ALEA01.Rnw

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%%%          SPONSOR: ABC
%%%             DRUG: WonderDrug(TM)
%%%      STUDY TITLE: Example Non-Interventional Study ABC-NIS-01 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%         STUDY NO: Alea01
%%%        R PROGRAM: ALEA01.Rnw
%%%          VERSION: 1.0
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%%%      DESCRIPTION: Tables, Listing, Figures
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%%% DEVELOPMENT DATE: 19Oct2017
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%%%     DEVELOPED BY: alea iacta
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%%%          RELEASE: 24Oct2017
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%%%             PATH: C:/Temp/ALEA01/
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\documentclass{article}                   % LaTeX document class;
\usepackage[english]{babel}               % english as default; 
\usepackage[scaled=.92]{helvet}           % Helvetica, scaled 92%;
\renewcommand{\familydefault}{\sfdefault} % default sans serif font;
\usepackage{pdflscape}                    % enables PDF landscape;
\usepackage{longtable}                    % enables "longtable" evironment;
\usepackage{booktabs}                     % enables \toprule \bottomrule;
\usepackage{geometry}                     % Flexible and complete interface to document dimensions;
\geometry{nomarginpar,a4paper,verbose,tmargin=2.5cm,bmargin=1.5cm,lmargin=1.5cm,
          rmargin=1.5cm,headheight =1.5cm,headsep=0.3cm}
\usepackage{lmodern}                      % high quality fonts;
\usepackage{lastpage}                     % allows page # of ##;
\usepackage{fancyhdr}                     % customize headers and footers;
\usepackage{float}                        % interface for floating objects;
\usepackage[utf8]{inputenc}               % standard input utf-8;
\usepackage[T1]{fontenc}                  % T1 font encoding;
\usepackage{calc}                         % allows \setcounter{};
\usepackage{epic}                         % Enhance LaTeX picture mode;
\usepackage{listings}                                 % allows code attachments with \lstinputlisting{};
\usepackage{fancyvrb}                                 % allows verbatim attachments with \VerbatimInput{};
\usepackage[colorlinks=true,linkcolor=blue]{hyperref} % hyperrefs in blue;
\usepackage[section]{placeins}                        % control float placement;
\usepackage{attachfile}                               % attach/embed files with \attachfile{};

% Global settings for \lstinputlisting (with line breaks);
\lstset{basicstyle=\sffamily,columns=fullflexible,keepspaces=true,breaklines=true}

% no indentation whole document;
\setlength{\parindent}{0pt} 

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%% BEGIN DOCUMENT;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\begin{document}

\pagestyle{fancy}
\fancyfoot[R]{Page \thepage\ of \pageref{LastPage}}  

<<POPULATION, echo=FALSE, results="hide">>=
# Enter Population (Analysis Set) here (for header and title page);
VAR_myset <- "Full Analysis Set (FAS)"

# Example: VAR_myset will not printed because results="hide";
VAR_myset
@

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%% CREATE TITLE PAGE;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

<<TITEL, child='00_TITLE_PAGE.Rnw'>>=
@

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%% CREATE TABLE OF CONTENTS;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\setcounter{page}{2}

\tableofcontents

\listoftables

\listoffigures

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%% ABBREVIATIONS;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

<<ABBREVIATIONS, child='00_ABBREVIATIONS.Rnw'>>=
@

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%% GLOBAL OPTIONS;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

<<set-options, echo=FALSE>>=
# Options
options(replace.assign = TRUE, width = 80)

# disabling scientific notation in R;
options(scipen = 999)

# Set digit option;
options(digits = 2)

pdf.options(family = "Helvetica-Narrow")

# Define knitr chunk options;
opts_chunk$set(fig.width  = 7, 
               fig.height = 7, 
               out.width  = '10cm', 
               fig.pos    = 'H',
               fig.align  = 'center',
               fig.path   = './figure/Plot-',
               fig.keep   = 'all',
               cache      = FALSE,
               echo       = FALSE,                  # FALSE: no output of R code;
               message    = FALSE,                  # FALSE: no output of R messages;
               warning    = FALSE,                  # FALSE: no output of warnings;
               dev        = 'pdf')
@

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%% READ SAS XPT FILES WITH USER-DEFINED FORMATS;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

<<external-code>>=
source("impsas_xpt.R")
@

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%% Read R Chunks and user defined R Functions;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

<<read-external, warning=TRUE>>=
### Read chunks;
read_chunk("00_chunks.R")

### Read R functions;
source("00_r_functions.R")
@

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%% ANALYSIS PROGRAMS - BEGIN;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%%%%%%%%%%%%%%%%%%%%% Include R program 01_DEMOG.Rnw;

<<DEMOG, child='01_DEMOG.Rnw'>>=
@

%%%%%%%%%%%%%%%%%%%%% Include R program 01_DEMO_FIG.Rnw;

<<DEMOG_FIG, child='01_DEMOG_FIG.Rnw'>>=
@

%%%%%%%%%%%%%%%%%%%%% Include R program 01_LINEAR_MODEL.Rnw;

<<LINEAR_MODEL, child='01_LINEAR_MODEL.Rnw'>>=
@

%%%%%%%%%%%%%%%%%%%%% Include R program 02_KAPLAN.Rnw;

<<KAPLAN, child='02_KAPLAN.Rnw'>>=
@

%%%%%%%%%%%%%%%%%%%%% Include R program 03_LAB_HGB.Rnw;

<<LABEXHGB, child='03_LAB_HGB.Rnw'>>=
@

%%%%%%%%%%%%%%%%%%%%% Include R program 03_LAB_WBC.Rnw;

<<LABEXWBC, child='03_LAB_WBC.Rnw'>>=
@

%%%%%%%%%%%%%%%%%%%%% Include R program 04_RESPONSE.Rnw;

<<RESPONSE, child='04_RESPONSE.Rnw'>>=
@

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%% ANALYSIS PROGRAMS - END;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%% APPENDIX INCLUDE ALL KNITR CODE;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\clearpage
\newpage

\begin{appendix}

\section{All Code for Generating this Report} \label{AllCode} 
\subsection{Master Rnw File ALEA01.Rnw}
\fvset{fontsize=\small} % fancyvrb option;
\VerbatimInput{ALEA01.Rnw}

\clearpage
\newpage
\subsection{File 00\_TITLE\_PAGE.Rnw}
\fvset{fontsize=\small}
\VerbatimInput{00_TITLE_PAGE.Rnw}

\clearpage
\newpage
\subsection{File 00\_ABBREVIATIONS.Rnw}
\fvset{fontsize=\small}
\VerbatimInput{00_ABBREVIATIONS.Rnw}

\clearpage
\newpage
\subsection{File impsas\_xpt.R}
Following \emph{.R script file} was generated automatically 
with \href{https://github.com/clindocu/sasxpt-r}{clindocu/sasxpt-r:}

\lstinputlisting{impsas_xpt.R} % input file with autom. line breaks;

\clearpage
\newpage
\subsection{File 00\_chunks.R}
\fvset{fontsize=\small}
\VerbatimInput{00_chunks.R}

\clearpage
\newpage
\subsection{File 00\_r\_functions.R}
\fvset{fontsize=\small}
\VerbatimInput{00_r_functions.R}

\clearpage
\newpage
\subsection{File 01\_DEMOG.Rnw}
\fvset{fontsize=\small}
\VerbatimInput{01_DEMOG.Rnw}

\clearpage
\newpage
\subsection{File 01\_DEMOG\_FIG.Rnw}
\fvset{fontsize=\small}
\VerbatimInput{01_DEMOG_FIG.Rnw}

\clearpage
\newpage
\subsection{File 01\_LINEAR\_MODEL.Rnw}
\fvset{fontsize=\small}
\VerbatimInput{01_LINEAR_MODEL.Rnw}

\clearpage
\newpage
\subsection{File 02\_KAPLAN.Rnw}
\fvset{fontsize=\small}
\VerbatimInput{02_KAPLAN.Rnw}

\clearpage
\newpage
\subsection{File 03\_LAB\_HGB.Rnw}
\fvset{fontsize=\small}
\VerbatimInput{03_LAB_HGB.Rnw}

\clearpage
\newpage
\subsection{File 03\_LAB\_WBC.Rnw}
\fvset{fontsize=\small}
\VerbatimInput{03_LAB_WBC.Rnw}

\clearpage
\newpage
\subsection{File 04\_RESPONSE.Rnw}
\fvset{fontsize=\small}
\VerbatimInput{04_RESPONSE.Rnw}

\clearpage
\newpage
\subsection{File 99\_HISTORY.Rnw}
\fvset{fontsize=\small}
\VerbatimInput{99_HISTORY.Rnw}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%% APPENDIX VERSION HISTORY;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

<<HISTORY, child='99_HISTORY.Rnw'>>=
@

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%% APPENDIX TECHNICAL DETAILS;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\clearpage
\newpage

\section{Technical Details}

\tiny{
  % \subsection{System Details}
  % <<echo=TRUE>>=
  %   Sys.info()
  % @
  \subsection{R Version}
  <<echo=TRUE>>=
    R.Version()
  @
  \subsection{Active R packages}
  <<echo=TRUE>>=
    sessionInfo()
  @
  \subsection{PDF \LaTeX{}}
  <<echo=TRUE>>=
    Sys.which("pdflatex")
  @
  \subsection{System Time}
  <<echo=TRUE>>=
    Sys.time()
  @
}

\end{appendix}

\end{document}

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%%%%%%%%%%% END DOCUMENT;
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