Duke University + Posit
mine.quarto.pub/manuscripts-conf23
Can run all code in a single file, and don’t mind running it over and over again with each edit.
e.g. Data Science 101 - HW 1, Stat 101 - Final project, a blog post, a tutorial, a not-too-extensive consulting report, etc.
Can run all code in a single file, and don’t mind running it over and over again with each edit, and need an output that conforms to journal style.
e.g., a not-too-computational journal article.
or
or
A notebook is a document that contains both code and narrative:
.ipynb
).qmd
) – a potential mindshiftMost computational science is born in notebooks
and dies ends in PDF or Word documents
that are not just PDFs that are the outputs of a single qmd file
An end-to-end scholarly publishing workflow that treats Jupyter and Quarto notebooks as a primary element of the scientific record.
A publication process that elevates transparent and reproducible work by authors, where data and software, together with narrative, are documented, shared, and archived.
New forms of credit to the wider research community, including research software engineers or rsearch software engineers.
type: manuscript
type: manuscript
Quarto manuscripts (Quarto 1.4+), in addition to doing everything you can do with journal articles, can
produce manuscripts in multiple formats (including LaTeX or MS Word formats required by journals), and give readers easy access to all of the formats through a website
publish computations from one or more notebooks alongside the manuscript, allowing readers to dive into your code and view it or interact with it in a virtual environment
quarto create project manuscript <name>
Manuscripts ♥️ Git + GitHub
Track your project with Git and host on GitHub for easy publishing.
In quarto.yml
of the project:
In index.qmd
of the project:
---
title: La Palma Earthquakes
author:
- name: Steve Purves
orcid: 0000-0002-0760-5497
corresponding: true
email: steve@curvenote.com
roles:
- Investigation
- Project administration
- Software
- Visualization
affiliations:
- Curvenote
- name: Rowan Cockett
orcid: 0000-0002-7859-8394
corresponding: false
roles: []
affiliations:
- Curvenote
license: CC BY-SA 4.0
keywords:
- La Palma
- Earthquakes
date: '2022-05-11'
abstract: |
In September 2021, a significant jump in seismic activity on the island of La Palma (Canary Islands, Spain) signaled the start of a volcanic crisis that still continues at the time of writing. Earthquake data is continually collected and published by the Instituto Geográphico Nacional (IGN). We have created an accessible dataset from this and completed preliminary data analysis which shows seismicity originating at two distinct depths, consistent with the model of a two reservoir system feeding the currently very active volcano.
keypoints:
- You may specify 1 to 3 keypoints for this PDF template
- These keypoints are complete sentences and less than or equal to 140 characters
- 'They are specific to this PDF template, so they will not appear in other exports'
citation:
container-title: Notebooks Now!
draft: false
bibliography: references.bib
echo: false
---
from source \(\rightarrow\) only relevant / required metadata in manuscript:
from source \(\rightarrow\) only relevant / required metadata in manuscript:
We’ve seen that you can peruse the code underlying the figures and tables in the manuscript
What if you wanted to interact with the code – in a computational environment that’s just a click away and that has all the software and packages needed to reproduce the manuscript?
with quarto use binder
:
mine.quarto.pub/manuscripts-conf23
github.com/mine-cetinkaya-rundel/quarto-manuscripts