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open_science_paper.Rnw
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open_science_paper.Rnw
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%%%------------------------------------------------------------------------------------%%
%%%------------------------------------------------------------------------------------%%
%%% Content: Open-Science-Paper LaTeX Scaffold
%%% Usage: Collaborative scientific paper writing
%%% Author: Claas-Thido Pfaff
%%%------------------------------------------------------------------------------------%%
%%%------------------------------------------------------------------------------------%%
%%%------------------------------------------------------------------------------%%%
%%% Document class: open_science_paper (Based on Koma-Script: article) %%%
%%%------------------------------------------------------------------------------%%%
%%
%
\documentclass[color=false, csvdata=false]{osp/subdocuments/open_science_paper}
%% Available class options [defaults]
% - color true/[false]: Changes between colored output and a black and white theme
% - csvdata true/[false]: With csv data enabled you can use the csv file under
% the data folder to insert title header information into the document.
% - 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.
% - 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.
% - sectionnumbers true/[false]: Switch between numbered and numberless sections
% - 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.
% - twosidelayout true/[false]: Switch between two and one side page layout.
% - reversepagelayout [false]/true reverse the order of odd and even side margins. This
% option can be used to start the paper on a left or right page.
% - resetdefaultclassoptions true/[false] resets the default options the open science paper
% loads the scrartcl class. After that you can modify every option via the open science
% paper class call. For example to change the calculated typearea you can use
% \documentclass[resetdefaultclassoptions=true, DIV=7]{osp/subdocuments/open_science_paper}
% - parindent true/[false] Switch paragraph indent on or off.
%%%------------------------------------------------------------------------------%%%
%%% Load user options %%%
%%%------------------------------------------------------------------------------%%%
\input{usr/subdocuments/options/osp_document_options.sty}
%%%------------------------------------------------------------------------------%%%
%%% Begin the document %%%
%%%------------------------------------------------------------------------------%%%
\begin{document}
%%%--------------------------------------------------------------%%%
%%% Document preparations %%%
%%%--------------------------------------------------------------%%%
%%
%
%%%-------------------------------------------------%%%
%%% Preferences for Knitr %%%
%%%-------------------------------------------------%%%
<<chunk_global_r_options, child='usr/subdocuments/options/osp_global_r_options.Rnw', eval=TRUE>>=
@
%%%--------------------------------------------------------------%%%
%%% Document content %%%
%%%--------------------------------------------------------------%%%
%%
%
%%%-------------------------------------------------%%%
%%% Include header %%%
%%%-------------------------------------------------%%%
\begin{ospHeader}
<<subdoc_content_header, child='usr/subdocuments/chapters/osp_header.Rnw', eval=T>>=
@
%%%-------------------------------------------------%%%
%%% Include abstract %%%
%%%-------------------------------------------------%%%
<<subdoc_content_abstract, child='usr/subdocuments/chapters/osp_abstract_section.Rnw', eval=T>>=
@
\end{ospHeader}
% Start column layout %
\begin{ospColumLayout}
%%%-------------------------------------------------%%%
%%% Include introduction %%%
%%%-------------------------------------------------%%%
<<subdoc_content_introduction, child='usr/subdocuments/chapters/osp_introduction_section.Rnw', eval=T>>=
@
%%%-------------------------------------------------%%%
%%% Include material and methods %%%
%%%-------------------------------------------------%%%
<<subdoc_content_material_methods, child='usr/subdocuments/chapters/osp_material_methods_section.Rnw', eval=T>>=
@
%%%-------------------------------------------------%%%
%%% Include results %%%
%%%-------------------------------------------------%%%
<<subdoc_content_results, child='usr/subdocuments/chapters/osp_results_section.Rnw', eval=T>>=
@
%%%-------------------------------------------------%%%
%%% Include discussion %%%
%%%-------------------------------------------------%%%
<<subdoc_content_discussion, child='usr/subdocuments/chapters/osp_discussion_section.Rnw', eval=T>>=
@
%%%-------------------------------------------------%%%
%%% Include acknowledgements %%%
%%%-------------------------------------------------%%%
<<subdoc_content_acknowledgement, child='usr/subdocuments/chapters/osp_acknowledgements_section.Rnw', eval=T>>=
@
%%%-------------------------------------------------%%%
%%% Include the bibliography %%%
%%%-------------------------------------------------%%%
<<options_bibliography, child='usr/subdocuments/chapters/osp_bibliography_section.Rnw', eval=T>>=
@
% End column layout %
\end{ospColumLayout}
% uncomment the following lines to get an appendix section.
% \begin{ospAppendix}
% <<subdoc_content_appendix, child='usr/subdocuments/chapters/osp_appendix_section.Rnw', eval=T>>=
% @
% \end{ospAppendix}
%%%------------------------------------------------------------------------------%%%
%%% End of document %%%
%%%------------------------------------------------------------------------------%%%
\end{document}