#LyX 2.1 created this file. For more info see http://www.lyx.org/
\lyxformat 474
\begin_document
\begin_header
\textclass jss
\begin_preamble
%the following commands are used only for articles and codesnippets

\author{First Author\\Affiliation of the first author \And 
        Second Author\\Affiliation of the second author \AND
        Third Author\\Affiliation of the third author}
\title{Article About the Use of Package \pkg{foo} in \proglang{R}}

% the same as above, without any formatting
\Plainauthor{First Author, Second Author, Third author}
\Plaintitle{Article About the Use of Package foo in R} 
%if necessary, provide a short title
\Shorttitle{Package foo in R} 

\Abstract{This is the abstract of the article.}
%at least one keyword is needed
\Keywords{keyword 1, keyword 2, \pkg{foo}, \proglang{R}}
%the same as above, without any formatting
\Plainkeywords{keyword 1, keyword 2, foo, R} 

%the following commands are used only for book or software reviews

%\Reviewer{Some Author\\University of Somewhere}
%\Plainreviewer{Some Author}

%the following commands are used only for book reviews
%\Booktitle{LyX and \proglang{R}: Secrets of the LyX Master}
%\Bookauthor{Book Author}
%\Pubyear{2008}
%\ISBN{0-12345-678-9}
%\Pages{500}

%the following command is used only for software reviews
%\Softwaretitle{\proglang{gretl 1.7.4}}

%the following commands are used only for book or software reviews
%\Publisher{LyX Publishing Inc.}
%\Pubaddress{LyX City}
%\Price{USD 59.95 (P), USD 99.95 (H)}
%\URL{http://www.lyx.org/}

%without any formatting
%\Plaintitle{LyX and R: Secrets of the LyX Master}
%\Shorttitle{LyX and R}

%the following commands are used for articles, codesnippets, book reviews and software reviews

%publication information
%do not use these commands before the article has been accepted
%\Volume{00}
%\Issue{0}
%\Month{Month}
%\Year{2000}
%\Submitdate{2000-00-00}
%\Acceptdate{2000-00-00}

%The address of at least one author should be given in the following format
\Address{
  First Author\\
  Department of Statistics\\
  University of Somewhere\\
  Somewhere, Somecountry\\
  E-mail: \email{first.author@lyx.org}\\
  URL: \url{http://www.lyx.org}
}
%you can add a telephone and fax number before the e-mail in the format
%Telephone: +12/3/4567-89
%Fax: +12/3/4567-89

%if you use Sweave,  include the following line (with % symbols):
%% need no \usepackage{Sweave.sty}
\end_preamble
\options article
\use_default_options false
\maintain_unincluded_children false
\language english
\language_package default
\inputencoding auto
\fontencoding global
\font_roman default
\font_sans default
\font_typewriter default
\font_math auto
\font_default_family default
\use_non_tex_fonts false
\font_sc false
\font_osf false
\font_sf_scale 100
\font_tt_scale 100
\graphics default
\default_output_format pdf2
\output_sync 0
\bibtex_command default
\index_command default
\paperfontsize default
\spacing single
\use_hyperref false
\papersize default
\use_geometry false
\use_package amsmath 0
\use_package amssymb 0
\use_package cancel 0
\use_package esint 0
\use_package mathdots 1
\use_package mathtools 0
\use_package mhchem 1
\use_package stackrel 0
\use_package stmaryrd 0
\use_package undertilde 0
\cite_engine natbib
\cite_engine_type authoryear
\biblio_style plainnat
\use_bibtopic false
\use_indices false
\paperorientation portrait
\suppress_date false
\justification true
\use_refstyle 0
\index Index
\shortcut idx
\color #008000
\end_index
\secnumdepth 3
\tocdepth 3
\paragraph_separation indent
\paragraph_indentation default
\quotes_language english
\papercolumns 1
\papersides 1
\paperpagestyle default
\tracking_changes false
\output_changes false
\html_math_output 0
\html_css_as_file 0
\html_be_strict false
\end_header

\begin_body

\begin_layout Standard
\begin_inset Note Note
status open

\begin_layout Plain Layout
This is a template LyX file for articles to be submitted to the Journal
 of Statistical Software (JSS).
 How to install the JSS LaTeX class to your LaTeX system is explained in
 
\begin_inset Flex URL
status open

\begin_layout Plain Layout

http://wiki.lyx.org/Layouts/JSS
\end_layout

\end_inset

.
\end_layout

\end_inset


\begin_inset Note Note
status open

\begin_layout Plain Layout
Note that title, author, address, abstract, keywords etc for this article
 style are written in the LaTeX preamble (accessed from Document\SpecialChar \menuseparator
Settings...\SpecialChar \menuseparator
LaTeX
 Preamble).
 
\end_layout

\begin_layout Plain Layout
To use the JSS codesnippet, bookreview or softwarereview styles, replace
 the option 
\begin_inset Quotes eld
\end_inset

article
\begin_inset Quotes erd
\end_inset

 in Document\SpecialChar \menuseparator
Settings...\SpecialChar \menuseparator
Document Class\SpecialChar \menuseparator
Options with 
\begin_inset Quotes eld
\end_inset

codesnippet
\begin_inset Quotes erd
\end_inset

, 
\begin_inset Quotes eld
\end_inset

bookreview
\begin_inset Quotes erd
\end_inset

 or 
\begin_inset Quotes eld
\end_inset

softwarereview
\begin_inset Quotes erd
\end_inset

 and remove/uncomment the relevant parts in the LaTeX Preamble.
 
\end_layout

\begin_layout Plain Layout
If you want to use this JSS article style for a non-JSS article, replace
 the option 
\begin_inset Quotes eld
\end_inset

article
\begin_inset Quotes erd
\end_inset

 with 
\begin_inset Quotes eld
\end_inset

nojss
\begin_inset Quotes erd
\end_inset

.
 This will suppress the JSS-specic parts of the layout.
\end_layout

\begin_layout Plain Layout
To include the JSS-specific parts of the layout, the article has to be processed
 with PDF, i.e.
 you cannot process it with DVI or PS.
 However, if the option 
\begin_inset Quotes eld
\end_inset

nojss
\begin_inset Quotes erd
\end_inset

 is used, it can be processed with DVI or PS.
\end_layout

\end_inset


\end_layout

\begin_layout Section
\begin_inset Note Note
status collapsed

\begin_layout Plain Layout
The opt field provides bookmarks for PDF files
\end_layout

\end_inset


\begin_inset Argument 1
status collapsed

\begin_layout Plain Layout
About package foo in R
\end_layout

\end_inset

About package 
\begin_inset ERT
status collapsed

\begin_layout Plain Layout


\backslash
pkg
\end_layout

\end_inset


\begin_inset ERT
status collapsed

\begin_layout Plain Layout

{
\end_layout

\end_inset

foo
\begin_inset ERT
status collapsed

\begin_layout Plain Layout

}
\end_layout

\end_inset

 in 
\begin_inset ERT
status collapsed

\begin_layout Plain Layout


\backslash
proglang
\end_layout

\end_inset


\begin_inset ERT
status collapsed

\begin_layout Plain Layout

{
\end_layout

\end_inset

R
\begin_inset ERT
status collapsed

\begin_layout Plain Layout

}
\end_layout

\end_inset


\end_layout

\begin_layout Standard
The special JSS style commands related to software and mathematical formulas
 are written as follows in LyX: 
\begin_inset ERT
status open

\begin_layout Plain Layout


\backslash
proglang{R}
\end_layout

\end_inset

 or 
\begin_inset ERT
status collapsed

\begin_layout Plain Layout


\backslash
proglang{
\end_layout

\end_inset

R
\begin_inset ERT
status collapsed

\begin_layout Plain Layout

}
\end_layout

\end_inset

 for the names of programming languages, 
\begin_inset ERT
status open

\begin_layout Plain Layout


\backslash
pkg{foo}
\end_layout

\end_inset

 or 
\begin_inset ERT
status collapsed

\begin_layout Plain Layout


\backslash
pkg{
\end_layout

\end_inset

foo
\begin_inset ERT
status collapsed

\begin_layout Plain Layout

}
\end_layout

\end_inset

 for software packages, and 
\begin_inset ERT
status open

\begin_layout Plain Layout


\backslash
code{some code}
\end_layout

\end_inset

 or 
\begin_inset ERT
status collapsed

\begin_layout Plain Layout


\backslash
pkg{
\end_layout

\end_inset

some code
\begin_inset ERT
status collapsed

\begin_layout Plain Layout

}
\end_layout

\end_inset

 for code; 
\begin_inset Formula $\E$
\end_inset

 
\begin_inset Note Note
status open

\begin_layout Plain Layout
written as 
\backslash
E
\end_layout

\end_inset

 for expectations, 
\begin_inset Formula $\VAR$
\end_inset

 
\begin_inset Note Note
status open

\begin_layout Plain Layout
written as 
\backslash
VAR
\end_layout

\end_inset

 for variances, 
\begin_inset Formula $\COV$
\end_inset

 
\begin_inset Note Note
status open

\begin_layout Plain Layout
written as 
\backslash
COV
\end_layout

\end_inset

 for covariances, and 
\begin_inset Formula $\Prob$
\end_inset

 
\begin_inset Note Note
status open

\begin_layout Plain Layout
written as 
\backslash
Prob
\end_layout

\end_inset

 for probabilities.
\end_layout

\begin_layout Standard
Writing several lines of code: 
\end_layout

\begin_layout Standard
\begin_inset ERT
status open

\begin_layout Plain Layout


\backslash
begin{CodeChunk}
\end_layout

\begin_layout Plain Layout


\backslash
begin{Code}
\end_layout

\begin_layout Plain Layout

first line of code
\end_layout

\begin_layout Plain Layout

second line of code
\end_layout

\begin_layout Plain Layout

third line of code
\end_layout

\begin_layout Plain Layout


\backslash
end{Code}
\end_layout

\begin_layout Plain Layout


\backslash
end{CodeChunk}
\end_layout

\end_inset


\end_layout

\begin_layout Standard
Alternatively, you can distinguish between input and output code:
\end_layout

\begin_layout Standard
\begin_inset ERT
status open

\begin_layout Plain Layout


\backslash
begin{CodeChunk}
\end_layout

\begin_layout Plain Layout


\backslash
begin{CodeInput}
\end_layout

\begin_layout Plain Layout

first line of input code
\end_layout

\begin_layout Plain Layout

second line of input code
\end_layout

\begin_layout Plain Layout


\backslash
end{CodeInput}
\end_layout

\begin_layout Plain Layout


\backslash
begin{CodeOutput}
\end_layout

\begin_layout Plain Layout

first line of output code
\end_layout

\begin_layout Plain Layout

second line of output code
\end_layout

\begin_layout Plain Layout

third line of output code
\end_layout

\begin_layout Plain Layout


\backslash
end{CodeOutput}
\end_layout

\begin_layout Plain Layout


\backslash
end{CodeChunk}
\end_layout

\end_inset


\end_layout

\begin_layout Section*
Acknowledgments
\end_layout

\begin_layout Standard
Here you can write some acknowledgments.
\end_layout

\end_body
\end_document
