439 lines
6.3 KiB
Plaintext
439 lines
6.3 KiB
Plaintext
#LyX 2.1 created this file. For more info see http://www.lyx.org/
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\lyxformat 474
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\begin_document
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\begin_header
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\textclass beamer
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\begin_preamble
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\usetheme{PaloAlto}
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\end_preamble
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\use_default_options true
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\begin_modules
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knitr
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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 none
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\inputencoding default
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\fontencoding global
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\font_roman default
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\font_sans default
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\font_typewriter default
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\font_math 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
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\font_tt_scale 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 10
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\spacing single
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\use_hyperref true
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\pdf_bookmarks true
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\pdf_bookmarksnumbered false
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\pdf_bookmarksopen false
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\pdf_bookmarksopenlevel 1
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\pdf_breaklinks false
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\pdf_pdfborder true
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\pdf_colorlinks false
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\pdf_backref false
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\pdf_pdfusetitle true
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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 1
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\use_package esint 1
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\use_package mathdots 1
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\use_package mathtools 1
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\use_package mhchem 1
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\use_package stackrel 1
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\use_package stmaryrd 1
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\use_package undertilde 1
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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 1
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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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\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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<<setup, include=FALSE>>=
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\end_layout
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\begin_layout Plain Layout
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library(knitr)
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\end_layout
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\begin_layout Plain Layout
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opts_chunk$set(fig.path='figure/beamer-',fig.align='center',fig.show='hold',size='f
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ootnotesize')
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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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\end_layout
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\begin_layout Title
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\begin_inset Argument 1
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status collapsed
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\begin_layout Plain Layout
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knitr, Beamer, and FragileFrame
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\end_layout
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\end_inset
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A Minimal Demo of knitr with Beamer and Fragile Frames
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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 open
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\begin_layout Plain Layout
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I thank Richard E.
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Goldberg for providing this demo.
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\end_layout
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\end_inset
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\end_layout
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\begin_layout Frame
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\begin_inset Argument 4
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status open
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\begin_layout Plain Layout
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Background
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\end_layout
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\end_inset
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\end_layout
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\begin_deeper
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\begin_layout Itemize
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The
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\series bold
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knitr
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\emph on
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\series default
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\emph default
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package allows you to embed R code and figures in LaTeX documents
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\end_layout
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\begin_deeper
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\begin_layout Itemize
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It has functionality similar to Sweave but looks nicer and gives you more
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control
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\end_layout
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\end_deeper
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\begin_layout Itemize
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If you already have Sweave working in LyX, getting
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\series bold
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knitr
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\series default
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to work is trivial
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\end_layout
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\begin_deeper
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\begin_layout Enumerate
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Install the
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\series bold
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knitr
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\series default
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package in
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\emph on
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R
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\end_layout
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\begin_layout Enumerate
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Read
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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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https://yihui.org/knitr/demo/lyx/
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\end_layout
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\end_inset
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\end_layout
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\end_deeper
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\begin_layout Itemize
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If you use Sweave or
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\series bold
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knitr
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\series default
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with Beamer in LyX, you must use the
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\emph on
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FragileFrame
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\emph default
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environment for the frames that contain R code chunks.
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Let's see if
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\series bold
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knitr
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\series default
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works with Beamer in this small demo.
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\end_layout
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\end_deeper
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\begin_layout Section
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First Test
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\end_layout
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\begin_layout FragileFrame
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\begin_inset Argument 4
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status open
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\begin_layout Plain Layout
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First Test
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\end_layout
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\end_inset
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\end_layout
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\begin_deeper
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\begin_layout Standard
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OK, let's get started with just some text:
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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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<<echo=FALSE,results='hide'>>=
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\end_layout
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\begin_layout Plain Layout
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# some setup
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\end_layout
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\begin_layout Plain Layout
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options(width=60) # make the printing fit on the page
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\end_layout
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\begin_layout Plain Layout
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set.seed(1121) # make the results repeatable
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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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\begin_layout Plain Layout
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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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\begin_layout Plain Layout
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# create some random numbers
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\end_layout
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\begin_layout Plain Layout
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(x=rnorm(20))
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\end_layout
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\begin_layout Plain Layout
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mean(x);var(x)
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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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\end_layout
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\begin_layout Standard
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BTW, the first element of
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\family typewriter
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x
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\family default
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is
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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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\backslash
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Sexpr{x[1]}
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\end_layout
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\end_inset
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.
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(Did you notice the use of
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\family typewriter
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\backslash
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Sexpr{}
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\family default
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?)
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\end_layout
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\end_deeper
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\begin_layout Section
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Second Test
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\end_layout
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\begin_layout FragileFrame
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\begin_inset Argument 4
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status open
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\begin_layout Plain Layout
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Second Test
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\end_layout
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\end_inset
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\end_layout
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\begin_deeper
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\begin_layout Standard
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Text is nice but let's see what happens if we make a couple of plots in
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our chunk:
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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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<<boring-plots,fig.width=4,fig.height=4,out.width='.45
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\backslash
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\backslash
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linewidth'>>=
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\end_layout
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\begin_layout Plain Layout
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par(las=1,mar=c(4,4,.1,.1)) # tick labels direction
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\end_layout
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\begin_layout Plain Layout
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boxplot(x)
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\end_layout
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\begin_layout Plain Layout
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hist(x,main='',col="blue",probability=TRUE)
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\end_layout
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\begin_layout Plain Layout
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lines(density(x),col="red")
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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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\end_layout
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\end_deeper
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\begin_layout Section
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The Big Question
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\end_layout
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\begin_layout Frame
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\begin_inset Argument 4
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status open
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\begin_layout Plain Layout
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The Big Question
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\end_layout
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\end_inset
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\end_layout
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\begin_deeper
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\begin_layout Standard
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Do the above chunks work? You should be able to compile the LyX document
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and get a nice-looking PDF slide presentation.
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If not, time to double-check everything...
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\end_layout
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\end_deeper
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\end_body
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\end_document
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