#LyX 2.4 created this file. For more info see https://www.lyx.org/
\lyxformat 614
\begin_document
\begin_header
\save_transient_properties true
\origin /systemlyxdir/examples/Modules/
\textclass article
\use_default_options true
\begin_modules
knitr
\end_modules
\maintain_unincluded_children no
\language english
\language_package default
\inputencoding utf8
\fontencoding auto
\font_roman "palatino" "default"
\font_sans "lmss" "default"
\font_typewriter "lmtt" "default"
\font_math "auto" "auto"
\font_default_family default
\use_non_tex_fonts false
\font_sc false
\font_roman_osf false
\font_sans_osf false
\font_typewriter_osf false
\font_sf_scale 100 100
\font_tt_scale 100 100
\use_microtype false
\use_dash_ligatures false
\graphics default
\default_output_format default
\output_sync 0
\bibtex_command default
\index_command default
\paperfontsize default
\spacing single
\use_hyperref false
\papersize default
\use_geometry true
\use_package amsmath 1
\use_package amssymb 1
\use_package cancel 1
\use_package esint 1
\use_package mathdots 1
\use_package mathtools 1
\use_package mhchem 1
\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
\justification true
\use_refstyle 1
\use_minted 0
\use_lineno 0
\index Index
\shortcut idx
\color #008000
\end_index
\leftmargin 2.5cm
\topmargin 2.5cm
\rightmargin 2.5cm
\bottommargin 2.5cm
\secnumdepth 3
\tocdepth 3
\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
\tablestyle default
\tracking_changes false
\output_changes false
\change_bars false
\postpone_fragile_content false
\html_math_output 0
\html_css_as_file 0
\html_be_strict false
\docbook_table_output 0
\docbook_mathml_prefix 1
\end_header

\begin_body

\begin_layout Title
Using knitr with \SpecialChar LyX

\end_layout

\begin_layout Author
Yihui Xie
\begin_inset Foot
status collapsed

\begin_layout Plain Layout
Department of Statistics,
 Iowa State University.
 Email:
 
\begin_inset CommandInset href
LatexCommand href
name "xie@yihui.name"
target "xie@yihui.name"
type "mailto:"
literal "false"

\end_inset


\end_layout

\end_inset


\end_layout

\begin_layout Standard
The R (
\begin_inset Flex URL
status collapsed

\begin_layout Plain Layout

http://www.r-project.org
\end_layout

\end_inset

) package 
\series bold
knitr
\series default
 is an alternative tool to Sweave based on a different design with more features.
 \SpecialChar LyX
 has native support to Sweave since version 2.0.0,
 and the support to 
\series bold
knitr
\series default
 was also added since 2.0.3.
 The usage is basically the same as the 
\family sans
Sweave
\family default
 module
\begin_inset Foot
status open

\begin_layout Plain Layout
read the \SpecialChar LyX
/Sweave manual from 
\family sans
Help\SpecialChar menuseparator
Specific Manuals
\end_layout

\end_inset

:
\end_layout

\begin_layout Enumerate
Open a new \SpecialChar LyX
 document;
\end_layout

\begin_layout Enumerate
Go to 
\family sans
Document\SpecialChar menuseparator
Settings\SpecialChar menuseparator
Modules
\family default
 and insert the module named 
\family sans
Rnw (knitr)
\family default
;
\end_layout

\begin_layout Enumerate
Then insert R code in the document with either 
\family sans
Insert\SpecialChar menuseparator
\SpecialChar TeX
 Code
\family default
 or the 
\family sans
Chunk
\family default
 environment;
\end_layout

\begin_layout Standard
The package website 
\begin_inset Flex URL
status collapsed

\begin_layout Plain Layout

http://yihui.name/knitr
\end_layout

\end_inset

 has full documentation and demos of 
\series bold
knitr
\series default
;
 many of the examples have links to the \SpecialChar LyX
 source documents.
\end_layout

\begin_layout Standard
Since \SpecialChar LyX
 2.3,
 it is necessary to enable the use of 
\emph on
needauth
\emph default
 converters in
\family sans
 Preferences\SpecialChar menuseparator
File Handling\SpecialChar menuseparator
Converters
\family default
 in order to compile with 
\series bold
knitr
\series default
.
\end_layout

\begin_layout Standard
Note the 
\series bold
knitr
\series default
 package requires R >= 2.14.1,
 so you need to update R if you are using an old version of R.
 Here we show one chunk as a simple example:
\end_layout

\begin_layout Standard
\begin_inset Flex Chunk
status open

\begin_layout Plain Layout

\begin_inset Argument 1
status open

\begin_layout Plain Layout

show-off
\end_layout

\end_inset


\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

\end_inset


\end_layout

\begin_layout Standard
Please contact the package author in case of any problems.
\end_layout

\end_body
\end_document