open_science_thesis.Rnw

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%%% Content: Open-Science-Thesis LaTeX Scaffold 
%%% Usage: Collaborative scientific thesis writing 
%%% Author: Claas-Thido Pfaff
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%%% Document class: open_science_thesis (Based on Koma-Script: scrbook) %%%
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\documentclass[autolayout=true]{ost/subdocuments/open_science_thesis} 

% linenumbers = true/[false] Enable or disable line numbering. This can be handy on revisions.
% colormode = [rgb]/cmyk The colormode can be switched between rgb which is optima for displays 
%			 and cmyk which is useful for professional printing.
% fancytocs = [true]/false Enable or disable fancy styled TOC.
% toctosection= [part]/chapter/false Add a partial toc to part, chapter or disable it completely.
% revision = true/[false] enables line numbers, extends paper size and allows to use the command \ostSetRevisor{name} to set
%		          up revisors for the document. Comments of revisors in the margin of the page. If you set up a revisor 
%                         for example with \ostSetRevisor{chris} the revisor can use the command \chris{Some note} in your text to
%			  place a note. If you set this option to true the notes get visible

% Available class options [defaults]

% titlepagestyle = [simple, plain, image, vertical]
% toctosection = [part, chapter]

% linenumbers=false, 
% colortheme=[orange, blue, green, red], 
% gitinfo=false, 
% sectionnumbers=true,
% autolayout=true,
% resetdefaultclassoptions=false, 
% parindent=false,

% backroundimage=false, enable background image for title page. use with onside only 


% - autolayout [true]/false: Switch between the nice automatic calculated typearea layout 
%   (Koma script) and a fixed geometry page layout (geometry package). You need to set the 
%   geometry inside of the style file if you choose false. (needs some work)

% - gitinfo true/[false]: Include git information into the title header of the 
%   document. This requires the setup of git hooks which you can do by issuing 
%   the make task (make githooks). After that you need to specify the URL of the 
%   git repository inside of the style file and you are done.  (needs some work)

% - print true/[false] switches between the color model rgb which is optimal for displays 
%   and the cmyk color model which is required for professional printing. 
% - linenumbers true/[false]: Switch on/off line numbers for the whole document. 



% - resetdefaultclassoptions true/[false] resets the default options the open science thesis 
%   loads the scrartcl class. After that you can modify every option via the open science 
%   thesis class call. For example to change the calculated typearea you can use 
%   \documentclass[resetdefaultclassoptions=true, DIV=7]{ost/subdocuments/open_science_thesis}   

% - parindent true/[false] Switch paragraph indent on or off.

%% scrbook class options 
% - oneside/[twoside] enables oneside or twoside layout with twoside layout as 
%   default.

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%%% Load user options %%%
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\input{usr/subdocuments/options/ost_document_options.sty} 

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%%% Load glossary definitions %%%
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<<glossary_definitions, child='usr/subdocuments/options/open_science_glossary.Rnw', eval=T>>=
@

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\begin{document}

% start front matter
\frontmatter

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%%% Document preparations %%%
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%

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%%% Preferences for Knitr %%%
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<<chunk_global_r_options, child='usr/subdocuments/options/ost_global_r_options.Rnw', eval=T>>=
@ 

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%%% Document content %%%
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%

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%%% Include header %%%
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<<subdoc_content_header, child='usr/subdocuments/chapters/ost_header.Rnw', eval=T>>=
@

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%%% Tables of content %%%
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% \tableofcontents
% \listoffigures 
% \listoftables 
\makealltables
\listofrevisions

\mainmatter

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%%% Include abstract %%%
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<<subdoc_content_abstract, child='usr/subdocuments/chapters/ost_abstract_section.Rnw', eval=T>>=
@

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%%% Include introduction %%%
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<<subdoc_content_introduction, child='usr/subdocuments/chapters/ost_introduction_section.Rnw', eval=T>>=
@

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%%% Include material and methods %%%
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<<subdoc_content_material_methods, child='usr/subdocuments/chapters/ost_material_methods_section.Rnw', eval=T>>=
@

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%%% Include results %%%
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<<subdoc_content_results, child='usr/subdocuments/chapters/ost_results_section.Rnw', eval=T>>=
@

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%%% Include discussion %%%
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<<subdoc_content_discussion, child='usr/subdocuments/chapters/ost_discussion_section.Rnw', eval=T>>=
@

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%%% Include acknowledgements %%%
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<<subdoc_content_acknowledgement, child='usr/subdocuments/chapters/ost_acknowledgements_section.Rnw', eval=T>>=
@

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%%% Include the appendix %%%
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% Appendix content 
\appendix

<<subdoc_content_appendix, child='usr/subdocuments/chapters/ost_appendix_section.Rnw', eval=T>>=
@ 

%%%-------------------------------------------------%%%
%%% Affidavit %%%
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% start main matter

<<subdoc_content_introduction, child='usr/subdocuments/chapters/ost_affidavit_section.Rnw', eval=T>>=
@

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%%% Include the bibliography %%%
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<<options_bibliography, child='usr/subdocuments/chapters/ost_bibliography_section.Rnw', eval=T>>=
@

% Literature and Index
\backmatter

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%%% Glossary %%%
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<<body_mainmatter_chapter_one, child='usr/subdocuments/chapters/ost_glossaries_section.Rnw', eval=T>>=
@

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\end{document}