After analysis · writing and sharing reproducible resources

name: title
class: Left, middle

# After analysis &#183; writing and sharing reproducible resources

### [Act II] Recomendations and practices for open and reproducible research

.large[Reproducible Research Practices (RRP'23) &#183; April 2023]

.right[Carlos Granell &#183; Sergi Trilles]

.right[Universitat Jaume I]

---
class: inverse, bottom, middle

## Nobel laureate and physics professor Wolfgang Pauli

.large["I do not mind if you think slowly, but I do object when you publish more quickly than you think.”]

???

[Wolfgang Pauli](https://es.wikipedia.org/wiki/Wolfgang_Pauli), [Quotes](https://en.wikiquote.org/wiki/Wolfgang_Pauli)

---
name: rec21
class: inverse, center, middle

# .blue.bg-white[\#21]

# Avoid *Data (or code) available upon request*

---
class: left
### Data (or code) available upon request

.huge[.small[<a name=cite-stodden2018></a>[[SSM18](https://www.pnas.org/doi/abs/10.1073/pnas.1708290115)]] -  An empirical analysis of journal policy effectiveness for computational reproducibility]

.large[...only .gray.bg-blue[44%] of requests led to receiving data and/or code from the original authors]

---
name: rec22
class: inverse, center, middle

# .blue.bg-white[\#22]

# Report the software version you use

---
class: left, top
### Software version

.huge[Specify versions of relevant software components (packages, libraries)]

.huge[A different version can lead to different results!]

.large[.small[<a name=cite-mesnard2017></a>[[MB17](https://doi.org/10.1109/MCSE.2017.3151254)]] - Reproducible and Replicable Computational Fluid Dynamics: It's Harder Than You Think]

-   .large[Check "Story 4: Different Versions of Code, External Libraries, or Compilers can Challenge Reproducibility"]

---
name: rec23
class: inverse, center, middle

# .blue.bg-white[\#23]

# Cite the software you use

---
class: left
### Software citation

.huge[Cite software that's important to the research outcome]

-   .large[[R engine](https://ropensci.org/blog/2021/11/16/how-to-cite-r-and-r-packages/)?]

- type  `citation()` to get reference publication in bibtex entry
  - add "All analyses were performed using R Statistical Software (v4.2.2; R Core Team 2022)" to **DASA section**

-   .large[[R packages](https://ropensci.org/blog/2021/11/16/how-to-cite-r-and-r-packages/)? It depends...]

- type `citation("<packageName>")` to get reference publication in bibtex format 
  - add "Temperature data was obtained from Environment and Climate Change Canada via the `weathercan` R package (v0.6.2; LaZerte and Albers 2018)" to **DASA section**.

---
class: left
### Software citation

.huge[[`report`](https://cran.r-project.org/package=report) R Package]

```r
report::report_system()
```

```
## Analyses were conducted using the R Statistical language (version 4.2.2; R Core
## Team, 2022) on Windows 10 x64 (build 22621)
```

```r
report::report_packages()
```

```
##   - xaringanthemer (version 0.4.2; Aden-Buie G, 2022)
##   - xaringanExtra (version 0.7.0; Aden-Buie G, Warkentin M, 2022)
##   - report (version 0.5.6; Makowski D et al., 2023)
##   - RefManageR (version 1.3.0; McLean MW, 2017)
##   - here (version 1.0.1; Müller K, 2020)
##   - R (version 4.2.2; R Core Team, 2022)
```

---
class: left
### Software citation

.pull-left[

.huge[Do not use URL to cite external library/code/software]

-   .large[Cite `SciPy` as a footnote: https://scipy.org/?]

]

.pull-right[

.huge[Cite software as any other paper instead]

-   .large[Cite `SciPy` as a paper: [Virtanen et al. (2020)](https://scholar.google.com/scholar?hl=en&as_sdt=0%2C5&q=SciPy+1.0%3A+fundamental+algorithms+for+scientific+computing+in+Python&btnG=)?]

]

.huge[Readings:]

-   .large[[Software Citation Checklist for Authors](https://zenodo.org/record/3479199#.YYmfT73MKAk)]

-   .large[Software citation principles .small[<a name=cite-smith2016></a>[[SKN16](https://doi.org/10.7717/peerj-cs.86)]]]

---
name: rec24
class: inverse, center, middle

# .blue.bg-white[\#24]

# Hello Quarto (and friends)