7 files changed, 172 insertions, 120 deletions
diff --git a/Master/texmf-dist/doc/latex/medstarbeamer/README.txt b/Master/texmf-dist/doc/latex/medstarbeamer/README.txt
index 1f5cc244ed6..7077e337176 100644
--- a/Master/texmf-dist/doc/latex/medstarbeamer/README.txt
+++ b/Master/texmf-dist/doc/latex/medstarbeamer/README.txt
@@ -1,44 +1,14 @@
 %%%%%%%%% MedStar Beamer Template %%%%%%%%%
 %%%%%%%% Written By: Anagha Kumar %%%%%
 %%%%%%%% License: lppl1.3  %%%%%%%%%%%%%%%%
+%%%%%%%% Version: 2015-11-12 %%%%%%%%%%%%%%%%
 
 % I wrote a beamer template for MedStar Health presentations. %% 
-%% I've included sample presentations using both .tex files and .rnw files%%
-%% The document class is obviously compatible with both %% 
-%% The advantage of the .rnw file is that it can be used with knitr such that you can weave your R code with your presentation %% 
+%% An example of how the slides would look is provided in example.tex %%%%%%%% 
 
-\NeedsTeXFormat{LaTeX2e}
-\ProvidesClass{medstarbeamer}
-\LoadClassWithOptions{beamer}
-\RequirePackage{anysize}
-\RequirePackage{hyperref}
-\RequirePackage{graphicx} 
-\RequirePackage{pgf} 
-\RequirePackage{xcolor}
-\RequirePackage{booktabs}
-\RequirePackage{soul}
-\RequirePackage{background} 
-\RequirePackage{cancel}
-\RequirePackage{amsmath} 
-\RequirePackage{enumerate}
+%%% I generated a separate style file (MedStarColors) %%% The user should download it as well as the .cls file
+%%%% % This is a helpful website: http://www.r-bloggers.com/create-your-own-beamer-template/
+% More information on colors available here: https://en.wikibooks.org/wiki/LaTeX/Presentations
 
-
-\usetheme{CambridgeUS} % for an extensive list of themes, this is a useful website: http://deic.uab.es/~iblanes/beamer_gallery/index_by_theme.html %
-\definecolor{citrine}{rgb}{0.89, 0.82, 0.04}
-\definecolor{coolblack}{rgb}{0.0, 0.18, 0.39}
-
-\usecolortheme{lily}
-\setbeamercolor{frametitle}{fg=white, bg=coolblack}
-\setbeamercolor{title}{fg=coolblack}
-\setbeamercolor{subtitle}{fg=coolblack}
-\setbeamercolor{palette primary}{fg=white, bg=coolblack} % controls the foreground and background colors for the strip at the bottom right 
-\setbeamercolor{palette secondary}{fg=white, bg=coolblack} % controls the foreground and background colors for the bottom left strip and the second strip at the top
-\setbeamercolor{palette tertiary}{fg=black, bg=citrine} %controls the foreground and background colors for the middle strip at the bottom and the top strip
-\useoutertheme{miniframes}
-\setbeamercolor{item}{fg=coolblack} %customizing the colors for the inner theme
-\logo{\includegraphics[ height=1cm, width=2cm]{medstarlogo}} %the size of the logo to be included in every frame
-
-\setbeamercovered{dynamic} %overlays appear faintly 
-\setbeamertemplate{navigation symbols}{}  % since I dislike the navigation symbols
-\setbeamertemplate{caption}[numbered] % since beamer does not number captions without setting this 
-\setbeamercolor{caption}{fg=coolblack}
-\ No newline at end of file
+%%% The beamer themes info lines and mini frames were useful resources to work off of though others can also be used %%% 
+%%% The two files (MedStarColors) and medstarbeamer.cls contain helpful comments to guide the user %%% 
diff --git a/Master/texmf-dist/doc/latex/medstarbeamer/example.tex b/Master/texmf-dist/doc/latex/medstarbeamer/example.tex
new file mode 100644
index 00000000000..67bb3658831
--- /dev/null
+++ b/Master/texmf-dist/doc/latex/medstarbeamer/example.tex
@@ -0,0 +1,51 @@
+\documentclass{medstarbeamer}
+\title[ Applied Bayesian Data Analysis]{Binary Response Regression and Model Selection}
+\institute[]{}
+\author[ Anagha Kumar]{Anagha Kumar}
+\date{August 26th, 2015} 
+\begin{document}
+
+\begin{frame} 
+\maketitle
+\end{frame}
+
+\sizecontentsoutline{2}
+\sizecontentscurrent{2}
+
+\section{The Problem of Interest}
+\begin{frame}{Dataset}
+\begin{enumerate}
+\item{The dataset used was from ``Survival Analysis - Techniques for Censored and Truncated Data".} 
+\item{It was a hypothetical study of the mortality experience of diabetics.}
+\item{30 diabetics were followed till death or the end of the study.}
+\item{The subject's age at entry into the study and the age at the end of the study or death were recorded.}
+\item{Rather than time to event analysis, I was interested in how ``entry age" and ``exit age", affected survival.} 
+\item{\alert{The response variable, survival, was binary (=1 if alive, =0 if dead).}}
+\end{enumerate}
+\end{frame}
+
+\section{New Section for Illustrative Purposes}
+\subsection{Does this work?}
+\subsubsection{This is an interesting example}
+\begin{frame}{Let's Try This Out}
+\end{frame}
+
+\section{Let's Try Another One}
+\subsection{Does this work as well?}
+\subsubsection{This is rather fun}
+\begin{frame}{Designing a custom color theme}
+\begin{itemize}
+\item{This is an interesting way of writing a beamer theme from scratch.}
+\end{itemize}
+\end{frame}
+
+
+\section{Let's Try Ansdsdsdsother One1}
+\subsection{Does this work as well111sdsds1?}
+\subsubsection{This is rather fu111sdsdsds111n}
+\begin{frame}{Designing a custom color theme}
+\begin{itemize}
+\item{This is an interesting way of writing a beamer theme from scratch.}
+\end{itemize}
+\end{frame}
+\end{document}
+\ No newline at end of file
diff --git a/Master/texmf-dist/doc/latex/medstarbeamer/medstarpresentation.Rnw b/Master/texmf-dist/doc/latex/medstarbeamer/medstarpresentation.Rnw
deleted file mode 100644
index 2f33e5935b1..00000000000
--- a/Master/texmf-dist/doc/latex/medstarbeamer/medstarpresentation.Rnw
+++ /dev/null
@@ -1,64 +0,0 @@
-\documentclass{medstarbeamer}
-\title[ Applied Bayesian Data Analysis]{Binary Response Regression and Model Selection}
-\author[ Anagha Kumar]{Anagha Kumar}
-\institute[MHRI]{\textit{MEDSTAR HEALTH RESEARCH INSTITUTE}}
-\date{August 26th, 2015} 
-\begin{document}
-
-\begin{frame} 
-\maketitle
-\end{frame}
-
-\begin{frame}{Table of Contents}
-\tableofcontents
-\end{frame}
-
-\section{The Problem of Interest}
-\begin{frame}{Dataset}
-\footnotesize{
-\begin{enumerate}
-\item{The dataset used was from ``Survival Analysis - Techniques for Censored and Truncated Data".} 
-\item{It was a hypothetical study of the mortality experience of diabetics. }
-\item{30 diabetics were followed till death or the end of the study.}
-\item{The subject's age at entry into the study and the age at the end of the study or death were recorded.}
-\item{Rather than time to event analysis, I was interested in how ``entry age" and ``exit age", affected survival.} 
-\item{The response variable, survival, was binary (=1 if alive, =0 if dead).}
-\item{The dataset contained no missing data.}
-\end{enumerate}
-}
-\end{frame}
-
-<<echo=FALSE, results='hide', warning=FALSE, message=FALSE>>= 
-options(repos = c(CRAN = "http://cran.rstudio.com"))
-install.packages("LearnBayes")
-library(LearnBayes)
-library(xtable)
-entry_age <- c(58, 58, 59, 60, 60, 61, 61, 62, 62, 62, 63, 63, 64, 66, 66, 67, 67, 67, 68, 69, 69, 69, 70, 70, 70, 71, 72, 72, 73, 73)
-exit_age <- c(60, 63, 69, 62, 65, 72, 69, 73, 66, 65, 68, 74, 71, 68, 69, 70, 77, 69, 72, 79, 72, 70, 76, 71, 78, 79, 76, 73, 80, 74)
-survive <- c(0, 0, 1, 0, 0, 1, 1, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 1, 1, 0, 0, 1, 0)
-@
-<<echo=FALSE, results='hide'>>= 
-table.entry_age <- t(table(entry_age))
-Xtable.entry_age <- xtable(table.entry_age, caption="Descriptive Statistics for Entry Age")
-table.exit_age <- t(table(exit_age))
-Xtable.exit_age <- xtable(table.exit_age, caption="Descriptive Statistics for Exit Age")
-table.survive <- t(table(survive))
-Xtable.survive <- xtable(table.survive, caption="Survival Counts")
-@
-\subsection{Exploratory Data Analysis}
-\begin{frame}{Descriptive Statistics}
-\tiny{
-<<echo=FALSE, results='asis'>>= 
-rownames(Xtable.entry_age) <- c("Counts")
-print(Xtable.entry_age, caption.placement="top", booktabs=TRUE, rownames=TRUE)
-rownames(Xtable.exit_age) <- c("Counts")
-print(Xtable.exit_age, caption.placement="top", booktabs=TRUE, rownames=TRUE)
-@
-<<echo=FALSE, results='asis'>>= 
-rownames(Xtable.survive) <- c("Counts")
-print(Xtable.survive, caption.placement="top", booktabs=TRUE, rownames=TRUE)
-@
-}
-\end{frame}
-
-\end{document}
-\ No newline at end of file
diff --git a/Master/texmf-dist/doc/latex/medstarbeamer/medstarpresentation.pdf b/Master/texmf-dist/doc/latex/medstarbeamer/medstarpresentation.pdf
deleted file mode 100644
index a4224c742f6..00000000000
--- a/Master/texmf-dist/doc/latex/medstarbeamer/medstarpresentation.pdf
+++ /dev/null
diff --git a/Master/texmf-dist/doc/latex/medstarbeamer/presentationtex.pdf b/Master/texmf-dist/doc/latex/medstarbeamer/presentationtex.pdf
deleted file mode 100644
index 55ab6a9593d..00000000000
--- a/Master/texmf-dist/doc/latex/medstarbeamer/presentationtex.pdf
+++ /dev/null
diff --git a/Master/texmf-dist/tex/latex/medstarbeamer/beamercolorthemeMedStarColors.sty b/Master/texmf-dist/tex/latex/medstarbeamer/beamercolorthemeMedStarColors.sty
new file mode 100644
index 00000000000..c140e4acedc
--- /dev/null
+++ b/Master/texmf-dist/tex/latex/medstarbeamer/beamercolorthemeMedStarColors.sty
@@ -0,0 +1,41 @@
+%%%%%%%%% MedStar Beamer Template %%%%%%%%%
+%%%%%%%% Written By: Anagha Kumar %%%%%
+%%%%%%%% License: lppl1.3  %%%%%%%%%%%%%%%%
+%%%%%%%% Version: 2015-11-12 %%%%%%%%%%%%%%%%
+%%%%%%%% Colortheme: MedStarColors %%%%%%%%%%%%
+
+\ProvidesPackage{beamercolorthemeMedStarColors}
+
+\definecolor{medstaryellow}{rgb}{0.91, 0.78, 0.04} % define your own colors 
+\definecolor{medstarblue}{rgb}{0.0, 0.18, 0.33} % define your own colors 
+\definecolor{medstarred}{rgb}{0.8, 0.0, 0.0} % taken from http://latexcolor.com/
+
+\setbeamercolor*{date in head/foot}{parent=palette primary} % see below
+\setbeamercolor{author in head/foot}{parent=palette secondary}
+\setbeamercolor{title in head/foot}{parent=palette tertiary}
+
+\setbeamercolor{frametitle}{fg=medstarblue, bg=medstaryellow}
+\setbeamercolor{title}{fg=medstarblue} % controls the color of the title on the front page 
+\setbeamercolor{subtitle}{fg=medstarblue}
+\setbeamercolor{palette primary}{fg=white, bg=medstarblue} % controls the foreground and background colors for the strip at the bottom right 
+\setbeamercolor{palette secondary}{fg=white, bg=medstarblue} % controls the foreground and background colors for the bottom left strip and the second strip at the top
+\setbeamercolor{palette tertiary}{fg=medstarblue, bg=medstaryellow} %controls the foreground and background colors for the middle strip at the bottom and the top strip
+\setbeamercolor{author}{fg=medstarblue}
+\setbeamercolor{date}{fg=medstarblue}
+\setbeamercolor{normal text}{fg=medstarblue} % controls the font color on each slide - can be altered to something other than black 
+\setbeamercolor{alerted text}{fg=medstarred}
+\setbeamercolor{caption}{fg=medstarblue} % because I want my captions in the medstar colors - this is an improvement over the default! 
+\setbeamercolor{caption name}{fg=medstarblue} 
+\setbeamercolor{item}{fg=medstarblue} % NOTE: works for other environments like enumerate. I think medstaryellow looks garish. 
+\setbeamercolor{section in toc}{fg = medstarblue}
+\setbeamercolor{section in toc shaded}{fg = medstaryellow}
+\setbeamercolor{subsection in toc}{fg = medstarblue}
+\setbeamercolor{subsection in toc shaded}{fg = medstaryellow}
+\setbeamercolor{subsubsection in toc}{fg = medstarblue}
+\setbeamercolor{subsubsection in toc shaded}{fg = medstaryellow}
+
+% Can also set background color to something other than white if needed
+% \setbeamercolor{background canvas}{bg = blue!5}
+
+
+
diff --git a/Master/texmf-dist/tex/latex/medstarbeamer/medstarbeamer.cls b/Master/texmf-dist/tex/latex/medstarbeamer/medstarbeamer.cls
index 43920d8f8c9..a06562b55ef 100644
--- a/Master/texmf-dist/tex/latex/medstarbeamer/medstarbeamer.cls
+++ b/Master/texmf-dist/tex/latex/medstarbeamer/medstarbeamer.cls
@@ -1,11 +1,7 @@
 %%%%%%%%% MedStar Beamer Template %%%%%%%%%
 %%%%%%%% Written By: Anagha Kumar %%%%%
 %%%%%%%% License: lppl1.3  %%%%%%%%%%%%%%%%
-
-% I wrote a beamer template for MedStar Health presentations. %% 
-%% I've included sample presentations using both .tex files and .rnw files%%
-%% The document class is obviously compatible with both
-%% The advantage of the .rnw file is that it can be used with knitr such that you can weave your R code with your presentation %% 
+%%%%%%%% Version: 2015-11-12 %%%%%%%%%%%%%%%%
 
 \NeedsTeXFormat{LaTeX2e}
 \ProvidesClass{medstarbeamer}
@@ -21,24 +17,82 @@
 \RequirePackage{cancel}
 \RequirePackage{amsmath} 
 \RequirePackage{enumerate}
+\RequirePackage{ifthen}
+
+\defbeamertemplate*{footline}{}
+{
+  \hbox{%
+  \begin{beamercolorbox}[wd=.3333333\paperwidth,ht=0.25cm,dp=0.2cm,center]{author in head/foot}%
+    \usebeamerfont{author in head/foot}\insertshortauthor
+  \end{beamercolorbox}%
+  \begin{beamercolorbox}[wd=.3333333\paperwidth,ht=0.25cm,dp=0.2cm,center]{title in head/foot}%
+    \usebeamerfont{title in head/foot}\insertshorttitle
+  \end{beamercolorbox}%
+  \begin{beamercolorbox}[wd=.3333333\paperwidth,ht=0.25cm,dp=0.2cm, center]{date in head/foot}%
+    \usebeamerfont{date in head/foot}\insertshortdate{}\hfill \insertframenumber{} / \inserttotalframenumber 
+  \end{beamercolorbox}}%
+}
+% ht controls the height of the boxes. %I want the text in the boxes to be centered. %dp controls the depth 
+
+\defbeamertemplate*{headline}{}
+{
+  \begin{beamercolorbox}{section in head/foot}
+    \vskip3pt\insertnavigation{\paperwidth}\vskip3pt
+  \end{beamercolorbox}%
+  \ifbeamer@theme@subsection%
+    \begin{beamercolorbox}[ht=0.25cm,dp=0.2cm, leftskip=0.5cm]{subsection in head/foot}
+      \usebeamerfont{subsection in head/foot}\insertsubsectionhead
+    \end{beamercolorbox}%
+  \fi
+}
+
+\setbeamersize{text margin left=0.5cm,text margin right=0.75 cm} % This is important to specify so that the margins and hence, typeset font can be controlled in each slide. I prefer cm over em. 
 
 
-\usetheme{CambridgeUS} % for an extensive list of themes, this is a useful website: http://deic.uab.es/~iblanes/beamer_gallery/index_by_theme.html %
-\definecolor{citrine}{rgb}{0.89, 0.82, 0.04}
-\definecolor{coolblack}{rgb}{0.0, 0.18, 0.39}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\usecolortheme{MedStarColors}
+\newif\ifbeamer@theme@subsection
+\beamer@theme@subsectiontrue %%%%%% adds in the blue line %%%% 
 
-\usecolortheme{lily}
-\setbeamercolor{frametitle}{fg=white, bg=coolblack}
-\setbeamercolor{title}{fg=coolblack}
-\setbeamercolor{subtitle}{fg=coolblack}
-\setbeamercolor{palette primary}{fg=white, bg=coolblack} % controls the foreground and background colors for the strip at the bottom right 
-\setbeamercolor{palette secondary}{fg=white, bg=coolblack} % controls the foreground and background colors for the bottom left strip and the second strip at the top
-\setbeamercolor{palette tertiary}{fg=black, bg=citrine} %controls the foreground and background colors for the middle strip at the bottom and the top strip
-\useoutertheme{miniframes}
-\setbeamercolor{item}{fg=coolblack} %customizing the colors for the inner theme
-\logo{\includegraphics[ height=1cm, width=2cm]{medstarlogo}} %the size of the logo to be included in every frame
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\logo{\includegraphics[ height=1cm, width=2.5cm]{medstarlogo}} %the size of the logo to be included in every frame
 
 \setbeamercovered{dynamic} %overlays appear faintly 
 \setbeamertemplate{navigation symbols}{}  % since I dislike the navigation symbols
 \setbeamertemplate{caption}[numbered] % since beamer does not number captions without setting this 
-\setbeamercolor{caption}{fg=coolblack}
+
+
+%%%%%%%%%%%%Shrinking the table of contents if needed %%%%%%%%%%%%%%%%%%%%%%%%%%
+\newcommand{\sizecontentsoutline}[1]
+{
+  \ifnum#1=1  
+     \begin{frame}
+    \tableofcontents 
+    \end{frame}
+    \else
+ \ifnum#1=2 
+    \begin{frame}
+    \footnotesize{\tableofcontents}
+    \end{frame}
+  \fi
+}
+
+\newcommand{\sizecontentscurrent}[1]
+{
+\AtBeginSection{
+\ifthenelse{\thesection > 1}{
+  \ifnum#1=1  
+     \begin{frame}
+    \tableofcontents[currentsection]
+    \end{frame}
+    \else
+ \ifnum#1=2 
+    \begin{frame}
+    \footnotesize{\tableofcontents[currentsection]}
+    \end{frame}
+  \fi
+}
+}
+}
+
+% Define Author, Date, Institute, Title using small caps and different fonts - theme
+\ No newline at end of file