Introduction

This page describes how to use Latex and Lyx to edit scientific publications.

Bibliography

How to add a page number to a bibliographic entry.

“Try using @inbook instead of @book. The .bst file of this journal has several definitions for citing books. When using @book in your .bib file you are implying that you are citing the whole book, and therefore there is no need for page numbergs. When using @inbook you mean to say that you are citing a certain part of the book. If you use @inbook the bibliography will show both pages and chapter of the book you are citing.”

In the bst file, you can also check for chapter entries.

Bibtex special character

bib file have an old encoding format. It’s possible to use utf8 in bibtex, but for compatibility reason I stick with the old format.

How to write “ä” and other umlauts and accented letters in bibliography?

{\"a} {\aa} 
{\c c}
{\^e} {\`e} {\'e} 
{\u g}
{\`i} {\.I} 
{\l}
{\~n}
{\o} {\H o}
{\'u}
{\v r} {\ss}

Sample bib file content

An article citation can usually be copied from the journal website or from a search engine

@article{,
title = {},
journal = {},
volume = {},
pages = {},
year = {},
issn = {},
doi = {},
url = {},
author = {},
keywords = {},
}

A website entry

@www{,
title = {},
author = {},
journal = {},
year = {},
url = {},
}

Compilation errors

Error: LaTeX Error: Something’s wrong–perhaps a missing

“In case the error keeps presenting even you already added a \cite{something} in your paper, then you have to clear the auxiliary files. In details, delete any files ended with .log .aux .bbl .blg.”

Error message:

! Argument of \UTFviii@two@octets has an extra }.

Tex.stackexchange answer Change ü to {"u} in Düsseldorf in the bibliography.

Merge and filter bibliographies

Answers to a question on merging 2 bibtex file recommend using Jabref file / import into current database.

Create a shorter bibliography with only cited documents from another bibliography Extracting only the BibTex records relevant to the paper. Answers recommend using bibtool or bibexport.

I have written an article in Lyx which cites 2 bibliographies and a colleague asked to have a .tex version of this article. Here is my recipe:

Use Jabref to merge two bibliographies. 
Export Lyx file to LaTeX (PDFLaTeX).
Edit the .tex file to insert a link to the merged bibliographies. 
    \phantomsection\addcontentsline{toc}{section}{\refname}\bibliography{long.bib} 
Compile the .tex with TeXstudio. 
Used bibexport to extract a short bibliography corresponding only to the citations used in one article.

bibexport -o short.bib article.aux 

Replace long.bib by short.bib in the .tex file.

I have done it 3 times already. Could I create a script that does all this automatically?

Latex

Diff

Install Latex diff on Debian:

sudo apt install latexdiff

Latexdiff and git

Latexdiff-git

Latexdiff can handle files in version control systems. I didn’t know this and checked out the old file by hand before performing the comparison. First I describe the way I should have done it as explained in man latexdiff-vc

latexdiff-git -r rev1 -r rev2 eutr_impact.tex
mv eutr_impact-diff*.tex eutr_impact.tex
latexmk -pdf -bibtex -f template.tex

You can also use --flatten:

“The generic usage of this function is :”latexdiff-vc –flatten -r rev1 [-r rev2] master.tex” where master.tex is the project file containing the highest level of includes etc.”

   latexdiff-git --flatten -r 5445bfd -r b47fefa template.tex
   latexmk -pdf -bibtex -f template-diff5445bfd-b47fefa.tex

But that document didn’t compile for some reason. So I used the solution above with the diff made on the sub-document subsequently moved to another document.

You may need to add some definiotniosn in the Latex preamble of the main document

%DIF PREAMBLE EXTENSION ADDED BY LATEXDIFF
%DIF UNDERLINE PREAMBLE %DIF PREAMBLE
\RequirePackage[normalem]{ulem} %DIF PREAMBLE
\RequirePackage{color}\definecolor{RED}{rgb}{1,0,0}\definecolor{BLUE}{rgb}{0,0,1} %DIF PREAMBLE
\providecommand{\DIFadd}[1]{{\protect\color{blue}\uwave{#1}}} %DIF PREAMBLE
\providecommand{\DIFdel}[1]{{\protect\color{red}\sout{#1}}}                      %DIF PREAMBLE
%DIF SAFE PREAMBLE %DIF PREAMBLE
\providecommand{\DIFaddbegin}{} %DIF PREAMBLE
\providecommand{\DIFaddend}{} %DIF PREAMBLE
\providecommand{\DIFdelbegin}{} %DIF PREAMBLE
\providecommand{\DIFdelend}{} %DIF PREAMBLE
%DIF FLOATSAFE PREAMBLE %DIF PREAMBLE
\providecommand{\DIFaddFL}[1]{\DIFadd{#1}} %DIF PREAMBLE
\providecommand{\DIFdelFL}[1]{\DIFdel{#1}} %DIF PREAMBLE
\providecommand{\DIFaddbeginFL}{} %DIF PREAMBLE
\providecommand{\DIFaddendFL}{} %DIF PREAMBLE
\providecommand{\DIFdelbeginFL}{} %DIF PREAMBLE
\providecommand{\DIFdelendFL}{} %DIF PREAMBLE
%DIF END PREAMBLE EXTENSION ADDED BY LATEXDIFF

Without latexdiff-git

Old way of doing things without using the latexdiff-vc helper. Generate diff version of latex files. In the instructions below, the manuscript was made of 2 documents template.tex  which called \input{content.tex}.

Checkout contents from commit 9ce6b9 on 2020 December 1st and prepare the diff in the /tmp dir:

# Delete and re-create a temp dir and copy everything in it
rm -rf /tmp/article_diff/
cp -r ~/repos/article_pub /tmp/article_diff
# Copy the old and new versions of the manuscript to the tmp folder
cd ~/repos/article_pub/latex_template
git show 9ce6b9:./content.tex > /tmp/article_diff/latex_template/content_before_review.tex
git show 9ce6b9:./template.tex > /tmp/article_diff/latex_template/template_before_review.tex
cp content.tex /tmp/article_diff/latex_template/content_now.tex
cp template.tex /tmp/article_diff/latex_template/template_now.tex

Generate the diff

cd /tmp/article_diff/latex_template
latexdiff template_before_review.tex template_now.tex > template.tex
latexdiff content_before_review.tex content_now.tex > content.tex

Compile the diff document, enter quiet mode with “Q” if there are error messages

 latexmk -pdf -bibtex -use-make template.tex

Fancy Headers

Fancy header on cusom page widths

“\fancyhfoffset{0pt} makes fancyhdr recalculate for each page, based on the then current .”

 \fancyhfoffset{0pt}

Makefile

Make can be use to automate the compilation of the latex file, place the supporting figures and documents in a zip archive and subsequently remove the intermediate files.

# Usage:
# make        # Generate the pdf and zip files for the submission. 
# make render # Render the pdf, keep all automatically generated files for Latex diagnostics.
# make clean  # Keep a copy of the pdf one level above and remove automatically generated files.
# make zip    # Generate the zip archive of the article and figures for the submission process.
#
all: render clean zip

render:
     latexmk -pdf -bibtex -use-make forests-1032372-proofreading.tex

clean:
     cp forests-1032372-proofreading.pdf ../manuscript.pdf || echo "forests-1032372-proofreading.tex not there."
     git clean -xf

zip: # Remove the zip archive otherwise deleted files will remain in the archive and it will be simply updated
     rm ../manuscript.zip ../figures.zip || echo "No existing zip archive to delete."
     zip ../manuscript.zip -r *
     zip ../figures.zip -r figures/*
     echo "Verify that the pdf and zip archives have been updated by checking their update time."
     ls -lh ../*.zip
     ls -lh ../*.pdf

Math

Equation numbering

Equations written in the format below are numbered automatically. It’s possible to set the counter to 8 so that equation numbering starts at 9.

\setcounter{equation}{8}
\begin{equation}
\sumᵢ\ cₒₙᵢfₑᵣₒᵤₛ{Fᵢ︐dᵗ} + \sumᵢ\ bᵣₒₐdₗₑₐᵥₑₛ Fᵢ︐dᵗ = 1
\end{equation}

Spacing

Overleaf spacing in math mode > Description of spacing commands

LaTeX code  Description
\quad   space equal to the current font size (= 18 mu)
\,  3/18 of \quad (= 3 mu)
\:  4/18 of \quad (= 4 mu)
\;  5/18 of \quad (= 5 mu)
\!  -3/18 of \quad (= -3 mu)
\ (space after backslash!)  equivalent of space in normal text
\qquad  twice of \quad (= 36 mu)

Multicol

Documentation of the Latex multicol package

\begin{multicols}{⟨number ⟩}
⟨multicolumn text⟩
\end{multicols}

“It is often convenient to spread some text over all columns, just before the multicolumn output, without any page break in be- tween. To achieve this the multi- cols environment has an optional second argument which can be used for this purpose. For exam- ple, the text you are now reading was started with”

\begin{multicols}{3}
[\section{The User
Interface}] ...

Lyx

The Lyx “What You See is What You Mean” editor is available at Lyx and from your package manager. Citations

Lyx nicely integrates with a bibtex bibliography. You can create a shortcut such as CTRL+SHIFT+C to insert a reference. A small menu will pop-up to choose from the references.

Unfortunately “BibTeX does not support files encoded in UTF-8”. To get characters such as “é” encoded correctly latin1 has to be used.This can be set as the database property in Jabref.

Shortcuts

Under Tools / preferences / Editing / Shortcuts / Stackoverflow question on how to find the command name for a shortcut. I mapped:

citation-insert to Ctrl+Alt+C 
href-insert to Ctrl+K
label-insert to Ctrl+Alt+L
statistics to Ctrl+Alt+T

See also the Lyx wiki page on shortcuts.

Lyx shortcuts are storred in bind files. The default bind file is called cua. To restore default bind file, one can simply delete the user directory, as explained on this forum post

See also the setup directory where I saved a bind file.

Encoding

Lyx wiki unicode

Since version 1.5, LyX uses Unicode internally; the LyX file is always encoded in utf8.

The Menu Document>Settings>Language offers the Tab Encoding to specify the encoding of the LaTeX-file LyX produces. It is described in the UserGuide in Attachment A.6 “The Document Menu”: The encoding specifies how the document content is exported to LaTeX

Conversion from lyx to Markdown

I use the encoding option mentionned above to convert to latex, exported from lyx using the pdflatex format option. Then used pandoc to convert from latex to markdown. It keeps the citation references which is the most important thing I wanted to keep.

Install dependencies

Tex packages

Tex packages are located at CTAN. Most of the time it’s sufficient to install them from the Debian repository. Some times the debian repository version is outdated. In that case you can try to install the packages from the backports:

sudo vim /etc/apt/sources.list
# Add deb http://ftp.debian.org/debian stretch-backports main 
# Or a mirror, for example
# deb http://ftp.it.debian.org/debian stretch-backports main
sudo apt update
sudo apt-get -t stretch-backports install texlive-bibtex-extra

Spell checker

A spell checker can be activated under Tools / preferences / language settings / spellchecker. On my system the only spell check engine available is Enchant, “a wrapper that provides automatic access to many spell checking libraries (ispell, aspell, hspell, hunspell, etc.)”.

The button displaying a red-underlined A can be activated to spell check continuously. Language of document

Under Document / Settings / Language, it’s possible to change the document language, which will have an impact on the language used for spell checking. In my system compiling a document in French returned an error:

"Package babel Error: Unknown option `french'."

This stackexchange post suggest installing the texlive-lang-french Debian package. This fixed the error. Math mode

Encoding

This question on “how do I prevent Lyx from loading inputenc?” explains where this part of the Latex preamble is defined.

In Document > Settings…, under Language > Encoding, choose “Other” and select “Language Default (no inputenc)”.

Instead I replaced Latin1 by utf8 as input encoding. This works for the moment.

Instead I replaced Latin1 by utf8 as input encoding. This works for the moment.

Math

Press CTRL+M at the cursor or on highlighted text to enter math mode. Latex syntax “”, “x_t” can be used to enter equations and is displayed directly as math symbols. Change input encoding

How to enter a column vector Has recommendations on how to enter matrix operations with sub-variables.

Fonts

Icons

Font-awesome is available in the Debian Package “texlive-fonts-extra”. It can be used in Lyx by insterting \usepackage{fontawesome} in the Latex preamble. Then insert an icon with:

\faComments
\faWrench

Encoding issues and Greek symbols used outside math mode

“Encoding file ‘lgrenc.def’ not found” was fixed by installing the debian package texlive-lang-greek (as explained here on stackoverflow). Other errors appeared related to the use of beta signs outside math mode. As one user explained on stackoverflow, placing signs in math mode usually fixes the issue. Hyperlinks in PDF

Elsevier article template

Elsevier provides a latex template for articles called elsarticle which is usable in Lyx. However compiling with this template doesn’t seem to work when using the hyperref package with the general option “automatically fill header”. After deactivating this option, compilation works again.

The elsarticle template uses numerical references by default. it is possible to activate author year reference according to this stack exchange answer. Tips

CTRL+D uses yap, a faster (on windows) previewer than the default PDF one. There is no noticeable difference on Linux.

Other templates

To produce a meeting report with a wider template than the default article.

I would have liked to find an overview of the templates with screenshots of PDF results. But I couldn't find such overview online. LyX wiki has a list of examples and a list of layouts. 
In fact all that was needed was to edit the Document \ Settings \ Page margins, I set the inner and out margins to 2 cm and was happy with the result.

knitr and Lyx

Yihui Xie: Using knitr and Lyx
 Krishna Devulapalli: Creation of research papers with embedded R results using LyX

My Lyx file uses many packages and formatting options. Export to RTF didn’t work and returned the error:

"An error occurred while running: latex2rtf"

I made a copy in a temporary directory (/tmp) and removed external packages and options in the latex preamble, before performing the conversion. Then the conversion to RTF worked.

Compare different versions of a document

Use Tools/Compare to highlight differences between a new and an old document. Then show changes in output to show changes in red and blue in the PDF output.

Alternatively, you can export the Lyx files to Latex and use Latexdiff as such:

latexdiff draft.tex revision.tex > diff.tex

Avoid complex tables or figures in the diff, as they can cause issues. I had to create a fake old documents with final figures and table for latexdiff to return a usable output.