Accept modifications in R examples

diff --git a/lib/examples/knitr.lyx b/lib/examples/knitr.lyx
index 9e4fbf05241eeae25a82a3bbf8d3dce12fd56f86..2034851c2b65adb9d94ec4720716fc3fcbaf6f39 100644 (file)
--- a/lib/examples/knitr.lyx
+++ b/lib/examples/knitr.lyx
@@ -1,5 +1,5 @@
 #LyX 2.3 created this file. For more info see http://www.lyx.org/
-\lyxformat 541
+\lyxformat 544
 \begin_document
 \begin_header
 \save_transient_properties true
@@ -55,6 +55,7 @@ knitr
 \suppress_date false
 \justification true
 \use_refstyle 1
+\use_minted 0
 \index Index
 \shortcut idx
 \color #008000
@@ -68,16 +69,17 @@ knitr
 \paragraph_separation indent
 \paragraph_indentation default
 \is_math_indent 0
+\math_numbering_side default
 \quotes_style english
+\dynamic_quotes 0
 \papercolumns 1
 \papersides 1
 \paperpagestyle default
-\tracking_changes true
+\tracking_changes false
 \output_changes false
 \html_math_output 0
 \html_css_as_file 0
 \html_be_strict false
-\author 2047637253 "Guillaume Munch"
 \end_header
 
 \begin_body
@@ -208,13 +210,9 @@ 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
@@ -231,8 +229,6 @@ Converters
 knitr
 \series default
 .
-\change_unchanged
-
 \end_layout
 
 \begin_layout Standard
@@ -246,24 +242,16 @@ 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
@@ -273,70 +261,22 @@ show-off
 
 \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
-
-\begin_layout Plain Layout
-
-<<show-off>>=
-\end_layout
-
-\begin_layout Plain Layout
-
-rnorm(5)
-\end_layout
-
-\begin_layout Plain Layout
-
-df=data.frame(y=rnorm(100), x=1:100)
-\end_layout
-
-\begin_layout Plain Layout
-
-summary(lm(y~x, data=df))
-\end_layout
-
-\begin_layout Plain Layout
-
-@
-\end_layout
-
-\end_inset
-
-
-\change_unchanged
-
 \end_layout
 
 \begin_layout Standard

diff --git a/lib/examples/sweave.lyx b/lib/examples/sweave.lyx
index 78ab805ab3752c9465ca6bf9e9d27d2991f7323c..342630e16419330159985d869937dc8a7b5fe4b0 100644 (file)
--- a/lib/examples/sweave.lyx
+++ b/lib/examples/sweave.lyx
@@ -1,5 +1,5 @@
 #LyX 2.3 created this file. For more info see http://www.lyx.org/
-\lyxformat 541
+\lyxformat 544
 \begin_document
 \begin_header
 \save_transient_properties true
@@ -67,6 +67,7 @@ sweave
 \suppress_date false
 \justification true
 \use_refstyle 0
+\use_minted 0
 \index Index
 \shortcut idx
 \color #008000
@@ -80,36 +81,31 @@ sweave
 \paragraph_separation indent
 \paragraph_indentation default
 \is_math_indent 0
+\math_numbering_side default
 \quotes_style english
+\dynamic_quotes 0
 \papercolumns 1
 \papersides 1
 \paperpagestyle default
-\tracking_changes true
+\tracking_changes false
 \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
-
-\change_inserted 2047637253 1483897614
 \begin_inset Note Note
 status open
 
 \begin_layout Plain Layout
-
-\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
 
@@ -121,8 +117,6 @@ prefix=TRUE,prefix.string=sweave-prefix,keep.source=FALSE
 \end_inset
 
 
-\change_unchanged
-
 \end_layout
 
 \begin_layout Standard
@@ -259,13 +253,9 @@ 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
@@ -278,8 +268,6 @@ File Handling\SpecialChar menuseparator
 Converters
 \family default
  in order to compile with Sweave.
-\change_unchanged
-
 \end_layout
 
 \begin_layout Section
@@ -347,21 +335,15 @@ bin
 \end_layout
 
 \begin_layout Standard
-
-\change_inserted 2047637253 1483897627
 \begin_inset Flex Chunk
 status open
 
 \begin_layout Plain Layout
 
-\change_inserted 2047637253 1483897627
-
 \begin_inset Argument 1
 status open
 
 \begin_layout Plain Layout
-
-\change_inserted 2047637253 1483897627
 where-is-R-bin,eval=FALSE
 \end_layout
 
@@ -372,16 +354,12 @@ where-is-R-bin,eval=FALSE
 
 \begin_layout Plain Layout
 
-\change_inserted 2047637253 1483897627
-
 R.home('bin')
 \end_layout
 
 \end_inset
 
 
-\change_unchanged
-
 \end_layout
 
 \begin_layout Standard
@@ -416,21 +394,15 @@ Sweave.sty
 \end_layout
 
 \begin_layout Standard
-
-\change_inserted 2047637253 1483897639
 \begin_inset Flex Chunk
 status open
 
 \begin_layout Plain Layout
 
-\change_inserted 2047637253 1483897639
-
 \begin_inset Argument 1
 status open
 
 \begin_layout Plain Layout
-
-\change_inserted 2047637253 1483897639
 sweave-sty,eval=FALSE
 \end_layout
 
@@ -441,16 +413,12 @@ sweave-sty,eval=FALSE
 
 \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
@@ -524,37 +492,20 @@ echo=FALSE
 
 \begin_layout Standard
 To write R code in \SpecialChar LyX
-, you can first 
-\change_inserted 2047637253 1483898412
-insert 
-\change_deleted 2047637253 1483898419
-switch to the 
-\change_unchanged
-
+, you can first insert 
 \family typewriter
 Chunk
 \family default
- 
-\change_inserted 2047637253 1483898437
-insets from 
+ 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
+ However, \SpecialChar LyX
  provides a summary of all the 
 \family typewriter
 Chunk
@@ -570,8 +521,6 @@ View\SpecialChar menuseparator
 Outline Pane
 \family default
  menus.
-\change_unchanged
-
 \end_layout
 
 \begin_layout Standard
@@ -591,21 +540,15 @@ useFancyQuotes
 \end_layout
 
 \begin_layout Standard
-
-\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
-
-\change_inserted 2047637253 1483897653
 setup, keep.source=TRUE
 \end_layout
 
@@ -616,15 +559,11 @@ setup, keep.source=TRUE
 
 \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
 
@@ -634,21 +573,15 @@ options(width = 70, useFancyQuotes = FALSE, digits = 4)
 \end_layout
 
 \begin_layout Standard
-
-\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
-
-\change_inserted 2047637253 1483897653
 sweave-manual, eval=FALSE, keep.source=TRUE
 \end_layout
 
@@ -659,23 +592,17 @@ sweave-manual, eval=FALSE, keep.source=TRUE
 
 \begin_layout Plain Layout
 
-\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
@@ -683,21 +610,15 @@ A simple example that will run in any S engine:
 \end_layout
 
 \begin_layout Standard
-
-\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
-
-\change_inserted 2047637253 1483897659
 print-integers, keep.source=TRUE
 \end_layout
 
@@ -708,15 +629,11 @@ print-integers, keep.source=TRUE
 
 \begin_layout Plain Layout
 
-\change_inserted 2047637253 1483897659
-
 ## the integers from 1 to 10 are
 \end_layout
 
 \begin_layout Plain Layout
 
-\change_inserted 2047637253 1483897659
-
 1:10
 \end_layout
 
@@ -726,21 +643,15 @@ print-integers, keep.source=TRUE
 \end_layout
 
 \begin_layout Standard
-
-\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
-
-\change_inserted 2047637253 1483897659
 hide-results, results=hide
 \end_layout
 
@@ -751,23 +662,17 @@ hide-results, results=hide
 
 \begin_layout Plain Layout
 
-\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
@@ -775,21 +680,15 @@ We can also emulate a simple calculator:
 \end_layout
 
 \begin_layout Standard
-
-\change_inserted 2047637253 1483897665
 \begin_inset Flex Chunk
 status open
 
 \begin_layout Plain Layout
 
-\change_inserted 2047637253 1483897665
-
 \begin_inset Argument 1
 status open
 
 \begin_layout Plain Layout
-
-\change_inserted 2047637253 1483897665
 calculator
 \end_layout
 
@@ -800,23 +699,17 @@ calculator
 
 \begin_layout Plain Layout
 
-\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
@@ -824,21 +717,15 @@ Now we look at some Gaussian data:
 \end_layout
 
 \begin_layout Standard
-
-\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
-
-\change_inserted 2047637253 1483897670
 rnorm
 \end_layout
 
@@ -849,37 +736,27 @@ rnorm
 
 \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
 
-\change_inserted 2047637253 1483897670
-
 t1 <- t.test(x)
 \end_layout
 
 \end_inset
 
 
-\change_unchanged
-
 \end_layout
 
 \begin_layout Standard
@@ -975,21 +852,15 @@ iris
 \end_layout
 
 \begin_layout Standard
-
-\change_inserted 2047637253 1483897677
 \begin_inset Flex Chunk
 status open
 
 \begin_layout Plain Layout
 
-\change_inserted 2047637253 1483897677
-
 \begin_inset Argument 1
 status open
 
 \begin_layout Plain Layout
-
-\change_inserted 2047637253 1483897677
 iris-summary
 \end_layout
 
@@ -1000,16 +871,12 @@ iris-summary
 
 \begin_layout Plain Layout
 
-\change_inserted 2047637253 1483897677
-
 summary(iris[,-5])
 \end_layout
 
 \end_inset
 
 
-\change_unchanged
-
 \end_layout
 
 \begin_layout Standard
@@ -1039,24 +906,16 @@ name "tab:xtable-demo"
 \end_inset
 
 
-\change_inserted 2047637253 1483897685
-
 \begin_inset Flex Chunk
 status open
 
 \begin_layout Plain Layout
 
-\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
 
 \end_inset
@@ -1066,33 +925,23 @@ xtable-demo,results=tex,echo=FALSE
 
 \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"
 )')
-\change_unchanged
-
 \end_layout
 
 \end_inset
 
 
-\change_unchanged
-
 \end_layout
 
 \end_inset
@@ -1179,24 +1028,16 @@ Both eps and pdf are set to true so that both latex and pdflatex work.
 
 \begin_layout Plain Layout
 \align center
-
-\change_inserted 2047637253 1483897765
 \begin_inset Flex Chunk
 status open
 
 \begin_layout Plain Layout
 
-\change_inserted 2047637253 1483897772
-
 \begin_inset Argument 1
 status open
 
 \begin_layout Plain Layout
-
-\change_inserted 2047637253 1483897770
 iris-pairs,fig=TRUE,width=4.5,height=4.5,eps=TRUE,pdf=TRUE
-\change_unchanged
-
 \end_layout
 
 \end_inset
@@ -1206,18 +1047,12 @@ iris-pairs,fig=TRUE,width=4.5,height=4.5,eps=TRUE,pdf=TRUE
 
 \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
@@ -1256,21 +1091,15 @@ status open
 
 \begin_layout Plain Layout
 \align center
-
-\change_inserted 2047637253 1483897883
 \begin_inset Flex Chunk
 status open
 
 \begin_layout Plain Layout
 
-\change_inserted 2047637253 1483897883
-
 \begin_inset Argument 1
 status open
 
 \begin_layout Plain Layout
-
-\change_inserted 2047637253 1483897883
 iris-boxplots,fig=TRUE,width=7,height=2,keep.source=F,eps=T,pdf=T
 \end_layout
 
@@ -1281,23 +1110,17 @@ iris-boxplots,fig=TRUE,width=7,height=2,keep.source=F,eps=T,pdf=T
 
 \begin_layout Plain Layout
 
-\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
@@ -1337,8 +1160,6 @@ R/S code
 R CMD Stangle
 \family default
 .
-\change_inserted 2047637253 1483898877
-
 \end_layout
 
 \begin_layout Section
@@ -1699,17 +1520,9 @@ label=
 \end_layout
 
 \begin_layout Standard
-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
+Another issue with the \SpecialChar TeX
+ code environment is the Sweave code chunk may fail
+ when we change the alignment of the chunk paragraph in \SpecialChar LyX
  (using 
 \family sans
 Paragraph settings
@@ -1761,36 +1574,10 @@ This is not a legitimate Sweave code chunk, since
 <<>>=
 \family default
  must start in a new line with nothing before it.
-
-\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
-\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
-
-.
-\change_unchanged
-
 \end_layout
 
 \begin_layout Section