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manual_booklet.tex
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manual_booklet.tex
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\documentclass[9pt]{report}
\usepackage[paperwidth=15.24cm, paperheight=22.86cm]{geometry}
\usepackage[pdftex]{graphicx}
\usepackage{setspace}
%\usepackage{lineno}
%\usepackage[letter,frame,center]{crop}
\usepackage{color}
\usepackage{float}
\usepackage{enumitem}
\usepackage{listings}
\lstset{basicstyle=\small\ttfamily,breaklines=true,backgroundcolor=\color{lightGrey}}
%\usepackage{bbm}
\usepackage{hyperref}
\usepackage{lscape}
\definecolor{PiranaOrange}{rgb}{0.9,0.4,0.1}
\definecolor{Blue}{rgb}{0.0,0.0,0.7}
\definecolor{Red}{rgb}{0.7,0.0,0.0}
\definecolor{Grey}{rgb}{0.4,0.4,0.4}
\definecolor{Grey}{rgb}{0.4,0.4,0.4}
\definecolor{LightGrey}{rgb}{0.92,0.92,0.92}
\definecolor{grey2}{rgb}{.92, .92, .92}
\bibliographystyle{unsrt}%Choose a bibliograhpic style}
%\usepackage{utopia} %\usepackage{charter} %\usepackage{palatino}
%\usepackage{bookman} %\usepackage{newcent} %\usepackage{times}
%\usepackage[options]{natbib} \sloppy
% font
%\renewcommand{\familydefault}{\sfdefault}
\usepackage{mathpazo}
\renewcommand{\familydefault}{\rmdefault}
%\oddsidemargin 1.5cm
%\textwidth 13cm
\textheight 17.5cm
\newcommand{\test}{\textcolor{Blue}{\textit{test}}\xspace}
\newcommand{\reference}{\textcolor{Green}{\textit{reference}}\xspace}
\newcommand{\valpsn}{\textcolor{Blue}{\textit{valpsn}}\xspace}
\newcommand{\ValPsN}{\textcolor{PiranaOrange}{\textit{ValPsN}}\xspace}
\newcommand{\psn}[1]{\textcolor{Grey}{#1}}
\newcommand{\fname}[1]{\textit{#1}}
\newcommand{\action}[1]{\textcolor{Red}{\textit{#1}}}
\newcommand{\command}[1]{{\ttfamily{#1}}}
%% code listings
\lstset{
language=fortran, % the language of the code
basicstyle=\ttfamily\small, % the size of the fonts that are used for the code
commentstyle=\color{Grey}\textit,
backgroundcolor=\color{LightGrey}, % choose the background color. You must add \usepackage{color}
captionpos=b, % sets the caption-position to bottom
columns=flexible,
showspaces=false,
showstringspaces=false,
showtabs=false,
morekeywords={*, ...} % if you want to add more keywords to the set
}
\begin{document}
\title{
\vspace{-100pt}
\textbf{
\textcolor{PiranaOrange}{\Large Pirana}
}\\
\vspace{5pt}
\small \textcolor{Grey}{Pharmacometrics workbench for NONMEM \& PsN} \\
\normalsize
\vspace{15pt}
\hspace{15pt}\includegraphics[scale=0.2]{images/pirana_logo.jpg}\\
\vspace{15pt}
\small Installation guide\\Manual\\Tutorial\\Quick Guides\\
\vspace{8pt} \textit{Pirana version $\geq$ 2.10.0}\\
\vspace{8pt}
% \scriptsize {\today} \\
\date{}
}
\maketitle
\null\vfill
\noindent
\vspace{5pt}
\small
\noindent Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. -- Pirana Software \& Consulting BV\\
\vspace{5pt}
\noindent Chapter 9, the tutorial on Pirana, PsN, and Xpose, has
earlier been published in the open access journal CPT-PSP (Nature
Publishing Group). This chapter is available under a creative commons
license (Commons Attribution-Noncommercial-No Derivative Works
3.0). In short, this means that you may reproduce the content for
non-commercial purposes, although you are required to attribute its
authors, and may not alter the content.
\normalsize
\newpage
\tableofcontents
\newpage % one page left blank intentially
\thispagestyle{empty}
\mbox{}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\input{manual_body.tex}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\newpage % one page left blank intentially
\thispagestyle{empty}
\mbox{}
\chapter{Tutorial: Pirana, PsN \& Xpose}
\input{manual_tutorial.tex}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\clearpage
\chapter{Quick Guides}
\clearpage
\section{Quick Guide: Configuring Pirana }
\input{7_quick_guide_configuration_pirana_body.tex}
\clearpage
\section{Quick Guide: Setting up NONMEM in Pirana}
\input{3_quick_guide_nonmem_installation_body.tex}
\clearpage
\section{Quick Guide: Setting up cluster connections}
\input{2_quick_guide_cluster_body.tex}
\clearpage
\section{Quick Guide: Working with models}
\input{4_quick_guide_working_with_models_body.tex}
\clearpage
\section{Quick Guide: Creating reports}
\input{10_quick_guide_reporting_body.tex}
\clearpage
\section{Quick Guide: Graphical output in R}
\input{8_quick_guide_graphics_withoutXpose_body.tex}
\clearpage
\section{Quick Guide: Creating a VPC}
\input{1_quick_guide_vpc_body.tex}
\clearpage
\section{Quick Guide: Using Xpose from Pirana }
\input{6_quick_guide_Xpose_graphics_body.tex}
\clearpage
\section{Quick Guide: Translating NM-TRAN }
\input{5_quick_guide_convertingODEs_body.tex}
\clearpage
\section{Quick Guide: Using PsN from Pirana}
\input{9_quick_guide_psn_body.tex}
\end{document}