mirror of
https://git.lyx.org/repos/lyx.git
synced 2024-12-21 05:00:59 +00:00
1602415b98
Also MacOSX ReadMe files. Note that a few lib/doc files are
also "updated" because trailing spaces are removed, but their file
formats are the same because they were recently updated at 83672113.
I did "git checkout LFUNs.lyx" because this file is generated
automatically and has a special header.
1656 lines
27 KiB
Plaintext
1656 lines
27 KiB
Plaintext
#LyX 2.2 created this file. For more info see http://www.lyx.org/
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\lyxformat 501
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\begin_document
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\begin_header
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\origin /systemlyxdir/examples/
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\textclass article
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\begin_preamble
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%% maxwidth is the original width if it's less than linewidth
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%% otherwise use linewidth (to make sure the graphics do not exceed the margin)
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\def\maxwidth{%
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\ifdim\Gin@nat@width>\linewidth
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\linewidth
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\else
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\Gin@nat@width
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\fi
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}
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\end_preamble
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\options nogin
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\use_default_options true
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\begin_modules
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sweave
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\end_modules
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\maintain_unincluded_children false
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\language english
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\language_package auto
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\inputencoding default
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\fontencoding global
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\font_roman "palatino" "default"
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\font_sans "lmss" "default"
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\font_typewriter "lmtt" "default"
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\font_math "auto" "auto"
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\font_default_family default
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\use_non_tex_fonts false
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\font_sc false
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\font_osf false
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\font_sf_scale 100 100
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\font_tt_scale 100 100
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\graphics default
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\default_output_format default
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\output_sync 0
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\bibtex_command default
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\index_command default
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\paperfontsize default
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\spacing single
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\use_hyperref false
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\papersize default
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\use_geometry true
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\use_package amsmath 1
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\use_package amssymb 1
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\use_package cancel 0
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\use_package esint 1
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\use_package mathdots 1
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\use_package mathtools 0
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\use_package mhchem 1
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\use_package stackrel 0
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\use_package stmaryrd 0
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\use_package undertilde 0
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\cite_engine basic
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\cite_engine_type default
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\biblio_style plain
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\use_bibtopic false
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\use_indices false
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\paperorientation portrait
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\suppress_date false
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\justification true
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\use_refstyle 0
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\index Index
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\shortcut idx
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\color #008000
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\end_index
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\leftmargin 3cm
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\topmargin 3cm
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\rightmargin 3cm
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\bottommargin 3cm
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\secnumdepth 3
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\tocdepth 3
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\paragraph_separation indent
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\paragraph_indentation default
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\quotes_language english
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\papercolumns 1
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\papersides 1
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\paperpagestyle default
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\tracking_changes false
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\output_changes false
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\html_math_output 0
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\html_css_as_file 0
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\html_be_strict false
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\end_header
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\begin_body
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\begin_layout Standard
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\begin_inset ERT
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status open
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\begin_layout Plain Layout
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%
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\backslash
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SweaveOpts{prefix=TRUE,prefix.string=sweave-prefix,keep.source=FALSE}
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\end_layout
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\end_inset
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\end_layout
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\begin_layout Standard
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\begin_inset ERT
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status open
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\begin_layout Plain Layout
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%%
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\backslash
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maxwidth was defined in the preamble; see document settings
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\end_layout
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\begin_layout Plain Layout
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\backslash
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setkeys{Gin}{width=
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\backslash
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maxwidth}
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\end_layout
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\end_inset
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\end_layout
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\begin_layout Title
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Using Sweave with \SpecialCharNoPassThru LyX
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\end_layout
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\begin_layout Author
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Yihui Xie
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\begin_inset Foot
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status collapsed
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\begin_layout Plain Layout
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Department of Statistics, Iowa State University.
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Email:
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\begin_inset CommandInset href
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LatexCommand href
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name "xie@yihui.name"
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target "xie@yihui.name"
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type "mailto:"
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\end_inset
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\end_layout
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\end_inset
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\begin_inset ERT
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status collapsed
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\begin_layout Plain Layout
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\backslash
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and
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\end_layout
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\end_inset
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Gregor Gorjanc
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\begin_inset ERT
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status collapsed
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\begin_layout Plain Layout
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\backslash
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and
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\end_layout
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\end_inset
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Jean-Marc Lasgouttes
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\end_layout
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\begin_layout Standard
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Sweave is a tool in the R language (
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\begin_inset Flex URL
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status collapsed
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\begin_layout Plain Layout
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http://www.r-project.org
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\end_layout
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\end_inset
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) for dynamic report generation using the ideas of literate programming.
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R code can be mixed into a \SpecialCharNoPassThru LaTeX
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document, and will be executed in R when
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the document is compiled; the results are written into the \SpecialCharNoPassThru TeX
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output.
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\end_layout
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\begin_layout Standard
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Since \SpecialCharNoPassThru LyX
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2.0, Sweave can be used out of the box with any document class
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using the
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\family sans
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Sweave
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\family default
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module.
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We can add the
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\family sans
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Sweave
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\family default
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module to a \SpecialCharNoPassThru LyX
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document from
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\family sans
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Document\SpecialChar menuseparator
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Settings\SpecialChar menuseparator
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Modules
|
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\family default
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.
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In this manual, we demonstrate some common features of Sweave and explain
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how the module works.
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A PDF version of this manual can be found at
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\begin_inset Flex URL
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status collapsed
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|
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\begin_layout Plain Layout
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https://github.com/downloads/yihui/lyx/sweave.pdf
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\end_layout
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\end_inset
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.
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\end_layout
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\begin_layout Section
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System Requirements
|
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\end_layout
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\begin_layout Standard
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The
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\family sans
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Sweave
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\family default
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module depends on the executable
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\family typewriter
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Rscript
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\family default
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, so it has to be in the
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\family sans
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PATH
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\family default
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variable of the system.
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It is usually not a problem for Linux and Mac OS users, but may be confusing
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to Windows users; if you do not understand what is
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\family sans
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PATH
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\family default
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under Windows, you may either use the R script
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\family sans
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|
add-R-path-win.R
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\family default
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in the repository
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\begin_inset Flex URL
|
|
status collapsed
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\begin_layout Plain Layout
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|
https://github.com/yihui/lyx
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\end_layout
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\end_inset
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to change it automatically (not recommended; you should learn
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\family sans
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PATH
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\family default
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anyway), or go to
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|
\family sans
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|
Tools\SpecialChar menuseparator
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Preferences\SpecialChar menuseparator
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Paths\SpecialChar menuseparator
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PATH prefix
|
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\family default
|
|
to add the bin path of R (recommended), which is often like
|
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\family sans
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C:
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|
\backslash
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|
Program Files
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\backslash
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|
R
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|
\backslash
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|
R-x.x.x
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\backslash
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bin
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\family default
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and you can find it in R:
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\end_layout
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\begin_layout Standard
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\begin_inset ERT
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status open
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|
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\begin_layout Plain Layout
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<<where-is-R-bin,eval=FALSE>>=
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\end_layout
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\begin_layout Plain Layout
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R.home('bin')
|
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\end_layout
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\begin_layout Plain Layout
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@
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\end_layout
|
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\end_inset
|
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|
|
|
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\end_layout
|
|
|
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\begin_layout Standard
|
|
After you have done these changes, you need to reconfigure \SpecialCharNoPassThru LyX
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by
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\family sans
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Tools\SpecialChar menuseparator
|
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Reconfigure
|
|
\family default
|
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.
|
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If
|
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\family typewriter
|
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Rscript
|
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\family default
|
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is not present in
|
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\family sans
|
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PATH
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\family default
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, the
|
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\family sans
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Sweave
|
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\family default
|
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module will be unavailable.
|
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It is recommended to use the latest version of R, since Sweave is still
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being updated.
|
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Another dependency is introduced by the \SpecialCharNoPassThru LaTeX
|
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style file
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\family sans
|
|
Sweave.sty
|
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\family default
|
|
which is shipped with R under this path (it is not on CTAN):
|
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\end_layout
|
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\begin_layout Standard
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\begin_inset ERT
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status open
|
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\begin_layout Plain Layout
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<<sweave-sty,eval=FALSE>>=
|
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\end_layout
|
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|
|
\begin_layout Plain Layout
|
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file.path(R.home('share'), 'texmf', 'tex', 'latex')
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\end_layout
|
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\begin_layout Plain Layout
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|
@
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\end_layout
|
|
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|
\end_inset
|
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|
|
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\end_layout
|
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|
|
\begin_layout Standard
|
|
Mik\SpecialCharNoPassThru TeX
|
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users may add the texmf directory to the list of root directories
|
|
in Mik\SpecialCharNoPassThru TeX
|
|
through Mik\SpecialCharNoPassThru TeX
|
|
settings.
|
|
Further note that
|
|
\family sans
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|
Sweave.sty
|
|
\family default
|
|
depends on the
|
|
\series bold
|
|
fancyvrb
|
|
\series default
|
|
package and
|
|
\emph on
|
|
may
|
|
\emph default
|
|
depend on
|
|
\series bold
|
|
ae
|
|
\series default
|
|
.
|
|
If \SpecialCharNoPassThru LyX
|
|
cannot find
|
|
\family sans
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|
Sweave.sty
|
|
\family default
|
|
, it will directly copy from R, so the Sweave module works even if you do
|
|
not know where is this style file.
|
|
\end_layout
|
|
|
|
\begin_layout Section
|
|
Sweave Examples
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
Before we write an Sweave document, we can set some Sweave options; the
|
|
command is
|
|
\family typewriter
|
|
|
|
\backslash
|
|
SweaveOpts{}
|
|
\family default
|
|
in Sweave and it can be inserted in a \SpecialCharNoPassThru LyX
|
|
document by
|
|
\family sans
|
|
Insert\SpecialChar menuseparator
|
|
Custom Insets\SpecialChar menuseparator
|
|
Sweave Options
|
|
\family default
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|
, or just use \SpecialCharNoPassThru TeX
|
|
code to write it (
|
|
\family sans
|
|
Insert\SpecialChar menuseparator
|
|
\SpecialCharNoPassThru TeX
|
|
Code
|
|
\family default
|
|
).
|
|
For example, we can set a global option
|
|
\family typewriter
|
|
echo=FALSE
|
|
\family default
|
|
in the beginning of a document to suppress all R code (by default, both
|
|
R code and its output will show up in the \SpecialCharNoPassThru LaTeX
|
|
document).
|
|
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
To write R code in \SpecialCharNoPassThru LyX
|
|
, you can first switch to the
|
|
\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 \SpecialCharNoPassThru TeX
|
|
code environment and write
|
|
Sweave code chunks in it.
|
|
The latter approach is recommended since it is more stable.
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
Some R options can be useful to the Sweave output as well, e.g.
|
|
|
|
\family typewriter
|
|
width
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\family default
|
|
and
|
|
\family typewriter
|
|
useFancyQuotes
|
|
\family default
|
|
.
|
|
The former option can adjust the width of the output, and the latter can
|
|
avoid a common problem with quotes.
|
|
Users are encouraged to read the Sweave manual in R for more details.
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
\begin_inset ERT
|
|
status open
|
|
|
|
\begin_layout Plain Layout
|
|
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|
<<setup, keep.source=TRUE>>=
|
|
\end_layout
|
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|
\begin_layout Plain Layout
|
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|
## the option 'digits' can set the (approximate) number of digits
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|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
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|
options(width = 70, useFancyQuotes = FALSE, digits = 4)
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|
\end_layout
|
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|
|
\begin_layout Plain Layout
|
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|
@
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\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
<<sweave-manual, eval=FALSE, keep.source=TRUE>>=
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
## view the Sweave vignette (requires R >= 2.13.0)
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
vignette("Sweave", package = "utils")
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
@
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\end_layout
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
A simple example that will run in any S engine:
|
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\end_layout
|
|
|
|
\begin_layout Standard
|
|
\begin_inset ERT
|
|
status open
|
|
|
|
\begin_layout Plain Layout
|
|
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|
<<print-integers, keep.source=TRUE>>=
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
## the integers from 1 to 10 are
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
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|
1:10
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
@
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
<<hide-results, results=hide>>=
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
## intentionally hide the output by setting results=hide
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
print(1:20)
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
@
|
|
\end_layout
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
We can also emulate a simple calculator:
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
\begin_inset ERT
|
|
status open
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
<<calculator>>=
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
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|
1 + pi
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
sin(pi/6)
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
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|
@
|
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\end_layout
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
Now we look at some Gaussian data:
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
\begin_inset ERT
|
|
status open
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
<<rnorm>>=
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
set.seed(123) # for reproducibility
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
x <- rnorm(20)
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
print(x)
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
t1 <- t.test(x)
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
@
|
|
\end_layout
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
Note that we can easily integrate some numbers into standard text; this
|
|
is done with the command
|
|
\family typewriter
|
|
|
|
\backslash
|
|
Sexpr{}
|
|
\family default
|
|
, and the corresponding \SpecialCharNoPassThru LyX
|
|
menu is
|
|
\family sans
|
|
Insert\SpecialChar menuseparator
|
|
Custom Insets\SpecialChar menuseparator
|
|
S/R expression
|
|
\family default
|
|
, or alternatively just use \SpecialCharNoPassThru TeX
|
|
code.
|
|
For example, the third element of the vector
|
|
\family typewriter
|
|
x
|
|
\family default
|
|
is
|
|
\begin_inset Flex S/R expression
|
|
status collapsed
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
x[3]
|
|
\end_layout
|
|
|
|
\end_inset
|
|
|
|
(i.e.
|
|
|
|
\family typewriter
|
|
x[3]
|
|
\family default
|
|
) and the
|
|
\begin_inset Formula $p$
|
|
\end_inset
|
|
|
|
-value of the test is
|
|
\begin_inset Flex S/R expression
|
|
status collapsed
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
format.pval(t1$p.value)
|
|
\end_layout
|
|
|
|
\end_inset
|
|
|
|
.
|
|
You can round these numbers using functions like
|
|
\emph on
|
|
round()
|
|
\emph default
|
|
in R.
|
|
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
|
|
\family roman
|
|
\series medium
|
|
\shape up
|
|
\size normal
|
|
\emph off
|
|
\bar no
|
|
\noun off
|
|
\color none
|
|
Now we look at a summary of the
|
|
\family typewriter
|
|
\series default
|
|
\shape default
|
|
\size default
|
|
\emph default
|
|
\bar default
|
|
\noun default
|
|
\color inherit
|
|
iris
|
|
\family roman
|
|
\series medium
|
|
\shape up
|
|
\size normal
|
|
\emph off
|
|
\bar no
|
|
\noun off
|
|
\color none
|
|
dataset:
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
\begin_inset ERT
|
|
status open
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
<<iris-summary>>=
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
summary(iris[,-5])
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
@
|
|
\end_layout
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
\begin_inset Float table
|
|
wide false
|
|
sideways false
|
|
status open
|
|
|
|
\begin_layout Plain Layout
|
|
\begin_inset Caption Standard
|
|
|
|
\begin_layout Plain Layout
|
|
Quantiles of the first four variables in the
|
|
\family typewriter
|
|
iris
|
|
\family default
|
|
data.
|
|
\begin_inset CommandInset label
|
|
LatexCommand label
|
|
name "tab:xtable-demo"
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
\align center
|
|
\begin_inset ERT
|
|
status open
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
<<xtable-demo,results=tex,echo=FALSE>>=
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
if (require('xtable')) {
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
print(xtable(sapply(iris[,-5], quantile)), floating=FALSE)
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
} else cat('the xtable package is not available! please install.packages("xtable"
|
|
)')
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
@
|
|
\end_layout
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
Usually people do not like such
|
|
\begin_inset Quotes eld
|
|
\end_inset
|
|
|
|
raw
|
|
\begin_inset Quotes erd
|
|
\end_inset
|
|
|
|
output, and we can polish these messy numbers with the
|
|
\series bold
|
|
xtable
|
|
\series default
|
|
package.
|
|
Table
|
|
\begin_inset CommandInset ref
|
|
LatexCommand ref
|
|
reference "tab:xtable-demo"
|
|
|
|
\end_inset
|
|
|
|
is an example demonstrating how to use the
|
|
\series bold
|
|
xtable
|
|
\series default
|
|
package with Sweave; note the chunk option
|
|
\family typewriter
|
|
results=tex
|
|
\family default
|
|
makes sure that the R output is written out as raw \SpecialCharNoPassThru LaTeX
|
|
code instead of
|
|
being wrapped in a special environment (
|
|
\family typewriter
|
|
Soutput
|
|
\family default
|
|
).
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
Figure
|
|
\begin_inset CommandInset ref
|
|
LatexCommand ref
|
|
reference "fig:iris-pairs"
|
|
|
|
\end_inset
|
|
|
|
and
|
|
\begin_inset CommandInset ref
|
|
LatexCommand ref
|
|
reference "fig:iris-boxplots"
|
|
|
|
\end_inset
|
|
|
|
are two simple examples of producing graphics output with Sweave.
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
\begin_inset Float figure
|
|
wide false
|
|
sideways false
|
|
status open
|
|
|
|
\begin_layout Plain Layout
|
|
\align center
|
|
\begin_inset Note Note
|
|
status open
|
|
|
|
\begin_layout Plain Layout
|
|
Both eps and pdf are set to true so that both latex and pdflatex work.
|
|
In practice, you would probably just choose one.
|
|
\end_layout
|
|
|
|
\end_inset
|
|
|
|
|
|
\begin_inset ERT
|
|
status open
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
<<iris-pairs,fig=TRUE,width=4.5,height=4.5,eps=TRUE,pdf=TRUE>>=
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
pairs(iris, col = iris$Species)
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
@
|
|
\end_layout
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
\begin_inset Caption Standard
|
|
|
|
\begin_layout Plain Layout
|
|
Scatter plot matrix of the
|
|
\family typewriter
|
|
iris
|
|
\family default
|
|
data.
|
|
\begin_inset CommandInset label
|
|
LatexCommand label
|
|
name "fig:iris-pairs"
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
\begin_inset Float figure
|
|
wide false
|
|
sideways false
|
|
status open
|
|
|
|
\begin_layout Plain Layout
|
|
\align center
|
|
\begin_inset ERT
|
|
status open
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
<<iris-boxplots,fig=TRUE,width=7,height=2,keep.source=F,eps=T,pdf=T>>=
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
par(mar=c(4,5,.1,.3), las=1)
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
boxplot(Sepal.Length~Species,data=iris,horizontal=TRUE,xlab='Sepal.Length')
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
@
|
|
\end_layout
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
\begin_inset Caption Standard
|
|
|
|
\begin_layout Plain Layout
|
|
Boxplots of sepal length grouped by species.
|
|
\begin_inset CommandInset label
|
|
LatexCommand label
|
|
name "fig:iris-boxplots"
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
We can also export all the R code in an Sweave document as a single R script
|
|
(
|
|
\family sans
|
|
File\SpecialChar menuseparator
|
|
Export\SpecialChar menuseparator
|
|
R/S code
|
|
\family default
|
|
), which is done via
|
|
\family typewriter
|
|
R CMD Stangle
|
|
\family default
|
|
.
|
|
\end_layout
|
|
|
|
\begin_layout Section
|
|
The
|
|
\family sans
|
|
Sweave
|
|
\family default
|
|
Module
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
The
|
|
\family sans
|
|
Sweave
|
|
\family default
|
|
module declares that a \SpecialCharNoPassThru LyX
|
|
document contains literate programming components
|
|
with R, so that \SpecialCharNoPassThru LyX
|
|
will handle such documents according to the specific
|
|
converters (see the Customization manual).
|
|
The
|
|
\family sans
|
|
Sweave
|
|
\family default
|
|
module uses the
|
|
\family sans
|
|
sweave
|
|
\family default
|
|
converter, which essentially consists of an R script
|
|
\family sans
|
|
lyxsweave.R
|
|
\family default
|
|
under the
|
|
\family sans
|
|
scripts
|
|
\family default
|
|
directory of \SpecialCharNoPassThru LyX
|
|
.
|
|
This script takes an
|
|
\family sans
|
|
Rnw
|
|
\family default
|
|
document from \SpecialCharNoPassThru LyX
|
|
and call Sweave to process it to a \SpecialCharNoPassThru TeX
|
|
document, then
|
|
\SpecialCharNoPassThru LyX
|
|
takes care of the rest of work.
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
The converter from the
|
|
\family sans
|
|
sweave
|
|
\family default
|
|
format to \SpecialCharNoPassThru LaTeX
|
|
is a call to R via the command line as:
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
\begin_inset ERT
|
|
status open
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
|
|
\backslash
|
|
begin{verbatim}
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
Rscript --no-save --no-restore $$s/scripts/lyxsweave.R $$p$$i $$p$$o $$e
|
|
$$r
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
|
|
\backslash
|
|
end{verbatim}
|
|
\end_layout
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
The \SpecialCharNoPassThru LyX
|
|
library directory
|
|
\family typewriter
|
|
$$s
|
|
\family default
|
|
can be found from the menu
|
|
\family sans
|
|
Help\SpecialChar menuseparator
|
|
About \SpecialCharNoPassThru LyX
|
|
\family default
|
|
.
|
|
All the rest of options passed to R are explained in the R script, and
|
|
the \SpecialCharNoPassThru LyX
|
|
Customization manual also has detailed explanations about
|
|
\family typewriter
|
|
$$i
|
|
\family default
|
|
,
|
|
\family typewriter
|
|
$$o
|
|
\family default
|
|
,
|
|
\family typewriter
|
|
$$e
|
|
\family default
|
|
and
|
|
\family typewriter
|
|
$$r
|
|
\family default
|
|
.
|
|
General users do not need to know clearly what they mean, but here we need
|
|
to explain a few issues in the R code:
|
|
\end_layout
|
|
|
|
\begin_layout Enumerate
|
|
the encoding string of the \SpecialCharNoPassThru LyX
|
|
document is passed to R as an command line
|
|
option; possible values are
|
|
\family typewriter
|
|
ISO-8859-15
|
|
\family default
|
|
and
|
|
\family typewriter
|
|
UTF-8
|
|
\family default
|
|
, etc.
|
|
The encoding is used for R to read the
|
|
\family sans
|
|
Rnw
|
|
\family default
|
|
document correctly.
|
|
\end_layout
|
|
|
|
\begin_layout Enumerate
|
|
the R code chunks in the Sweave document are executed under the directory
|
|
of the \SpecialCharNoPassThru LyX
|
|
document (if you are not sure, put
|
|
\family typewriter
|
|
getwd()
|
|
\family default
|
|
in a code chunk to see what is the current working directory).
|
|
In this case, you can put data files under the same directory and use relative
|
|
paths in R to guarantee reproducibility, i.e.
|
|
we do not need to write hard-coded paths which may not exist in other systems.
|
|
\end_layout
|
|
|
|
\begin_layout Enumerate
|
|
if \SpecialCharNoPassThru LaTeX
|
|
cannot find
|
|
\family sans
|
|
Sweave.sty
|
|
\family default
|
|
, this R script will copy it to the temporary directory automatically where
|
|
the \SpecialCharNoPassThru LaTeX
|
|
compilation takes place.
|
|
\end_layout
|
|
|
|
\begin_layout Enumerate
|
|
Sweave will use the filename of the Rnw file as the prefix string for the
|
|
graphics output by default; one known issue (
|
|
\begin_inset CommandInset href
|
|
LatexCommand href
|
|
name "#7551"
|
|
target "http://www.lyx.org/trac/ticket/7551"
|
|
|
|
\end_inset
|
|
|
|
) is that if the filename (without extension) contains dots, \SpecialCharNoPassThru LaTeX
|
|
can fail
|
|
to deal with such files in
|
|
\family typewriter
|
|
|
|
\backslash
|
|
includegraphics{}
|
|
\family default
|
|
.
|
|
Therefore, we have set the default value of the prefix to be the filename
|
|
with all the dots being replaced by
|
|
\begin_inset Quotes eld
|
|
\end_inset
|
|
|
|
-
|
|
\begin_inset Quotes erd
|
|
\end_inset
|
|
|
|
.
|
|
We can also solve this problem in Sweave directly: set the Sweave option
|
|
|
|
\family typewriter
|
|
prefix.string
|
|
\family default
|
|
to be a character string without dots, and this option will override the
|
|
default value.
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
We have pre-specified an option
|
|
\family typewriter
|
|
noae
|
|
\family default
|
|
for the Sweave package.
|
|
This option stops Sweave from loading these two packages:
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
\begin_inset ERT
|
|
status open
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
|
|
\backslash
|
|
begin{verbatim}
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
|
|
\backslash
|
|
RequirePackage[T1]{fontenc}
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
|
|
\backslash
|
|
RequirePackage{ae}
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
|
|
\backslash
|
|
end{verbatim}
|
|
\end_layout
|
|
|
|
\end_inset
|
|
|
|
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
\SpecialCharNoPassThru LyX
|
|
can deal with the font encoding by default, so there is no need to ask
|
|
Sweave to do this (furthermore, this may bring clashes of package options);
|
|
besides, the users can load the
|
|
\series bold
|
|
ae
|
|
\series default
|
|
package by themselves in the preamble if needed.
|
|
\end_layout
|
|
|
|
\begin_layout Section
|
|
Trouble Shooting
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
Since \SpecialCharNoPassThru LyX
|
|
2.0, we can see the detailed information during compilation via
|
|
|
|
\family sans
|
|
View\SpecialChar menuseparator
|
|
View Messages
|
|
\family default
|
|
.
|
|
This is extremely helpful for trouble shooting \twohyphens
|
|
the process of R will
|
|
be shown in the message panel, and we will be able to know which chunk
|
|
goes wrong in cases of errors.
|
|
For example, when you compile this document, you can see messages like
|
|
below:
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
\begin_inset ERT
|
|
status open
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
|
|
\backslash
|
|
begin{verbatim}
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
17:58:47.868: Processing code chunks with options ...
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
17:58:47.885: 1 : echo keep.source term verbatim (label=setup)
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
17:58:47.889: 2 : echo keep.source (label=sweave-manual)
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
17:58:47.908: 3 : echo keep.source term verbatim (label=print-integers)
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
....
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
17:58:47.941: Loading required package: xtable
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
17:58:47.976: 9 : echo term verbatim pdf (label=iris-pairs)
|
|
\end_layout
|
|
|
|
\begin_layout Plain Layout
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|
....
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\end_layout
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\begin_layout Plain Layout
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17:58:48.116: You can now run (pdf)latex on 'sweave.tex'
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\end_layout
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\begin_layout Plain Layout
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|
|
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\backslash
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|
end{verbatim}
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\end_layout
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|
\end_inset
|
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|
|
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
The string after
|
|
\family typewriter
|
|
label=
|
|
\family default
|
|
is the chunk label.
|
|
If any chunk causes an error in R, you will see the error message here
|
|
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 \SpecialCharNoPassThru LyX
|
|
(using
|
|
\family sans
|
|
Paragraph settings
|
|
\family default
|
|
), because \SpecialCharNoPassThru 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{}<<xtable-demo,results=tex,echo=FALSE>>=
|
|
\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
|
|
|
|
\begin_layout Standard
|
|
The homepage of Sweave is at
|
|
\begin_inset Flex URL
|
|
status collapsed
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
http://www.stat.uni-muenchen.de/~leisch/Sweave/
|
|
\end_layout
|
|
|
|
\end_inset
|
|
|
|
.
|
|
The CRAN task view on
|
|
\begin_inset Quotes eld
|
|
\end_inset
|
|
|
|
Reproducible Research
|
|
\begin_inset Quotes erd
|
|
\end_inset
|
|
|
|
has a list of Sweave-related packages which can be potentially useful;
|
|
see
|
|
\begin_inset Flex URL
|
|
status collapsed
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
http://cran.r-project.org/web/views/ReproducibleResearch.html
|
|
\end_layout
|
|
|
|
\end_inset
|
|
|
|
.
|
|
Questions about \SpecialCharNoPassThru LyX
|
|
and Sweave can be posted to the \SpecialCharNoPassThru LyX
|
|
mailing list (
|
|
\begin_inset Flex URL
|
|
status collapsed
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
http://www.lyx.org/MailingLists
|
|
\end_layout
|
|
|
|
\end_inset
|
|
|
|
).
|
|
More \SpecialCharNoPassThru LyX
|
|
examples are provided at
|
|
\begin_inset Flex URL
|
|
status collapsed
|
|
|
|
\begin_layout Plain Layout
|
|
|
|
https://github.com/yihui/lyx
|
|
\end_layout
|
|
|
|
\end_inset
|
|
|
|
.
|
|
\end_layout
|
|
|
|
\begin_layout Section
|
|
FAQ
|
|
\end_layout
|
|
|
|
\begin_layout Subsection
|
|
How to use Sweave with beamer?
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
You will end up with \SpecialCharNoPassThru LaTeX
|
|
errors if you use Sweave in normal beamer slides
|
|
in \SpecialCharNoPassThru LyX
|
|
; the reason is the beamer frame that contains verbatim R code.
|
|
The solution is to use a
|
|
\emph on
|
|
FragileFrame
|
|
\emph default
|
|
instead of a normal
|
|
\emph on
|
|
Frame
|
|
\emph default
|
|
, or to pass the option
|
|
\family typewriter
|
|
fragile
|
|
\family default
|
|
to the frame title via
|
|
\family sans
|
|
Insert\SpecialChar menuseparator
|
|
Frame Options
|
|
\family default
|
|
.
|
|
\end_layout
|
|
|
|
\begin_layout Subsection
|
|
Can I define my own R script to compile the Rnw document?
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
Yes, of course.
|
|
First you need to understand how the R script
|
|
\family typewriter
|
|
$$s
|
|
\family sans
|
|
/scripts/lyxsweave.R
|
|
\family default
|
|
works, which was introduced previously, and we recommend you to read the
|
|
R source code as well (on how R takes the paths and uses
|
|
\emph on
|
|
Sweave()
|
|
\emph default
|
|
to handle the Rnw document).
|
|
Then you put your customized
|
|
\family sans
|
|
lyxsweave.R
|
|
\family default
|
|
under the
|
|
\family sans
|
|
scripts
|
|
\family default
|
|
directory of your
|
|
\emph on
|
|
user directory
|
|
\emph default
|
|
(again, see
|
|
\family sans
|
|
Help\SpecialChar menuseparator
|
|
About \SpecialCharNoPassThru LyX
|
|
\family default
|
|
).
|
|
Note \SpecialCharNoPassThru LyX
|
|
will check the
|
|
\emph on
|
|
user directory
|
|
\emph default
|
|
before going to its own
|
|
\emph on
|
|
library directory
|
|
\emph default
|
|
; if an R script
|
|
\family sans
|
|
lyxsweave.R
|
|
\family default
|
|
is found in the user directory, it will be used.
|
|
It is not recommended to hack the script under the \SpecialCharNoPassThru LyX
|
|
library directory
|
|
directly, since updating \SpecialCharNoPassThru LyX
|
|
will override you modified script (the user
|
|
directory will not be affected).
|
|
\end_layout
|
|
|
|
\begin_layout Standard
|
|
Beside the support for the official Sweave in R, the
|
|
\series bold
|
|
knitr
|
|
\series default
|
|
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
|
|
\end_document
|