2  Reproducible Reports

The growing concern about the inability to reproduce published scientific research findings is known as the replication or reproducibility crisis.

A Nature paper by Baker (2016) states: “More than 70% of researchers have tried and failed to reproduce another scientist’s experiments, and more than half have failed to reproduce their own experiments.”

The failure to reproduce research is a function of systems pressure (defunding of public higher education), intentional actions (fraudulent scientific practices), unintentional decision-making (e.g., human error when clicking software, poor note-taking), and scientific training (e.g., methodology sections without clear protocols and details). Reproducible research is both an intentional practice and the outcome of scientific training emphasizing a specific workflow.

A primary objective of this playbook is to increase the reproducibility of public health research using line-by-line coding in R with Quarto for publishing the research with code chunks to confirm accuracy.

2.1 Reproducible Reports

You and your team will produce a reproducible Quarto Markdown report (.qmd) for your individual report and team manuscript. Specific instructions are provided in the next chapter.

Quarto provided two examples of a reproducible report and manuscript:

• Standard Quarto Report Example

• Standard Quarto Manuscript Example

The FRI Public Health Lab has produced Quarto manuscripts from active research projects:

• Health Avoiders Manuscript

• Zero Sum Full Manuscript

• Zero Sum Mini Manuscript