Software tools for research, writing & teaching

In my work, I now largely use:

• Research papers: Rmarkdown .Rmd for things R and mathy; MS Word for mostly text and images
• Presentations: Still using PPT; tried Quarto and reveal.js slides, but doesn’t work for my style
• Teaching: R notebooks (.R with #' comments) and.Rmd` works loverly!

But still old-school on tools that work very well for me.

Bibliographies

• I have been using BibTeX databases for many years.
  • Designed for LaTeX: \bibliography{graphics, statistics, Rpackages}. Cite with BibTeX keys: \cite{Agresti:90}

  @BOOK{Agresti:90,
  title = {Categorical Data Analysis},
  publisher = {Wiley-Interscience},
  year = {1990},
  author = {A. Agresti},
  address = {New York},
  isbn = {0-471-85301-1},
  lccn = {QA278 .A353 1990}
  }
  @book{FriendlyMeyer:2016:DDAR,
    Author = {Michael Friendly and Meyer, David},
    Title = {Discrete Data Analysis with {R}: Visualization and Modeling Techniques for Categorical and Count Data},
    Address = {Boca Raton, FL},
    Isbn = {978-1-4987-2583-5},
    Publisher = {Chapman \& Hall/CRC},
    Year = {2016}
    }

Methods for categorical data analysis are described by \cite{Agresti:90,FriendlyMeyer:2016:DDAR} …

• Change citation / biblio style easily for entire document: bibliographystyle{apa}
• Now works well with Rmarkdown / Pandoc and .csl style files: csl: apa.csl in YAML header

Methods for categorical data analysis are described by [@Agresti:90,@FriendlyMeyer:2016:DDAR] …

• R packages:
  • citr – RStudio add-in to search for references in a .bib file, inserting the key in the document;
  • knitcitations – also use DOIs and URLs to cite a paper. E.g. citet("10.1098/rspb.2013.1372") will create a citation to @Boettiger_2013
  • See: A Roundup of R Tools for Handling BibTeX for a good overview

Bibliography database manager

• As a biblio database manager, I use Jabref, https://www.jabref.org/
  • Easy import for over 15 reference formats
  • Fetch biblio info based on ISBN, DOI, …
  • Group references in hierarchical categories;
  • Browser extensions for Firefox, Chrome, …

Equations

• LaTeX is unsurpassed for writing simple or complex mathematical equations, but takes some time to learn work with it.

\begin{equation} \label{eq:linreg}
y = \mathbf{X} \beta + \epsilon
\end{equation}

Renders as: \[y = \mathbf{X} \beta + \epsilon\]

• Works more or less the same with Rmarkdown. In R Studio, this renders inline in the editor window

• For MS Word, Powerpoint, I use MathType, https://mathtype.en.softonic.com/, an interactive visual equation editor. Choose from the menu buttons, or just type y = \mathbf{X} \beta + \epsilon in the equation window.

• See an equation in a journal article, or written on paper? https://mathpix.com/ works reasonably well to convert that into LaTeX. Have to register, but there is a $0.00 option for Edu use.

Tables

• I used to use LaTeX exclusively

\begin{tabular}{llrr}
Model    &  Model symbol       &    df    &  \(G^2\)    \\ \hline
Marginal & [Hair] [Eye]        &     9    & 146.44      \\
Joint    & [Hair, Eye] [Sex]   &    15    &  19.86      \\ \hline
Mutual   & [Hair] [Eye] [Sex]  &    24    & 166.30
\end{tabular}

• With R, the xtable package generates tables in LaTeX or HTML, for data, model summaries, etc. knitr::kable() does as well, with fancier stuff in kableExtra.

• Other R table packages: GT

• Tables generator online: https://www.tablesgenerator.com/. Import a CSV, visually design your table, output in LaTeX, HTML, markdown, …