Hands On Working With Quarto Manuscript

Author
Affiliation

Joseph Bulbulia

Victoria University of Wellington, New Zealand

Published

May 13, 2025

Part 1: Quarto manuscripts

Note

Required Download Quarto here: - Use the prelease version: https://quarto.org/docs/download/ Optional - (Bulbulia 2024) link - (Hoffman et al. 2023) link

Hoffman, Katherine L., Diego Salazar-Barreto, Kara E. Rudolph, and Iván Díaz. 2023. “Introducing Longitudinal Modified Treatment Policies: A Unified Framework for Studying Complex Exposures,” April. https://doi.org/10.48550/arXiv.2304.09460.
Bulbulia, J. A. 2024. “A Practical Guide to Causal Inference in Three-Wave Panel Studies.” OSF. https://doi.org/10.31234/osf.io/uyg3d.
Key concepts
  • Writing up your manuscript
For the lab, download the script
  • We will go through this script step-by-step.

To Do

  • Download the script (from week 9) and store in our R directory: link to analysis script

  • Download the manuscript template and store in our R directory: link to manuscript template

  • Download the following tex file and save it to your R directory: latex macros

  • Download the followign tex file and save it to your R directory: title preamble

  • Download the following csl file and save it to your R directory: csl preamble

  • Make sure you can install all libraries required of the manuscript template.

  • Come to the seminar prepared to work through the analysis

What You Will Learn

  • How to create a publication quality manuscript

  • How to create a workflow for references

  • How to import results into your manuscript

  • How to make graphs of your results (using) margot

  • How to report your results

  • How to interpret your results

Packages

report::cite_packages()
  - Bulbulia J (2024). _margot: MARGinal Observational Treatment-effects_. doi:10.5281/zenodo.10907724 <https://doi.org/10.5281/zenodo.10907724>, R package version 0.3.1.0 Functions to obtain MARGinal Observational Treatment-effects from observational data., <https://go-bayes.github.io/margot/>.
  - Chang W (2023). _extrafont: Tools for Using Fonts_. R package version 0.19, <https://CRAN.R-project.org/package=extrafont>.
  - Grolemund G, Wickham H (2011). "Dates and Times Made Easy with lubridate." _Journal of Statistical Software_, *40*(3), 1-25. <https://www.jstatsoft.org/v40/i03/>.
  - Müller K, Wickham H (2023). _tibble: Simple Data Frames_. R package version 3.2.1, <https://CRAN.R-project.org/package=tibble>.
  - R Core Team (2024). _R: A Language and Environment for Statistical Computing_. R Foundation for Statistical Computing, Vienna, Austria. <https://www.R-project.org/>.
  - Wickham H (2016). _ggplot2: Elegant Graphics for Data Analysis_. Springer-Verlag New York. ISBN 978-3-319-24277-4, <https://ggplot2.tidyverse.org>.
  - Wickham H (2023). _forcats: Tools for Working with Categorical Variables (Factors)_. R package version 1.0.0, <https://CRAN.R-project.org/package=forcats>.
  - Wickham H (2023). _stringr: Simple, Consistent Wrappers for Common String Operations_. R package version 1.5.1, <https://CRAN.R-project.org/package=stringr>.
  - Wickham H, Averick M, Bryan J, Chang W, McGowan LD, François R, Grolemund G, Hayes A, Henry L, Hester J, Kuhn M, Pedersen TL, Miller E, Bache SM, Müller K, Ooms J, Robinson D, Seidel DP, Spinu V, Takahashi K, Vaughan D, Wilke C, Woo K, Yutani H (2019). "Welcome to the tidyverse." _Journal of Open Source Software_, *4*(43), 1686. doi:10.21105/joss.01686 <https://doi.org/10.21105/joss.01686>.
  - Wickham H, François R, Henry L, Müller K, Vaughan D (2023). _dplyr: A Grammar of Data Manipulation_. R package version 1.1.4, <https://CRAN.R-project.org/package=dplyr>.
  - Wickham H, Henry L (2023). _purrr: Functional Programming Tools_. R package version 1.0.2, <https://CRAN.R-project.org/package=purrr>.
  - Wickham H, Hester J, Bryan J (2024). _readr: Read Rectangular Text Data_. R package version 2.1.5, <https://CRAN.R-project.org/package=readr>.
  - Wickham H, Vaughan D, Girlich M (2024). _tidyr: Tidy Messy Data_. R package version 1.3.1, <https://CRAN.R-project.org/package=tidyr>.
  - Xie Y (2024). _tinytex: Helper Functions to Install and Maintain TeX Live, and Compile LaTeX Documents_. R package version 0.54, <https://github.com/rstudio/tinytex>. Xie Y (2019). "TinyTeX: A lightweight, cross-platform, and easy-to-maintain LaTeX distribution based on TeX Live." _TUGboat_, *40*(1), 30-32. <https://tug.org/TUGboat/Contents/contents40-1.html>.