253 1483899204
+
+summary(lm(y~x, data=df))
+\change_unchanged
+
+\end_layout
+
+\end_inset
+
+
+\change_unchanged
+
+\end_layout
+
+\begin_layout Standard
+
+\change_deleted 2047637253 1483899208
\begin_inset ERT
status open
@@ -247,6 +331,8 @@ summary(lm(y~x, data=df))
\end_inset
+\change_unchanged
+
\end_layout
\begin_layout Standard
diff --git a/lib/examples/sweave.lyx b/lib/examples/sweave.lyx
index bf770be..59d64df 100644
--- a/lib/examples/sweave.lyx
+++ b/lib/examples/sweave.lyx
@@ -1,4 +1,4 @@
-#LyX 2.2 created this file. For more info see http://www.lyx.org/
+#LyX 2.3 created this file. For more info see http://www.lyx.org/
\lyxformat 508
\begin_document
\begin_header
@@ -81,24 +81,33 @@ sweave
\papercolumns 1
\papersides 1
\paperpagestyle default
-\tracking_changes false
+\tracking_changes true
\output_changes false
\html_math_output 0
\html_css_as_file 0
\html_be_strict false
+\author 2047637253 "Guillaume Munch"
\end_header
\begin_body
\begin_layout Standard
-\begin_inset ERT
+
+\change_inserted 2047637253 1483897614
+\begin_inset Note Note
status open
\begin_layout Plain Layout
-%
-\backslash
-SweaveOpts{prefix=TRUE,prefix.string=sweave-prefix,keep.source=FALSE}
+\change_inserted 2047637253 1483897614
+\begin_inset Flex Sweave Options
+status open
+
+\begin_layout Plain Layout
+
+\change_inserted 2047637253 1483897614
+
+prefix=TRUE,prefix.string=sweave-prefix,keep.source=FALSE
\end_layout
\end_inset
@@ -106,6 +115,13 @@
SweaveOpts{prefix=TRUE,prefix.string=sweave-prefix,keep.source=FALSE}
\end_layout
+\end_inset
+
+
+\change_unchanged
+
+\end_layout
+
\begin_layout Standard
\begin_inset ERT
status open
@@ -239,6 +255,27 @@ https://github.com/downloads/yihui/lyx/sweave.pdf
\end_inset
.
+\change_inserted 2047637253 1483898587
+
+\end_layout
+
+\begin_layout Standard
+
+\change_inserted 2047637253 1483899123
+Since \SpecialChar LyX
+ 2.3, it is necessary to enable the use of
+\emph on
+needauth
+\emph default
+ converters in
+\family sans
+ Preferences\SpecialChar menuseparator
+File Handling\SpecialChar menuseparator
+Converters
+\family default
+ in order to compile with Sweave.
+\change_unchanged
+
\end_layout
\begin_layout Section
@@ -306,27 +343,41 @@ bin
\end_layout
\begin_layout Standard
-\begin_inset ERT
+
+\change_inserted 2047637253 1483897627
+\begin_inset Flex Chunk
status open
\begin_layout Plain Layout
-<<where-is-R-bin,eval=FALSE>>=
-\end_layout
+\change_inserted 2047637253 1483897627
+
+\begin_inset Argument 1
+status open
\begin_layout Plain Layout
-R.home('bin')
+\change_inserted 2047637253 1483897627
+where-is-R-bin,eval=FALSE
+\end_layout
+
+\end_inset
+
+
\end_layout
\begin_layout Plain Layout
-@
+\change_inserted 2047637253 1483897627
+
+R.home('bin')
\end_layout
\end_inset
+\change_unchanged
+
\end_layout
\begin_layout Standard
@@ -361,27 +412,41 @@ Sweave.sty
\end_layout
\begin_layout Standard
-\begin_inset ERT
+
+\change_inserted 2047637253 1483897639
+\begin_inset Flex Chunk
status open
\begin_layout Plain Layout
-<<sweave-sty,eval=FALSE>>=
-\end_layout
+\change_inserted 2047637253 1483897639
+
+\begin_inset Argument 1
+status open
\begin_layout Plain Layout
-file.path(R.home('share'), 'texmf', 'tex', 'latex')
+\change_inserted 2047637253 1483897639
+sweave-sty,eval=FALSE
+\end_layout
+
+\end_inset
+
+
\end_layout
\begin_layout Plain Layout
-@
+\change_inserted 2047637253 1483897639
+
+file.path(R.home('share'), 'texmf', 'tex', 'latex')
\end_layout
\end_inset
+\change_unchanged
+
\end_layout
\begin_layout Standard
@@ -455,15 +520,54 @@ echo=FALSE
\begin_layout Standard
To write R code in \SpecialChar LyX
-, you can first switch to the
+, you can first
+\change_inserted 2047637253 1483898412
+insert
+\change_deleted 2047637253 1483898419
+switch to the
+\change_unchanged
+
\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 \SpecialChar TeX
- code environment and write Sweave
- code chunks in it.
- The latter approach is recommended since it is more stable.
+
+\change_inserted 2047637253 1483898437
+insets from
+\family sans
+Insert\SpecialChar menuseparator
+Custom Insets\SpecialChar menuseparator
+Chunk
+\change_deleted 2047637253 1483898459
+
+\family default
+environment in the layout styles list (droplist in the top-left corner in
+ the toolbar)
+\change_unchanged
+, or you can simply open a \SpecialChar TeX
+ code environment and write Sweave code chunks
+ in it.
+
+\change_deleted 2047637253 1483898024
+The latter approach is recommended since it is more stable.
+\change_inserted 2047637253 1483961753
+However, \SpecialChar LyX
+ provides a summary of all the
+\family typewriter
+Chunk
+\family default
+ insets in the document in the
+\family sans
+Navigate\SpecialChar menuseparator
+Literate Programming
+\family default
+ and
+\family sans
+View\SpecialChar menuseparator
+Outline Pane
+\family default
+ menus.
+\change_unchanged
+
\end_layout
\begin_layout Standard
@@ -483,52 +587,91 @@ useFancyQuotes
\end_layout
\begin_layout Standard
-\begin_inset ERT
+
+\change_inserted 2047637253 1483897653
+\begin_inset Flex Chunk
+status open
+
+\begin_layout Plain Layout
+
+\change_inserted 2047637253 1483897653
+
+\begin_inset Argument 1
status open
\begin_layout Plain Layout
-<<setup, keep.source=TRUE>>=
+\change_inserted 2047637253 1483897653
+setup, keep.source=TRUE
+\end_layout
+
+\end_inset
+
+
\end_layout
\begin_layout Plain Layout
+\change_inserted 2047637253 1483897653
+
## the option 'digits' can set the (approximate) number of digits
\end_layout
\begin_layout Plain Layout
+\change_inserted 2047637253 1483897653
+
options(width = 70, useFancyQuotes = FALSE, digits = 4)
\end_layout
-\begin_layout Plain Layout
+\end_inset
+
-@
\end_layout
+\begin_layout Standard
+
+\change_inserted 2047637253 1483897653
+\begin_inset Flex Chunk
+status open
+
\begin_layout Plain Layout
-<<sweave-manual, eval=FALSE, keep.source=TRUE>>=
-\end_layout
+\change_inserted 2047637253 1483897653
+
+\begin_inset Argument 1
+status open
\begin_layout Plain Layout
-## view the Sweave vignette (requires R >= 2.13.0)
+\change_inserted 2047637253 1483897653
+sweave-manual, eval=FALSE, keep.source=TRUE
+\end_layout
+
+\end_inset
+
+
\end_layout
\begin_layout Plain Layout
-vignette("Sweave", package = "utils")
+\change_inserted 2047637253 1483897653
+
+## view the Sweave vignette (requires R >= 2.13.0)
\end_layout
\begin_layout Plain Layout
-@
+\change_inserted 2047637253 1483897653
+
+vignette("Sweave", package = "utils")
\end_layout
\end_inset
+\change_unchanged
+
\end_layout
\begin_layout Standard
@@ -536,52 +679,91 @@ A simple example that will run in any S engine:
\end_layout
\begin_layout Standard
-\begin_inset ERT
+
+\change_inserted 2047637253 1483897659
+\begin_inset Flex Chunk
+status open
+
+\begin_layout Plain Layout
+
+\change_inserted 2047637253 1483897659
+
+\begin_inset Argument 1
status open
\begin_layout Plain Layout
-<<print-integers, keep.source=TRUE>>=
+\change_inserted 2047637253 1483897659
+print-integers, keep.source=TRUE
+\end_layout
+
+\end_inset
+
+
\end_layout
\begin_layout Plain Layout
+\change_inserted 2047637253 1483897659
+
## the integers from 1 to 10 are
\end_layout
\begin_layout Plain Layout
-1:10
+\change_inserted 2047637253 1483897659
+
+1:10
\end_layout
-\begin_layout Plain Layout
+\end_inset
+
-@
\end_layout
+\begin_layout Standard
+
+\change_inserted 2047637253 1483897659
+\begin_inset Flex Chunk
+status open
+
\begin_layout Plain Layout
-<<hide-results, results=hide>>=
-\end_layout
+\change_inserted 2047637253 1483897659
+
+\begin_inset Argument 1
+status open
\begin_layout Plain Layout
-## intentionally hide the output by setting results=hide
+\change_inserted 2047637253 1483897659
+hide-results, results=hide
+\end_layout
+
+\end_inset
+
+
\end_layout
\begin_layout Plain Layout
-print(1:20)
+\change_inserted 2047637253 1483897659
+
+## intentionally hide the output by setting results=hide
\end_layout
\begin_layout Plain Layout
-@
+\change_inserted 2047637253 1483897659
+
+print(1:20)
\end_layout
\end_inset
+\change_unchanged
+
\end_layout
\begin_layout Standard
@@ -589,32 +771,48 @@ We can also emulate a simple calculator:
\end_layout
\begin_layout Standard
-\begin_inset ERT
+
+\change_inserted 2047637253 1483897665
+\begin_inset Flex Chunk
status open
\begin_layout Plain Layout
-<<calculator>>=
-\end_layout
+\change_inserted 2047637253 1483897665
+
+\begin_inset Argument 1
+status open
\begin_layout Plain Layout
-1 + pi
+\change_inserted 2047637253 1483897665
+calculator
+\end_layout
+
+\end_inset
+
+
\end_layout
\begin_layout Plain Layout
-sin(pi/6)
+\change_inserted 2047637253 1483897665
+
+1 + pi
\end_layout
\begin_layout Plain Layout
-@
+\change_inserted 2047637253 1483897665
+
+sin(pi/6)
\end_layout
\end_inset
+\change_unchanged
+
\end_layout
\begin_layout Standard
@@ -622,42 +820,62 @@ Now we look at some Gaussian data:
\end_layout
\begin_layout Standard
-\begin_inset ERT
+
+\change_inserted 2047637253 1483897670
+\begin_inset Flex Chunk
+status open
+
+\begin_layout Plain Layout
+
+\change_inserted 2047637253 1483897670
+
+\begin_inset Argument 1
status open
\begin_layout Plain Layout
-<<rnorm>>=
+\change_inserted 2047637253 1483897670
+rnorm
+\end_layout
+
+\end_inset
+
+
\end_layout
\begin_layout Plain Layout
+\change_inserted 2047637253 1483897670
+
set.seed(123) # for reproducibility
\end_layout
\begin_layout Plain Layout
+\change_inserted 2047637253 1483897670
+
x <- rnorm(20)
\end_layout
\begin_layout Plain Layout
+\change_inserted 2047637253 1483897670
+
print(x)
\end_layout
\begin_layout Plain Layout
-t1 <- t.test(x)
-\end_layout
-
-\begin_layout Plain Layout
+\change_inserted 2047637253 1483897670
-@
+t1 <- t.test(x)
\end_layout
\end_inset
+\change_unchanged
+
\end_layout
\begin_layout Standard
@@ -753,27 +971,41 @@ iris
\end_layout
\begin_layout Standard
-\begin_inset ERT
+
+\change_inserted 2047637253 1483897677
+\begin_inset Flex Chunk
status open
\begin_layout Plain Layout
-<<iris-summary>>=
-\end_layout
+\change_inserted 2047637253 1483897677
+
+\begin_inset Argument 1
+status open
\begin_layout Plain Layout
-summary(iris[,-5])
+\change_inserted 2047637253 1483897677
+iris-summary
+\end_layout
+
+\end_inset
+
+
\end_layout
\begin_layout Plain Layout
-@
+\change_inserted 2047637253 1483897677
+
+summary(iris[,-5])
\end_layout
\end_inset
+\change_unchanged
+
\end_layout
\begin_layout Standard
@@ -803,46 +1035,60 @@ name "tab:xtable-demo"
\end_inset
-\end_layout
+\change_inserted 2047637253 1483897685
+
+\begin_inset Flex Chunk
+status open
\begin_layout Plain Layout
-\align center
-\begin_inset ERT
+
+\change_inserted 2047637253 1483897698
+
+\begin_inset Argument 1
status open
\begin_layout Plain Layout
+\change_inserted 2047637253 1483897692
+xtable-demo,results=tex,echo=FALSE
+\change_unchanged
+
\end_layout
-\begin_layout Plain Layout
+\end_inset
+
-<<xtable-demo,results=tex,echo=FALSE>>=
\end_layout
\begin_layout Plain Layout
+\change_inserted 2047637253 1483897699
+
if (require('xtable')) {
\end_layout
\begin_layout Plain Layout
+\change_inserted 2047637253 1483897699
+
print(xtable(sapply(iris[,-5], quantile)), floating=FALSE)
\end_layout
\begin_layout Plain Layout
+\change_inserted 2047637253 1483897699
+
} else cat('the xtable package is not available! please
install.packages("xtable"
)')
-\end_layout
-
-\begin_layout Plain Layout
+\change_unchanged
-@
\end_layout
\end_inset
+\change_unchanged
+
\end_layout
\end_inset
@@ -925,27 +1171,49 @@ Both eps and pdf are set to true so that both latex and
pdflatex work.
\end_inset
-\begin_inset ERT
+\end_layout
+
+\begin_layout Plain Layout
+\align center
+
+\change_inserted 2047637253 1483897765
+\begin_inset Flex Chunk
status open
\begin_layout Plain Layout
-<<iris-pairs,fig=TRUE,width=4.5,height=4.5,eps=TRUE,pdf=TRUE>>=
-\end_layout
+\change_inserted 2047637253 1483897772
+
+\begin_inset Argument 1
+status open
\begin_layout Plain Layout
-pairs(iris, col = iris$Species)
+\change_inserted 2047637253 1483897770
+iris-pairs,fig=TRUE,width=4.5,height=4.5,eps=TRUE,pdf=TRUE
+\change_unchanged
+
+\end_layout
+
+\end_inset
+
+
\end_layout
\begin_layout Plain Layout
-@
+\change_inserted 2047637253 1483897776
+
+pairs(iris, col = iris$Species)
+\change_unchanged
+
\end_layout
\end_inset
+\change_unchanged
+
\end_layout
\begin_layout Plain Layout
@@ -984,32 +1252,48 @@ status open
\begin_layout Plain Layout
\align center
-\begin_inset ERT
+
+\change_inserted 2047637253 1483897883
+\begin_inset Flex Chunk
status open
\begin_layout Plain Layout
-<<iris-boxplots,fig=TRUE,width=7,height=2,keep.source=F,eps=T,pdf=T>>=
-\end_layout
+\change_inserted 2047637253 1483897883
+
+\begin_inset Argument 1
+status open
\begin_layout Plain Layout
-par(mar=c(4,5,.1,.3), las=1)
+\change_inserted 2047637253 1483897883
+iris-boxplots,fig=TRUE,width=7,height=2,keep.source=F,eps=T,pdf=T
+\end_layout
+
+\end_inset
+
+
\end_layout
\begin_layout Plain Layout
-boxplot(Sepal.Length~Species,data=iris,horizontal=TRUE,xlab='Sepal.Length')
+\change_inserted 2047637253 1483897883
+
+par(mar=c(4,5,.1,.3), las=1)
\end_layout
\begin_layout Plain Layout
-@
+\change_inserted 2047637253 1483897883
+
+boxplot(Sepal.Length~Species,data=iris,horizontal=TRUE,xlab='Sepal.Length')
\end_layout
\end_inset
+\change_unchanged
+
\end_layout
\begin_layout Plain Layout
@@ -1049,6 +1333,8 @@ R/S code
R CMD Stangle
\family default
.
+\change_inserted 2047637253 1483898877
+
\end_layout
\begin_layout Section
@@ -1408,8 +1694,17 @@ label=
\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 \SpecialChar LyX
+Another
+\change_deleted 2047637253 1483899012
+known
+\change_unchanged
+ issue
+\change_inserted 2047637253 1483898966
+with the \SpecialChar TeX
+ code environment
+\change_unchanged
+is the Sweave code chunk may fail when we change the alignment of the chunk
+ paragraph in \SpecialChar LyX
(using
\family sans
Paragraph settings
@@ -1461,7 +1756,16 @@ This is not a legitimate Sweave code chunk, since
<<>>=
\family default
must start in a new line with nothing before it.
- Therefore we recommend you to double check the real source code via
+
+\change_inserted 2047637253 1483899083
+ This does not happen when using the Chunk inset instead of the \SpecialChar
TeX
+ code environmen
+t.
+
+\change_unchanged
+
+\change_deleted 2047637253 1483898988
+Therefore we recommend you to double check the real source code via
\family sans
View\SpecialChar menuseparator
View Source
@@ -1480,6 +1784,8 @@ reference "tab:xtable-demo"
\end_inset
.
+\change_unchanged
+
\end_layout
\begin_layout Section
