Reproducible Reseach with Quarto

Demo for BDSI Workshop

Authors

Affiliation

Emi Tanaka

Australian National University

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Abstract

Reproducible research is indispensable for ensuring the trustworthiness of scientific findings. This abstract explores its significance, emphasizing open access to data, code, and documentation. Key practices such as version control and reproducible environments are highlighted for their role in enhancing verifiability. Additionally, the integration of reproducibility criteria in peer review is discussed. Overall, reproducible research serves as a vital framework for advancing scientific knowledge with transparency and integrity.

Keywords

reproducible research, quarto, markdown

1 Introduction

argued that we should clean data using their approach. The figure is using ggplot2 (Wickham 2016).

Reproducible research refers to the practice of making research methods, data, and results transparent and accessible so that others can verify and replicate the findings. The goal of reproducibility is to ensure that scientific findings are trustworthy and can be independently validated.

2 Background

This document is made using Allaire and Dervieux (2024). The figures are made using the ggplot2 R package (Wickham 2016).

3 Tasks

Warning

1. There is a Julia, Python and R code chunks in this document. Delete the code chunks that are not relevant to your work.
2. Look at Section 2 and Section 4.

4 Results

4.1 For R users

DELETE IF IRRELEVANT FOR YOU

Figure 1 shows that the setosa species is clearly separated from the other two species in terms of the of length and width of the sepal. We can see in Table 1 that setosa has a much larger length of the sepal and smaller width compared to the other two species.

Figure 1: The scatterplot of Sepal Length and Sepal Width by Species.

Figure 2: Scatter plot for cars dataset

Figure 1 shows a scatterplot!!!!

Table 1: The mean of Sepal Length and Sepal Width by Species.

Table 1 shows data!!

4.2 For Python users

DELETE IF IRRELEVANT FOR YOU

4.3 For Julia users

DELETE IF IRRELEVANT FOR YOU

5 Conclusion

Reproducible research not only fosters trust in scientific findings but also promotes collaboration and innovation by allowing others to build upon existing research. Many journals and funding agencies now require or encourage researchers to adopt reproducible practices to improve the reliability and credibility of scientific research.

References

Allaire, JJ, and Christophe Dervieux. 2024. Quarto: R Interface to ’Quarto’ Markdown Publishing System. https://CRAN.R-project.org/package=quarto.

Wickham, Hadley. 2016. Ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York. https://ggplot2.tidyverse.org.