capra-lab-manuscript-template

Forfatter
Evonne McArthur, Capra Lab
Sidst opdateret
3 år siden
Licens
Creative Commons CC BY 4.0
Resumé
More details and instructions can be found here: https://github.com/CapraLab/lab-manuscript-template The goal of this template is to make formatting and writing a scientific manuscript easier and more standardized. This should be appropriate as a basic academic journal template, but the Capra Lab is an evolutionary genomics lab (submitting to journals like MBE, AJHG, Genome Biology, Nat Eco Evo, etc). Some of these suggestions are subjective and there is ultimately no one-size-fits-all for writing a paper. However, this will hopefully serve as a great place to start.
Tags
University Reports
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%%% ------------ OVERVIEW OF THIS TEMPLATE ------------ %%%
% This is a Capra Lab Manuscript template! It was developed by the Capra
% Lab and converted to a LaTex document by Evonne McArthur 2/2022 and last
% edited 3/2022. 

% Find details and an MS word version here:
% https://github.com/CapraLab/lab-manuscript-template

% To use this template, you should probably read the whole compiled document
% because it contains lots of great tips. Once you are ready to go, you 
% should delete the tips in each section (\abstractTips \introTips \resultsTips 
% \captionTips \methodsTips \methodsDataTips, \methodsAnalysisTips \discussionTips and \generalTips). Then you should
% delete the REMOVEME_tips.tex file and the call to that file in this document
% (\input{REMOVEME_tips}). Then add your own content to the relevant subfiles.

% Figures should be uploaded to the ./main_figs and ./supplement/suppl_figs
% folders. Tables should be uploaded to ./supplement/suppl_tabs. When you work
% with main text figures, you should create a "code name" for them. You will
% follow the format in 4maintextFigs.tex to add a function that will generate
% the figure. When you want that figure to appear in the manuscript call that
% function (e.g. \codename).

% Note that this document contains info about how to customize these things:
% fontsize, font (to Arial), line spacing, line numbers, left vs. justified
% aligned, number or author-date citations, natbib vs bibLaTeX citations,
% sideways tables and figures, figure references and more!

% See these resources for more LaTeX tips:
%https://en.m.wikibooks.org/wiki/LaTeX
%https://tobi.oetiker.ch/lshort/lshort.pdf
%https://gangw.cs.illinois.edu/latex.pdf
%https://web.mit.edu/rsi/www/pdfs/new-latex.pdf
%http://hoffman.physics.harvard.edu/Hoffman-example-paper.pdf

%%% ------------ READ IN PACKAGES & SETUP ------------ %%%

% Basics, font size, page setup, link format, line spacing/numbering
\documentclass[11pt]{article} % font size
\usepackage[utf8]{inputenc}
\usepackage[english]{babel}
\usepackage[a4paper,margin=1in]{geometry} % page setup, margins
\usepackage{authblk} % author affiliations
\usepackage[colorlinks=true, linkcolor=black, citecolor=black, urlcolor=blue, filecolor=blue,breaklinks=true]{hyperref} % Hyperlinks, needed for biblatex, other option: allcolors=blue
\usepackage{setspace} % for linespacing
\usepackage{lineno} % line numbering (change with \linespacing below)
\usepackage{csquotes} % Recommended for biblatex, must load after lineno or will get a warning
\usepackage{ragged2e} % for left aligning
\setlength{\RaggedRightParindent}{\parindent} % for paragraph indent with left aligning

% Figure references and bolding them https://tex.stackexchange.com/questions/87903/bold-cross-references
\usepackage[capitalise, noabbrev, nameinlink]{cleveref}
\crefdefaultlabelformat{#2\textbf{#1}#3} % To bold figure refs
\Crefname{figure}{\textbf{Figure}}{\textbf{Figures}} % To bold figure refs
\Crefname{section}{\textbf{Section}}{\textbf{Sections}} % To bold section refs
\Crefname{table}{\textbf{Table}}{\textbf{Tables}} % To bold table refs
\newcommand{\crefrangeconjunction}{--} % change conjunction b/w figures
\newcommand{\crefpairconjunction}{, } % change conjunction b/w figures
\newcommand{\creflastconjunction}{, } % change conjunction b/w figures
\newcommand{\crefmiddleconjunction}{, } % change conjunction b/w figures

% Figures, Tables and captions
\usepackage{graphicx}
\graphicspath{{./main_figs/}{./supplement/suppl_figs/}} % paths for figs
\DeclareGraphicsExtensions{.pdf,.jpeg,.JPG,.png,.PNG, .eps, .tiff}
\usepackage{subcaption} % for subcaptions (panels), and add parentheses
\DeclareCaptionLabelFormat{bold}{\textbf{(#2)}} % bold subpanel letter in caption
\captionsetup{subrefformat=bold} % bold subpanel letter in caption
\renewcommand{\thesubfigure}{\Alph{subfigure}} % Make subpanel numbering capitalized
\newcommand{\labelphantom}[1]{%  To make subpanel references easier from https://tex.stackexchange.com/a/255790/121424 
  \parbox{0pt}{\phantomsubcaption\label{#1}}%
}
\usepackage{pgffor} % for function to make figures with subpanels
\usepackage{alphalph} % for function to make figures with subpanels
\usepackage[labelfont=bf, textfont=bf, singlelinecheck=off, textfont=footnotesize]{caption} % boldness of captions
\usepackage{booktabs}
\usepackage{multirow}
\usepackage{rotating}
%\usepackage{tabularx}
%\usepackage{makecell}

% Read in helper functions
\input{helperFunctions}

% Change Fonts
%\usepackage{fontspec} % To use arial font but you must change your compiler to XeLaTeX (upper left corner Menu > compilier) 
%\setmainfont{Arial} % To use arial font but you must change your compiler to XeLaTeX (upper left corner Menu > compilier) 

% Can remove, are for the tips
\usepackage[dvipsnames]{xcolor} % can remove, for coloring the tips
\usepackage{changepage} % can remove, for width on the tips
\usepackage{enumitem} % can remove, for width on the tips


%%% ------------ REFERENCES FORMAT ------------ %%% 
% Note: Change the print bibliography command if switching between BibLaTex and Natbib
% See this for a great comparison: https://tex.stackexchange.com/questions/25701/bibtex-vs-biber-and-biblatex-vs-natbib

%% BibLaTeX format %% (newer/better but not all journals accept)
% Numbered:
%\usepackage[sorting=none, backend=biber, style=numeric-comp,maxbibnames=10,minbibnames=3, maxcitenames= 2,giveninits=true, natbib=true, url=false,hyperref=true]{biblatex}
% Author Year:
\usepackage[backend=biber,style=authoryear-comp,sorting=nyt,natbib=true, url=false]{biblatex}

\addbibresource{library.bib} % add bibliography resource

%% Natbib format %% (more basic)
% Numbered:
% \usepackage[square,numbers]{natbib}
% \bibliographystyle{unsrtnat}
% Author Year:
%\usepackage{natbib}
%\bibliographystyle{unsrtnat}


%%% ------------ DOCUMENT ORGANIZATION ------------ %%%

\input{1titlepage}
\begin{document}

    %\RaggedRight % If you want left-aligned (ie ragged right text) rather than justified
    \setstretch{1.15} %\onehalfspace
    \linenumbers
    \input{REMOVEME_tips} % For the tips, eventually remove!
    
    \maketitle
    \makeAbstract
    \clearpage 
    \input{2intro} 
    \clearpage % can remove if you don't want a new page 
    \input{3results} 
    \clearpage % can remove if you don't want a new page
    \input{5discussion}
    \clearpage % can remove if you don't want a new page
    \input{6methods}

    \begin{singlespace}
        \printbibliography % for biblatex
        %\bibliography{library} % for natbib
    \end{singlespace}
    \clearpage

    \section*{Supplementary Information}
    \setcounter{page}{1} % Set page at 1
    \input{supplement/0suppl_text}
    \input{supplement/1suppl_figs}
    \input{supplement/2suppl_tabs}

\end{document}