#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
\use_geometry true
\use_package amsmath 1
\use_package amssymb 1
-\use_package cancel 0
+\use_package cancel 1
\use_package esint 1
\use_package mathdots 1
-\use_package mathtools 0
+\use_package mathtools 1
\use_package mhchem 1
-\use_package stackrel 0
-\use_package stmaryrd 0
-\use_package undertilde 0
+\use_package stackrel 1
+\use_package stmaryrd 1
+\use_package undertilde 1
\cite_engine basic
\cite_engine_type default
\biblio_style plain
\use_bibtopic false
\use_indices false
\paperorientation portrait
-\suppress_date false
+\suppress_date true
\justification true
\use_refstyle 0
+\use_minted 0
\index Index
\shortcut idx
\color #008000
\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
\end_inset
-\change_unchanged
-
\end_layout
\begin_layout Standard
\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
Converters
\family default
in order to compile with Sweave.
-\change_unchanged
-
\end_layout
\begin_layout Section
\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
\begin_layout Plain Layout
-\change_inserted 2047637253 1483897627
-
R.home('bin')
\end_layout
\end_inset
-\change_unchanged
-
\end_layout
\begin_layout Standard
\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
\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
\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
Outline Pane
\family default
menus.
-\change_unchanged
-
\end_layout
\begin_layout Standard
\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
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setup, keep.source=TRUE
\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
\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
\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
\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
\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
\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
\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
\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
\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
\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
\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
\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
\begin_layout Plain Layout
-\change_inserted 2047637253 1483897677
-
summary(iris[,-5])
\end_layout
\end_inset
-\change_unchanged
-
\end_layout
\begin_layout Standard
\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
\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
\begin_layout Plain Layout
\align center
-
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\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
\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
\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
\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
R CMD Stangle
\family default
.
-\change_inserted 2047637253 1483898877
-
\end_layout
\begin_layout Section
\begin_inset CommandInset href
LatexCommand href
name "#7551"
-target "http://www.lyx.org/trac/ticket/7551"
+target "https://www.lyx.org/trac/ticket/7551"
literal "false"
\end_inset
\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
<<>>=
\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
\end_layout
\begin_layout Standard
-The homepage of Sweave is at
+The user manual of Sweave is at
\begin_inset Flex URL
status collapsed
\begin_layout Plain Layout
-http://www.stat.uni-muenchen.de/~leisch/Sweave/
+https://stat.ethz.ch/R-manual/R-devel/library/utils/doc/Sweave.pdf
\end_layout
\end_inset
\begin_layout Plain Layout
-http://www.lyx.org/MailingLists
+https://www.lyx.org/MailingLists
\end_layout
\end_inset
projects / lyx.git / blobdiff