Elevate research projects with Quarto

MS Víctor Gauto
victor.gauto@ca.free.utn.edu.ar

GISTAQ (UTN-FRRe)

IIDTHH (UNNE, CONICET)

Instituto Gulich (UNC, CONAE)

Dr. Matías Bonansea

ICBIA (UNRC, CONICET)

Dr. Anabella Ferral

Instituto Gulich (UNC, CONAE)

Dr. Osvaldo Cardozo

IIDTHH (UNNE, CONICET)

Dr. Claudia Giardino

IREA (CNR)

2025-03-24

1 Content

  • Introduction ( 2)
  • Motivation ( 3)
  • Tools ( 4)
  • Conclusion ( 5)
  • Future improvements ( 6)
  • Resources ( 7)
https://vhgauto.quarto.pub/seminario2-gulich/

2 Introduction

Research project

To estimate water quality indicators in Paraná River middle basin for algorithm development using satellite remote sensing techniques

Collaborative website with automatic running, interactive and open source.

2.1 Front page

  • Authors
  • Affiliation
  • Last modified date
  • Keywords
  • More resources links

2.2 Table of content

  • Sections and subsections
  • Ease website navigation
  • Variable content according to the development

2.3 Notebooks

  • Source code description
  • Processing data justification
  • Calculus methodology explanation to promote reproducibility

2.4 References

  • Formatted references according to desired style (.csl)
  • Reference preview on citation hover

2.5 Maps, tables & interactive plots

  • Results visualization
  • Correlation between parameters exploration
  • Spectral properties description
  • Sample site location

Web site 

https://vhgauto.quarto.pub/gistaq-parana/

3 Motivation

Research project typical life journey.

%%{
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    }
  }
}%%

flowchart LR
    a1[Thinking] ==> a2[Beginning]
    a2 ====> |<span class="svg-spinners--clock"></span>| a3[Main goal]

    a3 ==> a4([Paper])
    a3 ==> a5([Conference])
    a3 ==> a6([Report])

classDef default stroke:#FFC0CB,color:#FFFFFF,fill:#224289;

  • Water sampling
  • Physicochemical test
  • Partial results analyses
  • Reference reading
  • Other tasks

3.1 During the project development

  • Dynamic document, that adapts to the current project state.

  • Easy access site to check the latest results.

  • Unified reference search.

  • Script code execution and results reproducibility.

  • All project members can work seamless and without problems and no fear of disarranging the document.

  • Consultation resource and to admire all the effort done.

4 Tools

  • R y Python: reading and data collection; processing and results storage; plots, tables and maps generation.

  • Git y GitHub: version control management and project members collaboration.

  • Quarto: to content compilation and website publishing.

    • manuscript allows website creation with an emphasis in reproducibility and targeted to scientific and academic documents.

4.1 R

targets allows automatic functions execution and dependencies management between them.

Check current workflow state and execute only outdated targets.

File monitoring and code re-execution when change detection.

4.2 R

graph LR
  x3d474db92cf09724>"mensaje"] ==> xc5ec810879cc40ee>"recorte"]
    x3d474db92cf09724>"mensaje"] ==> x32cb0d977e75588d>"elimino"]
    x3d474db92cf09724>"mensaje"] ==> x0dc39fa9e42347ba>"reflectancia"]
    x3d474db92cf09724>"mensaje"] ==> x0e71b645b3e50d0c>"script_descarga_py"]
    x3d474db92cf09724>"mensaje"] ==> x70dd0adf732b9ac4>"estado_descarga"]
    xfabd587be49f2fed>"fecha"] ==> x0dc39fa9e42347ba>"reflectancia"]
    xfabd587be49f2fed>"fecha"] ==> x38637a02f9b83fc8>"lab"]
    x0e71b645b3e50d0c>"script_descarga_py"] ==> x70dd0adf732b9ac4>"estado_descarga"]
    x2eb57580dd338e28(["excel"]) ==> x1a91c1978c7a143b(["datos_lab"])
    x38637a02f9b83fc8>"lab"] ==> x1a91c1978c7a143b(["datos_lab"])
    x3975d57dc4a04f5c>"descarga"] ==> x0a08cea06a6d211f(["producto_zip"])
    xe56f95f4237d1e66(["script_py"]) ==> x0a08cea06a6d211f(["producto_zip"])
    xd2e55a6b497fb062(["fecha_descarga"]) ==> x4b150ba8dbe4203d(["recorte_tif"])
    x0a08cea06a6d211f(["producto_zip"]) ==> x4b150ba8dbe4203d(["recorte_tif"])
    xc5ec810879cc40ee>"recorte"] ==> x4b150ba8dbe4203d(["recorte_tif"])
    x29bd13377b9e6171>"archivo_excel"] ==> x2eb57580dd338e28(["excel"])
    x2eb57580dd338e28(["excel"]) ==> xd2e55a6b497fb062(["fecha_descarga"])
    xfabd587be49f2fed>"fecha"] ==> xd2e55a6b497fb062(["fecha_descarga"])
    xd2e55a6b497fb062(["fecha_descarga"]) ==> xe56f95f4237d1e66(["script_py"])
    x0e71b645b3e50d0c>"script_descarga_py"] ==> xe56f95f4237d1e66(["script_py"])
    x2eb57580dd338e28(["excel"]) ==> x75ae8feee719d1e2(["datos_gis"])
    xd2e55a6b497fb062(["fecha_descarga"]) ==> x75ae8feee719d1e2(["datos_gis"])
    x4b150ba8dbe4203d(["recorte_tif"]) ==> x75ae8feee719d1e2(["datos_gis"])
    x0dc39fa9e42347ba>"reflectancia"] ==> x75ae8feee719d1e2(["datos_gis"])

  classDef default stroke:#FFC0CB,color:#FFFFFF,fill:#224289;

4.3 R

renv execution environment management, package version and its dependencies.

Log file that allows environment reproducibility.

4.4 R

tidyverse with multiple packages for general purpose data processing and manipulation.

terra for geographic data processing and vector and raster reading.

corrr linear correlation coefficient calculation.

4.5 R

ggplot2 for basic plot creation (.png).

ggiraph for interactive plot creation (.html).

leaflet for interactive map creation (.html).

4.6 PYTHON

Copernicus Data Space

  • Collection
  • Processing level
  • Region of interest
  • Time range
  • Credentials

4.7 GIT

Version control management and simultaneous collaboration between project members.

github cloud storage service.

branch per member, so each one works in a specific section without interfering with the remaining repository.

pull request to request adding changes.

merge to combine changes once checked and accepted.

4.8 QUARTO

  • Combines code execution by programming language and narrative text to create a product in multiple formatted options

  • Offers a publishing platform for the output and to access it as a website

%%{
  init: {
    'themeVariables': {
      'edgeLabelBackground': '#224289',
      'edgeLabel': 'red'
    }
  }
}%%

flowchart LR
  s1[<span class="ant-design--code-filled"></span><br>scripts]:::e1 ==> q1[<span class="simple-icons--quarto"></span><br>quarto]:::e1

  s2[<span class="material-symbols--markdown"></span><br>markdown]:::e1 ===> q1

  s3[<span class="fe--document"></span><br>text]:::e1 ===> q1

  s4[<span class="file-icons--latex"></span>]:::e1 ==> q1

  q1 ==> h1[<span class="qlementine-icons--file-html-16"></span><br>html]:::e1

  h1 ==>|<b style='color:white'>quarto pub</b>| w1[<span class="mdi--web"></span><br>website]:::e1

  classDef e1 stroke:none,color:#FFFFFF,fill:none;

4.9 QUARTO

4.10 QUARTO

  • Manuscript is design for scientific document authoring, with emphasis in reproducibility, since it encourages the readers to explore processing scripts (notebooks).

  • Offers multiple static outputs that follow an specific template from a magazine.

  • It allows to deploy the website in Quarto Pub or GitHub Pages .

  • In combination with targets, plots/tables/maps are regenerated with new data input, or script modification, updating the results.

4.11 QUARTO

File and directories tree.

quarto_manuscript
├── bibliography
│   ├── ieee.csl
│   └── reference.bib
├── data
│   ├── laboratory.csv
│   └── reflectance.csv
├── plot
│   ├── boxplot.png
│   └── time_series.png
├── manuscript.qmd
├── notebooks
│   ├── plots.qmd
│   └── data_reading.qmd
├── _publish.yml
├── raster
├── scripts
│   ├── functions.R
│   └── support.R
├── vectors
├── _quarto.yml
└── _targets.R

4.12 QUARTO

manuscript.qmd
---
title: Research Project
author: Víctor Gauto
date: last modified
---

# Introducción

**Paraná River** has <i>water</i>.

````{r}
ggplot(data, aes(x, y)) +
  geom_point()
````

4.13 QUARTO

_quarto.yml
project:
  type: manuscript

manuscript:
  article: manuscrito.qmd
  notebooks:
    - notebooks/data_reading.qmd

format:
  html:
    lang: es
    include-in-header:
      - extras/favicon.html
    theme:
      - extras/my_style.scss
    toc: true
    code-link: true
    code-copy: true
    tbl-cap-location: margin
    fig-cap-location: bottom
    bibliography: bibliography/reference.bib
    csl: bibliography/ieee.csl
    html-math-method: katex

4.14 QUARTO

_publish.yml
- source: project
  quarto-pub:
    - id: ff90d76c-20c0-4210-8791-5d868ede4c50
      url: https://vhgauto.quarto.pub/gistaq-parana

5 Conclusion

The Research Project development allowed us to learn a new set of tools.

6 Future improvements

  • Rewrite functions used by targets.
    • Define arguments clearly.
    • Return descriptive messages during runtime and in case of errors.
    • Incorporate website rendering.
  • Optimize satellite data download, avoiding to get the entire product.
    • Google Earth Engine.
    •  rsi package.
  • Organice website visual features (colors, fonts, styles, margins) in the .scss file.
  • Use the full potential of Manuscript, so the results are created by the notebooks.

Thanks for your time

MS Víctor Gauto

victor.gauto@ca.frre.utn.edu.ar

/vhgauto

7 Resources

Download

This presentation repository

Reproducible Manuscripts with Quarto - posit::conf(2023)

Quarto for Academics | Mine Çetinkaya-Rundel

Quarto | Get started

Quarto Manuscripts

The {targets} R package user manual

Introduction to renv

R for Data Science (2e)

ggiraph-book

Quarto: The Definitive Guide

Website repository

Quarto Extensions

Official repository for Citation Style Language (CSL) citation styles

8

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