commit 47612b3839f8915c982ba1bec00f7e0dd958e44f
Author: Guillaume MM <[email protected]>
Date: Mon Jul 17 22:15:12 2017 +0200
Accept modifications in R examples
---
lib/examples/knitr.lyx | 70 +-------------
lib/examples/sweave.lyx | 235 ++--------------------------------------------
2 files changed, 16 insertions(+), 289 deletions(-)
diff --git a/lib/examples/knitr.lyx b/lib/examples/knitr.lyx
index 9e4fbf0..2034851 100644
--- 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 78ab805..342630e 100644
--- 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
