R Reporting Part 8: Using LaTeX to Create Posters

This is the eigth of a series of articles on how to use R, RStudio and TexMaker to prepare presentations and batch jobs for automated reporting on a web server or Microsoft SharePoint server. The series is based upon the presentation that I did at the February 27, 2016 Dallas R User Group Meetup. Because the presentation was primarily a demonstration, there really isn’t a presentation to distribute; this series covers the topics from the presentation/demonstration. The series will eventually include the following articles as I complete them over the next couple of weeks:

The series of articles describes the process for daily batch jobs that generate the Daily Econometric Graphs web page which includes links to the same econometric charts in several formats, all generated through the same R code:

All of the examples are based upon the knitr R package; you should reference the knitr documentation, as this article is not a replacement for the knitr documentation.

Example source is available in images/documents/econometric_source.zip.

LaTeX Poster Styles

Because LaTeX was written by and for academics and professionals in math and science who need to create posters for conferences and other displays, several authors have created LaTeX packages to make it easy to create posters. Here are a few of the major packages:

Baposter from Brian Amberg is easy to use but has a relatively fixed display style.
Beamerposter uses Beamer style operations.
A0poster is perhaps the most flexible of the various poster packages, but with flexibility comes some complexity.

The example that follows will use BAposter, as it is probably the easiest to get working. The example poster is a PDF file Useful Econometrics Poster.

BAPoster Example

The code for the example poster uses the knitr chunk syntax discussed earlier in this series of articles in R Reporting Part 3: Using Rhtml for Batch Web Reporting and set up using the read_chunk("econometric_charts_chunks.R") call in the prologue of the LaTeX/knitr file:


<<prolog,message=FALSE,echo=FALSE,error=FALSE,warning=FALSE,dev=c('pdf','png','jpeg')>>=
#install.packages(c("dplyr","magrittr","assertr","ggvis","googleVis","htmlwidgets","networkD3","rCharts","qtlcharts","dygraphs","d3heatmap"))
require(ggplot2)
require(dplyr)
require(magrittr)
require(assertr)
require(ggplot2)
require(fImport)
require(reshape2)
require(scales)
require(knitr)
#library(RCurl)

setwd("~/svn_work/Consulting_Business/web_site/articles/econometric_charts/src/R")
options('download.file.method'='wget')
read_chunk("econometric_charts_chunks.R")

@
\documentclass[a0paper,portrait]{baposter}
\usepackage{color}
\definecolor{mssDeepBlue}{rgb}{0.1367188,0.375,0.5742188} % new RGB values
\definecolor{mssCyan}{rgb}{0.0,0.6210938,0.8515625}
\definecolor{mssGreen}{rgb}{0.4101562,0.7421875,0.15625}

\definecolor{mssCyanLight}{rgb}{0.0,0.3105469,0.4257812}


\usepackage{hyperref}
\usepackage{hyperxmp}
\usepackage{ifplatform}
%
%
%
\ifwindows 
   \newcommand{\mssPathDef}{C:/Users/bwmoore/Documents} 
\else
  \newcommand{\mssPathDef}{/home/bwmoore} 
\fi

\begin{document}
\background{}
\begin{poster}{
   background=none,
   colspacing=0.7em,
   textborder=roundedleft,
   headerborder=none,
   headershape=roundedright,
   headerheight=0.134\textheight,% this defines height of box reserved for title, name, etc.
   %another declarations
}
{}
{Useful Econometrics}
{Bruce Moore \\
Moore Software Services LLC \\
Coppell, TX  USA \\
moorebw@mooresoftwareservices.com}
{ \includegraphics[width=7cm,angle=0]{"/home/bwmoore/svn_work/Consulting_Business/VG_Visuals/Dropbox/LOGOS/Logo - Tagline Below/MOORE LOGO Tagline"}}
\setlength\parindent{24pt}
%
%
%
%
%
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Column 1
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\headerbox{Purpose}{name=purpose,column=0,borderColor=mssDeepBlue,headerColorOne=mssDeepBlue,headerColorTwo=mssDeepBlue,boxshade=none,headerFontColor=white}{

\paragraph{}This poster provides example econometrics to demonstrate using RStudio to generate a poster.
}
%
% Column 1 Box 2
%
\headerbox{Data Source}{name=dataSource,column=0,below=purpose,borderColor=mssDeepBlue,headerColorOne=mssDeepBlue,headerColorTwo=mssDeepBlue,boxshade=none,headerFontColor=white}{
\paragraph{}The data for this poster was pulled from the St. Louis Federal Reserve FRED2 system using the fImport R package.

\paragraph{}The poster uses the \LaTeX\ \href{http://www.brian-amberg.de/uni/poster/}{BAposter} package and was composed in RStudio and generated using the knitr R package.  It was formatted for A0 printing (33.11 by 46.81 inches), although BAposter supports other page sizes.

\paragraph{}Lists use the normal \LaTeX\ list itemize environment.  For example, the data series used in this poster are

\begin{itemize}
\item Swap rates
\item Used Car and Rruck Consumer Price Index
\item Median Household Income
\item Unemployment Rate
\item Mortgage Delinquency
\end{itemize}
}
%
% Column 1 Box 3
%
\headerbox{Contact Information}{name=contact,column=0,below=dataSource,borderColor=mssDeepBlue,headerColorOne=mssDeepBlue,headerColorTwo=mssDeepBlue,boxshade=none,headerFontColor=white}{
  \begin{center}
  Bruce Moore \\
  bwmoore@mooresoftwareservices.com \\
  +1 (972) 652-0254 \\
  \includegraphics[width=.27\textwidth]{"/home/bwmoore/svn_work/Consulting_Business/sales_presentations/business_cards/images/bwmoore_tiny"}
  \end{center}
}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Column 2
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\headerbox{Cost of Funds}{name=costOfFunds,column=1,span=2,borderColor=mssDeepBlue,headerColorOne=mssDeepBlue,headerColorTwo=mssDeepBlue,boxshade=none,headerFontColor=white}{
<< costOfFunds,echo=FALSE,message=FALSE,warning=FALSE,error=FALSE,pdf.compress=TRUE,eval=TRUE,fig.path="images/figures/",dev=c("png","pdf","svg"),fig.width=6,fig.height=3,dpi=200>>=
@
%\includegraphics[width=\linewidth]{\mssPathDef/svn_work/Consulting_Business/web_site/articles/econometric_charts/src/R/images/figures/costOfFunds-1.png}

}
%
% Column 2 Box 2
%
\headerbox{Auto CPI}{name=autoCPI,column=1,below=costOfFunds,boxheaderheight=1.0cm,borderColor=mssDeepBlue,headerColorOne=mssDeepBlue,headerColorTwo=mssDeepBlue,boxshade=none,headerFontColor=white}{
<< autoCPI,echo=FALSE,message=FALSE,warning=FALSE,error=FALSE,pdf.compress=TRUE,eval=TRUE,fig.path="images/figures/",dev=c("png","pdf","svg")>>=
@
}
%
% Column 2 Box 3
%
\headerbox{Mortgage Delinquency}{name=mortDelinquncy,column=1,below=autoCPI,boxheaderheight=1.0cm,borderColor=mssDeepBlue,headerColorOne=mssDeepBlue,headerColorTwo=mssDeepBlue,boxshade=none,headerFontColor=white}{
<< mortDelinquency,echo=FALSE,message=FALSE,warning=FALSE,error=FALSE,pdf.compress=TRUE,eval=TRUE,fig.path="images/figures/",dev=c("png","pdf","svg")>>=
@
}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Column 3
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Column 3 Box 2
%
\headerbox{Median Household Income}{name=medianHouseholdIncome,column=2,below=costOfFunds,boxheaderheight=1.0cm,borderColor=mssDeepBlue,headerColorOne=mssDeepBlue,headerColorTwo=mssDeepBlue,boxshade=none,headerFontColor=white}{
<< medianHouseholdIncome,echo=FALSE,message=FALSE,warning=FALSE,error=FALSE,pdf.compress=TRUE,eval=TRUE,fig.path="images/figures/",dev=c("png","pdf","svg")>>=
@
}
%
% Column 3 Box 3
%
\headerbox{Unemployment}{name=unemployment,column=2,below=medianHouseholdIncome,boxheaderheight=1.0cm,borderColor=mssDeepBlue,headerColorOne=mssDeepBlue,headerColorTwo=mssDeepBlue,boxshade=none,headerFontColor=white}{
<< medianHouseholdIncome,echo=FALSE,message=FALSE,warning=FALSE,error=FALSE,pdf.compress=TRUE,eval=TRUE,fig.path="images/figures/",dev=c("png","pdf","svg")>>=
@
}


\end{poster}
\end{document}

Set Up Defaults

The first step is to set the various global parameters for the poster, for complete information on the various options, see the BAPoster documentation.


\background{}
\begin{poster}{
   background=none,
   colspacing=0.7em,
   textborder=roundedleft,
   headerborder=none,
   headershape=roundedright,
   headerheight=0.134\textheight,% this defines height of box reserved for title, name, etc.
   %another declarations
}
{}
{Useful Econometrics}
{Bruce Moore \\
Moore Software Services LLC \\
Coppell, TX  USA \\
This email address is being protected from spambots. You need JavaScript enabled to view it.}
{ \includegraphics[width=7cm,angle=0]{"/home/bwmoore/svn_work/Consulting_Business/VG_Visuals/Dropbox/LOGOS/Logo - Tagline Below/MOORE LOGO Tagline"}}
\setlength\parindent{24pt}

The bracket pairs contain the following:

The first bracket pair contains the key value options that set up the block shapes and other parameters
The second bracket pair contains the eyecatcher text; this is not used on this poster
The third bracket pair contains the poster title
The fourth bracket pair contains the poster authors
The final bracket pair contains the logo or header graphic for the poster

Creating a Text Box for a Single Column

BAPoster uses the headerbox tag to generate each box on the poster:


\headerbox{Purpose}{name=purpose,column=0,borderColor=mssDeepBlue,headerColorOne=mssDeepBlue,headerColorTwo=mssDeepBlue,boxshade=none,headerFontColor=white}{

\paragraph{}This poster provides example econometrics to demonstrate using RStudio to generate a poster.
}

The bracket pairs on the tag are as follows:

The first bracket pair contains the text for the heading
The second bracket pair contains the keywords for the tag, including these important tags:

name is required and is needed to establish the relative position of boxes within a column.
column is required to determine in which column the box should be placed
borderColor and the other keywords are optional but will be used in almost all cases.

The third bracket pair contains the text for the box. This can include any LaTeX tags for tables, lists, math, as long as the output will fit on the poster.

Creating the Second Text Box in a Column

The second and subsequent text boxes in a column are identical to the first but must have a below keyword to reference the text box that is immediately above:


\headerbox{Data Source}{name=dataSource,column=0,below=purpose,borderColor=mssDeepBlue,headerColorOne=mssDeepBlue,headerColorTwo=mssDeepBlue,boxshade=none,headerFontColor=white}{
\paragraph{}The data for this poster was pulled from the St. Louis Federal Reserve FRED2 system using the fImport R package.

\paragraph{}The poster uses the \LaTeX\ \href{http://www.brian-amberg.de/uni/poster/}{BAposter} package and was composed in RStudio and generated using the knitr R package.  It was formatted for A0 printing (33.11 by 46.81 inches), although BAposter supports other page sizes.

\paragraph{}Lists use the normal \LaTeX\ list itemize environment.  For example, the data series used in this poster are

\begin{itemize}
\item Swap rates
\item Used Car and Rruck Consumer Price Index
\item Median Household Income
\item Unemployment Rate
\item Mortgage Delinquency
\end{itemize}
}

Creating a Text Box that Spans Columns

To emphasize a point, it will frequently be useful to create a text box that spans columns, as is done in the “Cost of Funds” block on this poster using the span keyword:


\headerbox{Cost of Funds}{name=costOfFunds,column=1,span=2,borderColor=mssDeepBlue,headerColorOne=mssDeepBlue,headerColorTwo=mssDeepBlue,boxshade=none,headerFontColor=white}{
<< costOfFunds,echo=FALSE,message=FALSE,warning=FALSE,error=FALSE,pdf.compress=TRUE,eval=TRUE,fig.path="images/figures/",dev=c("png","pdf","svg"),fig.width=6,fig.height=3,dpi=200>>=
@
}

This text box incorporates R code that will be evaluated by the knitr package. knitr does not know the size of the LaTeX text box, so you will probably want to use the fig.width and fig.height keywords for the chunk to set the relative dimensions that you want for any graphics so that the proportions match what you need in the text box.

Details: Written by Bruce Moore; Published: 19 April 2016; Created: 19 April 2016; Last Updated: 10 May 2016; Hits: 3696

R Reporting Part 7: Converting R Documents to E-books

This is the seventh of a series of articles on how to use R, RStudio and TexMaker to prepare presentations and batch jobs for automated reporting on a web server or Microsoft SharePoint server. The series is based upon the presentation that I did at the February 27, 2016 Dallas R User Group Meetup. Because the presentation was primarily a demonstration, there really isn’t a presentation to distribute; this series covers the topics from the presentation/demonstration. The series will eventually include the following articles as I complete them over the next couple of weeks:

All of the examples are based upon the knitr R package; you should reference the knitr documentation, as this article is not a replacement for the knitr documentation.

Example source is available in images/documents/econometric_source.zip.

Software Required

Creating epub files requires software that converts from html to epub format. Calibre is the one of the better open source tools for e-book generation and management. It is available for Linux, Windows and OS X. For converting LaTeX files to epub, it is necessary to create an HTML file as an intermediate step. There are several tools to do this; Latex2html is one of the tools that can do this and is arguably the best, but it is not being actively maintained. The LaTeX to HTML FAQ has a list of alternatives.

In looking at alternatives, it is helpful to use one that does not generate pages with headers and footers, as these can create problems during the epub generation process.

Creating an E-book from Rhtml

The first step in creating an E-book is to create an HTML file as input to the process. You can generate the document as the output from running an .RHTML or by using one of several utilities for converting LaTeX files to HTML. The script below is a very simplified script to generate an epub. For simplicity, error checking and recovery are omitted:


#!/bin/bash
echo $HOME
cd ~/svn_work/Consulting_Business/web_site/articles/econometric_charts/src/R
#
# Run RScript and knitr to generate the HTML file
#
/usr/bin/Rscript -e "require('knitr'); knit('econometric_charts_home_page.Rhtml')"
#
# Compress images
#
optipng images/figures/*.png
optipng *.png
#
# Use Calibre ebook-convert to convert the HTML file to an epub file
#
ebook-convert econometric_charts_home_page.html .epub --authors "Bruce Moore" --language en --no-default-epub-cover
#
# Upload to the web site
#
cd ~/svn_work/Consulting_Business/web_site/articles/econometric_charts/src/R
scp -i /home/batchuser/.ssh/webuser econometric_charts_home_page_article/econometric_charts_home_page_article.epub This email address is being protected from spambots. You need JavaScript enabled to view it.:/home/webuser/www/images/documents/

Run RScript and Knitr

The first section of the script calls Rscript to run R from the command line and pass two statements. The first is require('knitr') while the second is to knit() the Rhtml file which runs all of the R code and creates an HTML file.


#
# Run RScript and knitr to generate the HTML file
#
/usr/bin/Rscript -e "require('knitr'); knit('econometric_charts_home_page.Rhtml')"

Compress Images

The second segment uses optipng to compress the .png images that are created as graphics when running the Rhtml file:


#
# Compress images
#
optipng images/figures/*.png
optipng *.png

Ebook-convert

The third segment uses the ebook-convert program from Calibre to create the epub file. There are numerous options for the ebook-convert command but the --authors, --language and --no-default-epub-cover options are a minimal set. The first two are self explainatory and are useful for all files. The --no-default-epub-cover option is useful for input files that have content that generates a good cover page, or where no cover page is needed.


#
# Use Calibre ebook-convert to convert the HTML file to an epub file
#
ebook-convert econometric_charts_home_page.html .epub --authors "Bruce Moore" --language en --no-default-epub-cover

Upload to Server

The final segment is a command to upload files to a web server or other server. In this case, the scp secure copy command is used. In this use, it is assumed that public key authentication has previously been configured. The -i option is not normally needed for interactive use, but is necessary for reliable use under cron. The -i option points to the private key file to be used for authentication.


#
# Upload to the web site
#
cd ~/svn_work/Consulting_Business/web_site/articles/econometric_charts/src/R
scp -i /home/batchuser/.ssh/webuser econometric_charts_home_page_article/econometric_charts_home_page_article.epub This email address is being protected from spambots. You need JavaScript enabled to view it.:/home/webuser/www/images/documents/

Converting LaTeX to Epub

When using a LaTeX input file, there is one additional step in between the RScript and ebook-convert segments. Option -split +0 causes the output to be placed into a single HTML file rather than splitting it into files based upon sections.


#
# Generate the epub version of the article
#
latex2html -split +0 econometric_charts_home_page_slides.tex

Details: Written by Bruce Moore; Published: 18 April 2016; Created: 18 April 2016; Last Updated: 10 May 2016; Hits: 2266

R Reporting Part 5: Using LaTeX/Beamer for PDF Presentations

This is the fifth of a series of articles on how to use R, RStudio and TexMaker to prepare presentations and batch jobs for automated reporting on a web server or Microsoft SharePoint server. The series is based upon the presentation that I did at the February 27, 2016 Dallas R User Group Meetup. Because the presentation was primarily a demonstration, there really isn’t a presentation to distribute; this series covers the topics from the presentation/demonstration. The series will eventually include the following articles as I complete them over the next couple of weeks:

All of the examples are based upon the knitr R package; you should reference the knitr documentation, as this article is not a replacement for the knitr documentation.

Example source is available in images/documents/econometric_source.zip.

Using Rnw for LaTeX/Beamer Presentations

LaTeX’s Beamer presentations allow easy use of math symbols, cross referencing, citation, and a create presentation table of contents. To create a LaTeX/Beamer presentation create an .Rnw file as shown in Figure 1. RStudio will populate the file with the basic LaTeX tags as shown in Figure 2, but for a Beamer presentation, you can probably start with something like the tags in Figure 3.

Creating an Rhtml file in RStudio — Figure 1. Create the .Rnw file in RStudio.

Figure 2. Default LaTeX stub in RStudio.


\documentclass{article}

\begin{document}




\end{document}

Figure 3. Basic Beamer presentation file with title page


\documentclass{beamer}
\title[Selected Econometrics]{Selected Econometrics for \today}
\subject{Selected Econometrics for \today}
%\copyright{Copyright \copyright 2014 by Moore Software Services, LLC.  All rights reserved.}
\author[Bruce Moore]{Bruce Moore, DEng}
\institute[Moore Software Services]{Moore Software Services, LLC\\
P.O. Box 183\\
Coppell, TX  75019\\
(972) 652-0254\\
\texttt{This email address is being protected from spambots. You need JavaScript enabled to view it.} \\
\texttt{www.mooresoftwareservices.com} \\
}



\date{\today}
\begin{document}

%
% Titlepage
%
\begin{frame}[plain]
 \titlepage
\end{frame}
%\SweaveOpts{concordance=TRUE}
\section{Swap}
%
%
%
\begin{frame}[fragile]{Heading for slide 1}
\begin{itemize}
\item Item 1
\item Item 2
\end{itemize}
\end{frame}




\end{document}

Call all Needed Libraries in the Prologue knitr Chunk

Next, add the "prologue" in the file where all of the required R libraries are included and options are set:


<<prologue,message=FALSE,echo=FALSE,error=FALSE,warning=FALSE>>=
#install.packages(c("dplyr","magrittr","assertr","ggvis","googleVis","htmlwidgets","networkD3","rCharts","qtlcharts","dygraphs","d3heatmap"))
require(ggplot2)
require(dplyr)
require(magrittr)
require(assertr)
require(ggplot2)
require(fImport)
require(reshape2)
require(scales)
#library(RCurl)

setwd("~/svn_work/Consulting_Business/web_site/articles/econometric_charts/src/R")
options('download.file.method'='wget')
read_chunk("econometric_charts_chunks.R")

@

It does not matter where you put this as long as it occurs before the first slide that uses R to generate the output. All of this should be familiar except for the lines


options('download.file.method'='wget')
read_chunk("econometric_charts_chunks.R")

The options line changes the download method used by the Rcurl package (a dependency loaded by fImport) to one that works on my Linux machine, as the default download method does not work on my machine. The read_chunk line is the one that is important for including code into Markdown presentations and reports.

When you create an R report that will be compiled by knitr, you can either put the code inline, or create it in a separate .R file that can be called from multiple .Rhtml, .Rmd, .RPres or .Rnw files; knitr reads these chunks from the file specified in the read_chunk("filename.R") call at the beginning of your .Rhtml or .Rnw file. From a re-use perspective, the chunk method is very helpful.

“Prologue” is not a reserved word nor does knitr require this label; this is just a personal standard for all of the .Rhtml and .Rnw files that I create.

Writing the Knitr Chunk File econometric_charts_chunks.R With an Interactive Graphic

The previous articles in this series talk about how to create the chunk file for reuse; see R Reporting Part 4: Using Markdown for Presentations for instructions on creating the chunk file.

Create a Slide and Call an R Chunk to Create a Graphic

Once the chunk file is ready, you can call it from your Beamer presentation:


%
%
%
\begin{frame}[fragile]{Swap rates are a useful proxy for top-of-market CD rates and for transfer prices}
<<costOfFunds,message=FALSE,echo=FALSE,error=FALSE,warning=FALSE,fig.path="images/figures",out.height='0.6\\textheight'>>=
@
\footnote{Board of Governors of the Federal Reserve System (US), 1-Year Swap Rate [MSWP1], 2-Year Swap Rate [MSWP2], 3-Year Swap Rate [MSWP3], and 5-Year Swap Rate [MSWP5] retrieved from FRED, Federal Reserve Bank of St. Louis \url{https://research.stlouisfed.org/fred2/series/series_name}, \today.}
\end{frame}

Adding the Epilog

Finally, if there are things that you want to do after the R code for your graphics run and before pdflatex runs, add a epilogue to run additional commands. This is a personal coding practice and is not a standard or requirement. I usually run optipng or some other image compression utility as the last step in all of my Rhtml, Rmd and Rnw files:


<<epilogue,message=FALSE,echo=FALSE,error=FALSE,warning=FALSE,fig.path="images/figures",out.width='\\textwidth',out.height='0.8\\textheight'>>=
system('optipng images/figures/*.png')
@

Running `knitr` to Generate the HTML File

The final step is to run knitr to process the file; to do this, click on the “Knit” icon at the top of the active tab in RStudio, as shown in Figure 2:

Running knitr in RStudio to generate a PDF file from the Rnw source file — Figure 4. Running `knitr` to generate the PDF file and all figures.

The output from this will be a PDF file that you can view on any machine without any dependencies. You cannot do interactive visualizations in Beamer.

Details: Written by Bruce Moore; Published: 06 April 2016; Created: 06 April 2016; Last Updated: 10 May 2016; Hits: 3389

R Reporting Part 6: Using LaTeX for PDF Articles

This is the sixth of a series of articles on how to use R, RStudio and TexMaker to prepare presentations and batch jobs for automated reporting on a web server or Microsoft SharePoint server. The series is based upon the presentation that I did at the February 27, 2016 Dallas R User Group Meetup. Because the presentation was primarily a demonstration, there really isn’t a presentation to distribute; this series covers the topics from the presentation/demonstration. The series will eventually include the following articles as I complete them over the next couple of weeks:

All of the examples are based upon the knitr R package; you should reference the knitr documentation, as this article is not a replacement for the knitr documentation.

Example source is available in images/documents/econometric_source.zip.

Using Rnw for LaTeX/Beamer Presentations

LaTeX’s For most true automated reporting requirements, LaTex offers some very useful capabilities:

Table of Contents
List of Figures
Footnotes, in-line citations and automated bibliography for data references
Indexing

To create a LaTeX article, create an .Rnw file as shown in Figure 1. RStudio will populate the file with the basic LaTeX tags as shown in Figure 2, but for a more realistic document, you can probably start with something like the tags in Figure 3.

Figure 2. Default LaTeX stub in RStudio.


\documentclass{article}

\begin{document}




\end{document}

Figure 3. Basic LaTeX article with title page, Table of Contents and


\documentclass{article}         %% Print version for presentation
%
% Printing options
%
\usepackage[]{tikz}
\usepackage{hyperref}
\usepackage{hyperxmp}
\usepackage{multimedia}   % allows video?
\usepackage{ifplatform}
\usepackage{verbatim}
\usepackage{endnotes}
%\let\enotesize=\tiny
%\let\footnote=\endnote
%
% Determine the OS and set the path prefix
% Note that \iflinux always retURs false unless shell escape is enabled
%

\ifwindows 
   \newcommand{\mssPathDef}{C:/Users/bwmoore/Documents} 
\else
  \newcommand{\mssPathDef}{/home/bwmoore} 
\fi
%\iflinux
%\fi
%
%
\hypersetup{
   pdfcopyright={Copyright \copyright \the\year by Moore Software Services, LLC.  All rights reserved.}
   pdfsubject={}
   }

%
%
%
\begin{document}
\begin{titlepage}
\begin{center}
\begin{huge}
\textbf{Selected Econometrics for \today} \\
\end{huge}
Bruce Moore, DEng \\
Moore Software Services, LLC \\
P.O. Box 183\\
Coppell, TX  75019\\
(972) 652-0254\\
\texttt{This email address is being protected from spambots. You need JavaScript enabled to view it.} \\
\href{https://www.mooresoftwareservices.com}{www.mooresoftwareservices.com} \\
%\includegraphics[height=\textheight]{\mssPathDef/svn_work/Consulting_Business/VG_Visuals/IncludeLogos/MOORE_LOGO_Tagline.pdf}
\includegraphics[width=\textwidth]{\mssPathDef/svn_work/Consulting_Business/VG_Visuals/IncludeLogos/MOORE_LOGO_Tagline.png}
\includegraphics[scale=3.0]{\mssPathDef/svn_work/Consulting_Business/sales_presentations/business_cards/images/bwmoore_d600.png}

\end{center}
\end{titlepage}
\tableofcontents
\listoffigures


\end{document}

Figure 3 has an example of how to prepare all of the major items in a large document, but this is just touching the tip of the iceberg on what can be done with LaTeX. The main unusual feature in this example is the /ifwindows segment; this sets up a variable with a path structure for my windows laptop or my Ubuntu desktop, so that I can work on the files on either machine.

For more information on LaTeX tags, read one or more of the following tutorials and books:

Beginning LaTeX at Cornell University
LaTeX Tutorial at Rensselaer Polytechnic Institute
LaTeX Documentation at the LaTeX project

Call all Needed Libraries in the Prologue knitr Chunk

Next, add the "prologue" in the file where all of the required R libraries are included and options are set:


<<prologue,message=FALSE,echo=FALSE,error=FALSE,warning=FALSE>>=
#install.packages(c("dplyr","magrittr","assertr","ggvis","googleVis","htmlwidgets","networkD3","rCharts","qtlcharts","dygraphs","d3heatmap"))
require(ggplot2)
require(dplyr)
require(magrittr)
require(assertr)
require(ggplot2)
require(fImport)
require(reshape2)
require(scales)
#library(RCurl)

setwd("~/svn_work/Consulting_Business/web_site/articles/econometric_charts/src/R")
options('download.file.method'='wget')
read_chunk("econometric_charts_chunks.R")

@

It does not matter where you put this as long as it occurs before the first slide that uses R to generate the output. All of this should be familiar except for the lines


options('download.file.method'='wget')
read_chunk("econometric_charts_chunks.R")

“Prologue” is not a reserved word nor does knitr require this label; this is just a personal standard for all of the .Rhtml and .Rnw files that I create.

Writing the Knitr Chunk File econometric_charts_chunks.R With an Interactive Graphic

The previous articles in this series talk about how to create the chunk file for reuse; see R Reporting Part 4: Using Markdown for Presentations for instructions on creating the chunk file.

Create a Section in the Article and Call an R Chunk to Create a Graphic

Once the chunk file is ready, you can call it from your article:


\section{Pricing}
There are several econometric series available on the St. Louis Federal Reserve System FRED2 web site that are useful in setting prices for loans and deposits.  This section contains plots of recent downloads of common series from FRED2.
\subsection{Swap Rates}
Swap rates are a useful proxy for top-of-market CD rates and for transfer prices, since an institution can both borrow and deposit funds at approximately the swap rate.  Rational institutions with access to markets rarely go significantly higher than the swap rate.  Typically, wholesale funders like the Federal Home Loan Bank (FHLB) offer rates that are generally about 50 basis points higher than the swap rate; it is very unusual for an institution to gather deposits at rates above these rates.
<<costOfFunds,message=FALSE,echo=FALSE,error=FALSE,warning=FALSE,fig.path="images/figures",fig.cap="Swap rates are a useful proxy for top-of-market CD rates and for transfer prices.",dev=c('pdf','png','jpeg')>>=
@
\footnote{Board of Governors of the Federal Reserve System (US), 1-Year Swap Rate [MSWP1], 2-Year Swap Rate [MSWP2], 3-Year Swap Rate [MSWP3], and 5-Year Swap Rate [MSWP5] retrieved from FRED, Federal Reserve Bank of St. Louis \url{https://research.stlouisfed.org/fred2/series/series_name}, \today.}

%
%
%
\newpage
\section{Severity of Loss}
This section contains plot of econometrics that are useful in forecasting the severity of loss when a loss occurs on loan products.
\subsection{CPI for Used Cars and Trucks}
The CPI for Used Cars and Trucks is useful in forecasting the severity of loss for auto loans.  As the index increases, the severity of loss will decrease, while a decreasing index will potentially cause an increase in the severity of loss.  Understanding the seasonality in the index can help in decision making on whether to hold a vehicle in inventory for one or two months to get a better price at auction or to sell the vehicle as quickly as possible during periods when the market is expected to decline.
<<autoCPI,message=FALSE,echo=FALSE,error=FALSE,warning=FALSE,fig.path="images/figures",fig.cap="The CPI for Used Cars and Trucks is useful in forecasting the severity of loss for auto loans.",dev=c('pdf','png','jpeg')>>=
@
\footnote{US. Bureau of Labor Statistics, Consumer Price Index for All Urban Consumers: Used cars and trucks [CUUR0000SETA02], retrieved from FRED, Federal Reserve Bank of St. Louis \url{https://research.stlouisfed.org/fred2/series/CUUR0000SETA02}, \today.}

Adding Mid-sentence R Output

If you are preparing a report that will have to be re-run with new data on a regular basis, you may want to use number generated by R in the report. Knitr (or Sweave) make this easy using the \Sexpr{} tag. In most cases, you will want to use the round or format functions to limit the number of digits. The I() function is mainly useful for Rhtml files, where it removes a code-like font; this is included here only because you may run across it in files that have been converted from .Rhtml to .Rnw.


\section{Summary}
<<sumP,message=FALSE,echo=FALSE,error=FALSE,warning=FALSE,fig.path="images/figures",fig.cap="Mortgage Delinquency is useful in forecasting frequency of loss.",dev=c('pdf','png','jpeg')>>=
swpTs<-fredSeries(c("MSWP5","MSWP3","MSWP2","MSWP1"),nDaysBack=365*10,to=Sys.timeDate())
swpTs$dateVal = as.Date(rownames(swpTs))


swpDf <- data.frame(swpTs)
swpDf$dateVal <- as.character(swpDf$dateVal)   # melt doesn't work with Date data types
swpDf$dateVal <- as.Date(swpDf$dateVal)        # ggplot's scale_x_date doesn't work with character data types
colnames(swpDf)[2] <- "Series"

max5year <- mean(swpDf$MSWP5)
max1year <- mean(swpDf$MSWP1)
summary(swpDf)
@
There are several different ways to format output for in-line R:
\begin{itemize}
\item The mean rate in the 5-year swap series is \Sexpr{mean(swpDf$MSWP5)}.
\item The mean rate in the 5-year swap series is \Sexpr{round(mean(swpDf$MSWP5),2)}.
\item The mean rate in the 5-year swap series is \Sexpr{format(round(mean(swpDf$MSWP5),2), nsmall=0)}.
\item The mean rate in the 5-year swap series is \Sexpr{I(format(round(mean(swpDf$MSWP5),2), nsmall=0))}.
\end{itemize}

Adding the Epilogue


<<epilogue,message=FALSE,echo=FALSE,error=FALSE,warning=FALSE,fig.path="images/figures",out.width='\\textwidth',out.height='0.8\\textheight'>>=
system('optipng images/figures/*.png')
@

Running `knitr` to Generate the HTML File

The final step is to run knitr to process the file; to do this, click on the “Knit” icon at the top of the active tab in RStudio, as shown in Figure 2:

The output from this will be a PDF file that you can view on any machine without any dependencies. You cannot do interactive visualizations in Beamer.

Details: Written by Bruce Moore; Published: 07 April 2016; Created: 07 April 2016; Last Updated: 10 May 2016; Hits: 2814

R Reporting Part 4: Using Markdown for Presentations

This is the fourth of a series of articles on how to use R, RStudio and TexMaker to prepare presentations and batch jobs for automated reporting on a web server or Microsoft SharePoint server. The series is based upon the presentation that I did at the February 27, 2016 Dallas R User Group Meetup. Because the presentation was primarily a demonstration, there really isn’t a presentation to distribute; this series covers the topics from the presentation/demonstration. The series will eventually include the following articles as I complete them over the next couple of weeks:

All of the examples are based upon the knitr R package; you should reference the knitr documentation, as this article is not a replacement for the knitr documentation.

Example source is available in images/documents/econometric_source.zip.

Using Rmd for Interactive Presentations

The first step in creating the interactive presentation is to create the .Rmd file in RStudio as shown in Figure 1. RStudio will prompt you for the output type as shown in Figure 2, where there are three choices:

HTML (ioslides)–this type allows interactive graphics and math markup (using MathJax). The math markup is not portable to other machines unless the machine has either an Internet connection or has MathJax installed.
HTML (Slidy)–this type allows interactive graphics and math markup (using MathJax). The math markup is not portable to other machines unless the machine has either an Internet connection or has MathJax installed.
PDF (Beamer)–this type does not allow interactive graphics and math markup (using LaTeX). The math markup in the PDF file is portable to other machines.

You can change the output type later if you want.

Modify the Title and Other Header Information

The first step is to modify the header information in the Markdown file to set the title, author, output type and footer. The snippet below shows the major header settings that you are likely to need for a basic presentation. The incremental setting allows you to step through the bullet points in a presentation. The use of “:” and indention in the header is syntactically important; the “:” is a line end terminator.


---
title: "Using RStudio for Presentations and Reports" 
author: "Bruce Moore" 
date: "February 26, 2016" 
output: 
  ioslides_presentation:
    incremental: true  
    footer: "Bruce Moore, Moore Software Services" 
---

The Markdown Reference Guide has complete information on the options that you can include in the header.

Call all Needed Libraries in the Prologue knitr Chunk

Next, add the "prologue" in the file where all of the required R libraries are included and options are set:


‘‘‘{r,prologue,message=FALSE,echo=FALSE,error=FALSE,warning=FALSE}
require(ggplot2)
require(dplyr)
require(magrittr)
require(assertr)
require(ggplot2)
require(fImport)
require(reshape2)
require(scales)
require(googleVis)
#library(RCurl)

setwd("~/svn_work/Consulting_Business/web_site/articles/econometric_charts/src/R")
options('download.file.method'='wget')
read_chunk("econometric_charts_chunks.R")
‘‘‘

All of this should be familiar except for the lines


options('download.file.method'='wget')
read_chunk("econometric_charts_chunks.R")

“Prologue” is not a reserved word nor does knitr require this label; this is just a personal standard for all of the .Rhtml and .Rnw files that I create.

Create a Slide and call the R Chunk to Generate the Graphic

The next step is to add the ## tag followed by the slide heading and other Markdown tags for a slide. This is followed by the knitr markup to call our code chunk from the econometric_charts_chunks.R file:


‘‘‘{r,  costOfFunds,fig.path="images/figures/",fig.width=7, fig.height=5,fig.dpi=100,message=FALSE,warning=FALSE,echo=FALSE,cache=FALSE}

‘‘‘

All R code in the .Rmd file must be enclosed with the knitr tags:


‘‘‘{r, }

and


‘‘‘

This is a special Markdown code delimiters that knitr looks uses to identify and run any R code that is enclosed. Most of the knitr options in this example are self explanatory, but the fig.path option requires some discussion. By default, knitr will create a figure directory in whatever the root directory is–your home directory unless you otherwise set it, as was done in the prologue section in this example.

Writing the Knitr Chunk File econometric_charts_chunks.R With an Interactive Graphic

The last step is to add the R code to the generate the interactive graphic to the econometric_charts_chunks.R so that knitr will generate the graphic. In the .R file, the costOfFundsInteractive


## ---- costOfFundsInteractive ----

label for the chuck must match the chunk label ## ---- costOfFundsInteractive ---- in the econometric_charts_chunks.R file:


## ---- costOfFundsInteractive ----
#
# Make the figure with swap rates
#
swpTs<-fredSeries(c("MSWP5","MSWP3","MSWP2","MSWP1"),nDaysBack=365*10,to=Sys.timeDate())
swpTs$dateVal = as.Date(rownames(swpTs))


swpDf <- data.frame(swpTs)
swpDf$dateVal <- as.Date(swpDf$dateVal)        # ggplot's scale_x_date doesn't work with character data types
colnames(swpDf)[2] <- "Series"

chart <- googleVis::gvisLineChart(data=swpDf
                                  ,xvar="dateVal",yvar=c("MSWP5","MSWP2","MSWP1")
                                  ,options=list(width=800,height=600,gvis.editor="Edit",title='Swap Rates'))
#plot(chart) # use this for console debugging
print(chart) # use this for output in Markdown

In the .Rmd file

## Interactive graphic ‘‘‘{r, costOfFundsInteractive,fig.path="images/figures/",message=FALSE,warning=FALSE,echo=FALSE,cache=FALSE,results='asis'} ‘‘‘

While debugging in the console, uncomment the plot command; for output in knitr use the plot statement.

Adding the Epilog

The final chunk in the presentation file is probably a good practice or perhaps a time saving measure but is not a requirement; an epilogue to run image compression on any image files that were created by the script:


‘‘‘{r, epilogue,echo=FALSE,message=FALSE,warning=FALSE,cache=FALSE}
system('optipng("images/figures/*.png")')
‘‘‘

The optipng utility compresses .png files and will improve the load time for your page. If you choose to generate .jpg or other file types, you can call other utilities to compress them.

Running `knitr` to Generate the HTML File

The final step is to run knitr to process the file; to do this, click on the “Knit” icon at the top of the active tab in RStudio, as shown in Figure 2:

Running knitr in RStudio to generate an HTML file from the Rhtml source file — Figure 4. Running `knitr` to generate the HTML file and all figures.

The output from this will be an HTML file that you can open in a browser. If you use interactive visualizations that depend upon libraries from the web, you may have problems running your presentation without an Internet connection, so make sure to test your presentation with networking turned off to understand what will and will not render or work.

Details: Written by Bruce Moore; Published: 30 March 2016; Created: 30 March 2016; Last Updated: 10 May 2016; Hits: 3249

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R Reporting Part 8: Using LaTeX to Create Posters

LaTeX Poster Styles

BAPoster Example

Set Up Defaults

Creating a Text Box for a Single Column

Creating the Second Text Box in a Column

Creating a Text Box that Spans Columns

R Reporting Part 7: Converting R Documents to E-books

Software Required

Creating an E-book from Rhtml

Run RScript and Knitr

Compress Images

Ebook-convert

Upload to Server

Converting LaTeX to Epub

R Reporting Part 5: Using LaTeX/Beamer for PDF Presentations

Using Rnw for LaTeX/Beamer Presentations

Call all Needed Libraries in the Prologue knitr Chunk

Writing the Knitr Chunk File econometric_charts_chunks.R With an Interactive Graphic

Create a Slide and Call an R Chunk to Create a Graphic

Adding the Epilog

Running knitr to Generate the HTML File

R Reporting Part 6: Using LaTeX for PDF Articles

Using Rnw for LaTeX/Beamer Presentations

Call all Needed Libraries in the Prologue knitr Chunk

Writing the Knitr Chunk File econometric_charts_chunks.R With an Interactive Graphic

Create a Section in the Article and Call an R Chunk to Create a Graphic

Adding Mid-sentence R Output

Adding the Epilogue

Running knitr to Generate the HTML File

R Reporting Part 4: Using Markdown for Presentations

Using Rmd for Interactive Presentations

Modify the Title and Other Header Information

Call all Needed Libraries in the Prologue knitr Chunk

Create a Slide and call the R Chunk to Generate the Graphic

Writing the Knitr Chunk File econometric_charts_chunks.R With an Interactive Graphic

Adding the Epilog

Running knitr to Generate the HTML File

Running `knitr` to Generate the HTML File

Running `knitr` to Generate the HTML File

Running `knitr` to Generate the HTML File