Writing scientific papers in LaTex (Tips and Tricks)

• TeX Engine Settings
• Aesthetics
  • Highlighting
    • Round label
    • Grey highlight
• Meta
  • Finding weird Unicode
  • Highlight updates or inline comments
• Math
• Glossaries
• Bibliography
  • Clean bib files
  • Use Biblatex
• Tables
  • Hide columns
• SI-units
• Clever reference
• Figures
  • Python to Tikz
  • Extract data from existing figures
  • Indicate lines in a plot
• Preparing for submission
  • Clean-up Project
    • LaTeX cleaner's main features:
  • Shortening a Paper
    • Biblatex hacks

TeX Engine Settings

Settings in VSCode with increased memory size (pgfplots) and shell escape:

{
			"name": "lualatexmk",
			"command": "latexmk",
			"args": [
                "-shell-escape",                // <---- added this line
                "--extra-mem-bot=10000000",     // <---- added this line
                "--extra-mem-top=10000000",     // <---- added this line
				"-synctex=1",
				"-interaction=nonstopmode",
				"-file-line-error",
				"-lualatex",
				"-outdir=%OUTDIR%",
				"%DOC%"
			],
			"env": {}
		}

Aesthetics

Highlighting

Round label

\usepackage{tikz}
\usepgfplotslibrary{external}

\definecolor{mycolor}{RGB}{112,45,128}
\newcommand{\roundlabel}[1]{\tikzexternaldisable \tikz[baseline=(char.base)]{
            \node[rectangle, rounded corners=0.65mm,inner sep=0.65mm,fill=mycolor, draw=mycolor, text=white, font=\itshape](char) {#1};}\tikzexternalenable}

Example usgae: \roundlabel{Message 5/Conclusion:}

Grey highlight

\newcommand{\syntaxHighlight}[1]{\colorbox{black!10}{#1}}

Example usage: \syntaxHighlight{chapters/contributors.tex}

Meta

Finding weird Unicode

Add in the preamble the following to easily find a weird unicode in Overleaf.

\DeclareUnicodeCharacter{2500}{\color{red} FIX ME!!!!}

Highlight updates or inline comments

\usepackage[dvipsnames]{xcolor} %required package
\newcommand{\update}[1]{{\color{YellowOrange} #1}} %usage \update{this is changed.}

\usepackage[dvipsnames,svgnames, table]{xcolor} % Required to specify custom colors

\usepackage{listofitems}
\usepackage{pgffor}

\makeatletter
% Define your own list of colors
\def\myColorList{LimeGreen,BrickRed,Fuchsia,Bittersweet,YellowOrange, YellowGreen, WildStrawberry}
\readlist\ColorList\myColorList


\newcommand{\defineauthors}[1]{
    Personal commands for comments are:
    \begin{itemize}
    \foreach \x [count=\xi from 1] in {#1} {   
        \item \textcolor{\ColorList[\xi]}{\textbackslash\unexpanded\expandafter{\x}\{\}}
        }
    
    \end{itemize}

    \foreach \x [count=\xi from 1] in {#1} { 
    \expandafter\xdef\csname\x\endcsname####1{\noexpand\textcolor{\ColorList[\xi]}{[\unexpanded\expandafter{\x}: ####1]}}%
    }
}
\makeatother

%usage after begin document
\defineauthors{all, gilles, emma, ozlem, lianet, nicola}

Math

Typesetting and defining symbols:

\usepackage{xifthen}
\newcommand{\prob}[1][]{%requires xifthen package%
\ifthenelse{\isempty{#1}}%
      {\ensuremath{P}}%
    {\ensuremath{P\left\(#1\right\)}}%
}
\newcommand{\vect}[1]{\boldsymbol{\mathrm{#1}}}
\newcommand{\mat}[1]{\boldsymbol{\mathrm{#1}}}
\newcommand{\MSE}{\mathrm{MSE}}
\newcommand{\tr}{\mathrm{tr}}
\newcommand{\moddef}{\mathrm{mod}}
\newcommand{\diag}{\mathrm{diag}}
\newcommand{\vecop}{\text{vec}}
\newcommand{\CP}{L}
\newcommand{\hddots}{\hdots}
\newcommand*{\inC}[1]{\in\mathbb{C}^{#1}}
\newcommand{\norm}[1]{\left\lVert#1\right\rVert}
\newcommand{\abs}[1]{\left\lvert#1\right\rvert}
\newcommand{\expt}[1]{\mathbb{E} \left\{#1\right\}}
\newcommand{\cn}[2]{\ensuremath{\sim\mathcal{C}\mathcal{N}\left(#1,#2\right)}}

Glossaries

\usepackage[xindy, toc, numberedsection, acronym]{glossaries}
\usepackage{hyperref}
\loadglsentries{abbr.tex}
\makeglossaries 

More information: https://www.overleaf.com/learn/latex/Glossaries Base LaTex file is located here.

Scripting files to format the file, remove duplicates, merge different abbr files is located here.

Bibliography

Clean bib files

• Clean-up your bib files: https://flamingtempura.github.io/bibtex-tidy/
• I also always enable the "Enclose values in double braces" option to keep the capitalization in titles.
• My default setup

Use Biblatex

No cite or natbib package is required. For more info check: https://www.overleaf.com/learn/latex/Bibliography_management_with_biblatex. Always be aware there is a difference in citation style and bibliography style.

\usepackage[backend=biber,style=ieee]{biblatex}
%\usepackage[backend=biber,language=dutch]{biblatex}
\addbibresource{bib.bib}
\AtBeginBibliography{\footnotesize}

\begin{document}

\printbibliography
\end{document}

Tables

• Handy table generator: https://www.tablesgenerator.com/
• I prefer to use the Booktabs table style. An example can be found in the following link: https://nhigham.com/2019/11/19/better-latex-tables-with-booktabs/

Hide columns

%% to hide a column in table 
\usepackage{array}
\newcolumntype{H}{>{\setbox0=\hbox\bgroup}c<{\egroup}@{}}

SI-units

\usepackage[per-mode=symbol]{siunitx}  %usage \SI{35}{\meter\squared}
\DeclareSIUnit{\dBm}{dBm}	% add SI unit "dBm"

Clever reference

\usepackage[capitalise]{cleveref}  %usage \cref{fig:figureReference}

• Standard figure reference gives (\ref) gives: 1
• Cleveref figure references gives (\cref): fig. 1

Figures

Python to Tikz

tikzplotlib

Extract data from existing figures

https://automeris.io/WebPlotDigitizer/

Indicate lines in a plot

%draw arc
\draw (x0, y0) arc
    [
        start angle=50,
        end angle=310,
        x radius=0.1cm,
        y radius =0.6cm
    ] ;
    
%draw line 
\draw[] (x1, y1) -- (x2, y2);

%add text
\node[] (x3,  y3) {my text};

example:

Preparing for submission

Clean-up Project

LaTeX cleaner from Google Research.

Usage:

pip install arxiv_latex_cleaner
arxiv_latex_cleaner ./ --keep_bib --verbose
tar -jcvf arxiv.tar.gz gwffzkzgrjgpqksqdkfgtvzkfnjwghny_arXiv/

LaTeX cleaner's main features:

• Removes all auxiliary files (.aux, .log, .out, etc.).
• Removes all comments from your code (yes, those are visible on arXiv and you do not want them to be). These also include \begin{comment}\end{comment}, \iffalse\fi, and \if0\fi environments.
• Optionally removes user-defined commands entered with commands_to_delete (such as \todo{} that you redefine as the empty string at the end).
• Optionally allows you to define custom regex replacement rules through a cleaner_config.yaml file.

There is a 50MB limit on arXiv submissions, so to make it fit:

• Removes all unused .tex files (those that are not in the root and not included in any other .tex file).
• Removes all unused images that take up space (those that are not actually included in any used .tex file).
• Optionally resizes all images to im_size pixels, to reduce the size of the submission. You can allowlist some images to skip the global size using images_allowlist.
• Optionally compresses .pdf files using ghostscript (Linux and Mac only). You can allowlist some PDFs to skip the global size using images_allowlist.

Shortening a Paper

Biblatex hacks

• You can check how many times a certain reference is cited in the text. In this example, every reference which is only cited once is colored red.

\usepackage[backend=biber, style=ieee, citestyle=numeric-comp, maxcitenames=1,mincitenames=1, maxbibnames=1, minbibnames=1,isbn=false, doi=false,citecounter=true]{biblatex}
\addbibresource{bib.bib}
\AtBeginBibliography{\footnotesize}
\renewcommand{\finentrypunct}{%
  \addperiod\space
  \ifnum \value{citecounter} < 2
  \color{red}
  \else
   \color{Green}
    \fi
  (Cited \arabic{citecounter})%
}

• The number of names shown in the bibliography can be altered by the maxbibnames=1, minbibnames=1 option.
• What if linebreaking of titles in bibliography not working correctly. Possible solutions:
  • remove \usepackage{ulem}
  • remove \usepackage{cite}
  • remove \usepackage{natbib}