Share-data-code-presentation.qmd

---
title: "Share your data and code!"
subtitle: "CES Skills Seminars"  
author: 
  - "José R. Ferrer-Paris" 
  - "(a.k.a. Jose Ferrer; JR)"
date: '`r Sys.Date()`'
format: 
  revealjs:
    theme: simple
    footer: "CES Skills seminar / 20th April 2023 / JR Ferrer-Paris"
    logo: img/ces-logo-transparent.png
    css: 
      - css/logo.css
      - css/inat.css
preview-links: true
title-slide-attributes:
    data-background-image: "https://inaturalist-open-data.s3.amazonaws.com/photos/268028588/large.jpg"
    data-background-size: contain
    data-background-color: "black"
    data-background-opacity: ".6"
editor_options: 
  chunk_output_type: console
---

# My observation of the weekend

[{{< fa solid fish-fins >}} inaturalist.org/observations/155084844](https://www.inaturalist.org/observations/155084844)


## Community id {.smaller}

```{r}
#| echo: true
library(rinat)
library(dplyr) 
user_obs <- get_inat_obs_user("NeoMapas")  %>% 
  filter(common_name %in% "Girdled Scalyfin")
```

```{r}
user_obs %>% 
  DT::datatable(filter="none",options=list(searching=FALSE, paging=FALSE))
```

## My collection of observations

```{r}
#| echo: true
#| output-location: slide
library(leaflet)
library(sf)
obs_df <- 
get_inat_obs_user("NeoMapas")  %>% 
  select(longitude, latitude, datetime, common_name, 
      scientific_name, image_url) %>%
  st_as_sf(coords=c("longitude", "latitude"), crs=4326)
popup_html <- with(obs_df, 
                   sprintf("<p><b>%s</b><br/><i>%s</i></p>
                           <p>Observed: %s<br/>
                           <p><img src='%s'/></p>", 
                           common_name,  scientific_name,
                           datetime, image_url))
leaflet(obs_df) %>% 
  addProviderTiles("Esri.WorldStreetMap") %>% 
  addMarkers(data = obs_df,
                   popup = ~popup_html)
```


# What is Open Science

> Open science is the movement to make scientific research (including publications, data, physical samples, and software) and its dissemination accessible to all levels of society, amateur or professional.

https://en.wikipedia.org/wiki/Open_science

## Why Open Science ? {.smaller}

::: columns
::: {.column width="60%"}
> Open Science has the potential of making the scientific process more transparent, inclusive and democratic.  It is increasingly recognized as a critical accelerator for the achievement of the United Nations Sustainable Development Goals and a true game changer in bridging the science, technology and innovation gaps and fulfilling the human right to science.

https://www.unesco.org/en/open-science
:::
::: {.column width="40%"}

<a title="UNESCO.org, CC BY-SA 4.0 &lt;https://creativecommons.org/licenses/by-sa/4.0&gt;, via Wikimedia Commons" href="https://commons.wikimedia.org/wiki/File:UNESCO-Open_science-pillars-en.png"><img width="512" alt="UNESCO-Open science-pillars-en" src="https://upload.wikimedia.org/wikipedia/commons/thumb/d/d8/UNESCO-Open_science-pillars-en.png/512px-UNESCO-Open_science-pillars-en.png"></a>

:::
:::

## But seriously, why?

<a title="Roche DG, Lanfear R, Binning SA, Haff TM, Schwanz LE, et al. (2014), CC BY 4.0 &lt;https://creativecommons.org/licenses/by/4.0&gt;, via Wikimedia Commons" href="https://commons.wikimedia.org/wiki/File:To_deposit_or_not_to_deposit,_that_is_the_question_-_journal.pbio.1001779.g001.png"><img width="512" alt="To deposit or not to deposit, that is the question - journal.pbio.1001779.g001" src="https://upload.wikimedia.org/wikipedia/commons/thumb/6/65/To_deposit_or_not_to_deposit%2C_that_is_the_question_-_journal.pbio.1001779.g001.png/512px-To_deposit_or_not_to_deposit%2C_that_is_the_question_-_journal.pbio.1001779.g001.png"></a>

## We all benefit from Open Science

- Everybody wins
- Be **more efficient**
- Avoid common problems / **find solutions faster**
- Increases **collaboration**
- **Contribute** what you can, **use** what you need
- Get **credit for your work**

::: aside
Emma MacKenzie, Sophie Winterbourne, Felicity Anderson, Edward Wallace; The benefits of an open-science approach in student research projects. Biochem (Lond) 23 December 2021; 43 (6): 66–73. doi: https://doi.org/10.1042/bio_2021_198
:::


---

![Kramer, Bianca, & Bosman, Jeroen. (2018, January 14). Rainbow of open science practices. Zenodo. https://doi.org/10.5281/zenodo.1147025](img/rainbow-of-open-science-practices.png)

# {{< fa book-open-reader >}} Prepare yourself

To maximise discovery and reuse you should employ best practices in preparing and publishing your code and data to make it [*F*indable *A*ccesible *I*nteroperational *R*eusable](https://www.go-fair.org/fair-principles/). 

## {{< fa book-open-reader >}} Think about

### Intelectual property

### Data availability policies of journals/funders

### File formats

### Do you work with [sensitive data](https://research.unsw.edu.au/handling-sensitive-data)?

:::aside
Check also ARDC's [Research Data Rights Management Guide](https://ardc.edu.au/resource/research-data-rights-management-guide/)
:::

---

![](https://research.unsw.edu.au/sites/default/files/uploads/groups/pvcri/RTS/DataClassificationGuide_Web%20Ver.%20Aug%202019-page-002.jpg)

## {{< fa book-open-reader >}} Persistent identifiers


:::: r-stack
::: {.fragment .fade-out}
### Identify yourself

Use a unique identifier like ORC{{< fa brands orcid >}} 

<blockquote class="twitter-tweet"><p lang="en" dir="ltr">Should I pronounce <a href="https://twitter.com/ORCID_Org?ref_src=twsrc%5Etfw">@ORCID_Org</a> as orchid or orc-I-D? The latter seems like an evil Tolkien monster. <a href="https://twitter.com/hashtag/DigID17?src=hash&amp;ref_src=twsrc%5Etfw">#DigID17</a> <a href="https://twitter.com/hashtag/DHSI2017?src=hash&amp;ref_src=twsrc%5Etfw">#DHSI2017</a></p>&mdash; Dr. Laura Estill (@Laura_Estill) <a href="https://twitter.com/Laura_Estill/status/874688177910431745?ref_src=twsrc%5Etfw">June 13, 2017</a></blockquote> <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
:::
::: {.fragment .fade-in-then-out}
### Identify your institution

UNSW Sydney: 

- Research Organization Registry [ror.org/03r8z3t63](https://ror.org/03r8z3t63)
- Wikidata [Q734764]([https://www.wikidata.org/wiki/Q734764)
:::
::: {.fragment .fade-in-then-out}
### Identify your data

A Digital Object Identifier (DOI) is a unique, persistent identifier for research outputs.
:::
::::


## {{< fa book-open-reader >}} Ask for help!

### Multiple resources available at UNSW

[Research Technology Services (ResTech)](https://research.unsw.edu.au/research-technology-services-restech)

[UNSWorks](https://unsworks.unsw.edu.au) is UNSW’s [open access repository](https://www.library.unsw.edu.au/research/publishing-and-sharing-your-research/open-access).

<div>
<span style="vertical-align: top;">[UNSW codeRs](https://unsw-coders.netlify.app/)</span>
![UNSW codeRs logo](https://unsw-coders.netlify.app/images/logo_hu20be6c44ea68e676024b4aa4f3296560_161224_0x70_resize_lanczos_2.png){height=50} 
</div>


# {{< fa solid code-branch >}} Share your code 

Shared code helps you and your collaborators to analyse and/or visualise your data. It supports validation of your findings and help others to build upon your work.

## {{< fa solid code-branch >}} Why?

1. Encourage reproducibility
1. Meet journal/funder requirements
1. You'll learn a lot
1. Extend the half-life of your research
1. Be more employable

::: aside
Check this [blog post](https://towardsdatascience.com/how-and-why-to-share-scientific-code-64fbd385a67) from Nathan C. Frey
:::

## {{< fa solid code-branch >}} Version control, please!

You can use any flavour^[`git`, `svn`, or whichever else is out there] of version control you like ! 

There are plenty of [tutorials](https://www.w3schools.com/git/default.asp) and [workshops](https://carpentries-incubator.github.io/git-novice-branch-pr/) to learn from.

If you learn all the command-line tricks, great!

But you can do a lot from the browser or in RStudio {{< fa brands r-project >}}.

## {{< fa solid code-branch >}} Where?

If you use git you can share your code with:

- [Github {{< fa brands github >}}](https://docs.github.com/en/get-started/quickstart) 
- [Bitbucket {{< fa brands bitbucket >}}](https://bitbucket.org/product/guides) 
- [Gitlab {{< fa brands gitlab >}}](https://docs.gitlab.com/ee/tutorials/) 

# {{< fa up-right-from-square >}} Share your data

Research data should be accessible to support validation and facilitate data reuse. For sensitive data provide the descriptive metadata.

## {{< fa up-right-from-square >}} Ask your librarians!

[UNSWorks](https://unsworks.unsw.edu.au) allows researchers to [publish datasets](https://subjectguides.library.unsw.edu.au/publishing/data) on their platform of choice and then create a record and link to their publications to increase discoverability of their data. Small datasets (up to 5GB) can be uploaded to UNSWorks. 

## {{< fa up-right-from-square >}} UNSWorks benefits

- Support for Creative Commons Licenses
- Automated DOI assignment
- Automated publication to Research Data Australia (RDA)
- Embargo functionality
- Integration with InfoEd grants

## {{< fa up-right-from-square >}} Subject-specific repositories

Increase the visibility of your data among researchers in your field. 

For example [iNaturalist](https://www.inaturalist.org) for wildlife observations!

Check the Registry of Research Data Repositories ([r3data](https://www.re3data.org)) to find a repository in your discipline.

## {{< fa up-right-from-square >}} Generalist publishing platforms

:::: r-stack
::: {.fragment .fade-out}
### [Figshare](figshare.com)

Anyone can sign up for an account, simple up-load and very easy to download and reuse data.

I uploaded my `Rdata` file [here](https://figshare.com/articles/dataset/IUCN_Red_List_of_Ecosystem_assessment_results_for_IVC_Forest_Macrogroups_in_the_Americas_region/7488872), now I can:

```{r}
#| echo: true
#| eval: false
figshare.url <- "https://figshare.com/ndownloader/files/13874333"
con <- url(figshare.url)
load(con)
close(con)
```
:::
::: {.fragment .fade-in-then-out}
### [Zenodo](zenodo.org)

Developed by CERN to support the open access and open science movement in Europe, but available for use by researchers worldwide.

<div>
<span style="vertical-align: top;">
Great for github integration: now your repo has a DOI!</span> [![](https://zenodo.org/badge/DOI/10.5281/zenodo.5234108.svg)](https://doi.org/10.5281/zenodo.5234108)
</div>

:::
::: {.fragment .fade-in-then-out}
### [Dryad](https://datadryad.org)

- UNSW researchers have institutional access 
- File upload of up to 300GB per dataset record
- Curation support
- Automatic DOI assignment
- ORCID log in
- CC0 license
:::

::::


# {{< fa solid puzzle-piece >}} Combine data and code?

Did you pre-register your analysis? have a pre-print? have input and output data? code? photos? 

Sooo many DOIs...

## {{< fa solid puzzle-piece >}} OSF

> The Open Science framework or ([OSF](https://osf.io)) is an online platform that enables researchers to transparently plan, collect, analyze, and share their work throughout the entire research life cycle. 

I use OSF to organise different [components of a project](https://osf.io/ak2w3/)


# Thank you!{background-image="https://inaturalist-open-data.s3.amazonaws.com/photos/101251571/medium.jpeg" background-opacity="0.9"}

Remember, we are here to help:

[Research Technology Services (ResTech)](https://research.unsw.edu.au/research-technology-services-restech)

[UNSWorks](https://unsworks.unsw.edu.au) 

<div>
<span style="vertical-align: top;">[UNSW codeRs](https://unsw-coders.netlify.app/)</span>
![UNSW codeRs logo](https://unsw-coders.netlify.app/images/logo_hu20be6c44ea68e676024b4aa4f3296560_161224_0x70_resize_lanczos_2.png){height=50} 
</div>

## {.smaller background-image="https://inaturalist-open-data.s3.amazonaws.com/photos/101251571/medium.jpeg" background-opacity="0.3"}

This presentation was prepared by:

José R. Ferrer-Paris ( [{{< fa brands orcid >}} 0000-0002-9554-3395](https://orcid.org/0000-0002-9554-3395) / [{{< fa brands github >}} @jrfep](https://github.com/jrfep))

and is shared with license: [ Atribution 4.0 Internacional ({{< fa brands creative-commons >}} {{< fa brands creative-commons-by >}} 4.0)](https://creativecommons.org/licenses/by/4.0/)

::: panel-tabset
### Links

This presentation is available at:

[rpubs.com/jrfep/...](https://rpubs.com/jrfep/)

This presentation was created using [RStudio](https://posit.co/products/open-source/rstudio/), [Quarto v.1.3.330](https://quarto.org/docs/presentations/) with [fontawesome extension](https://github.com/quarto-ext/fontawesome), and [reveal.js](https://revealjs.com/). Original content, code and instructions available at: [{{< fa brands github >}} UNSW-codeRs/how-to-share-data-and-code](https://github.com/UNSW-codeRs/how-to-share-data-and-code)

### Image credits

UNESCO.org [CC BY 4.0](https://creativecommons.org/licenses/by/4.0), via Wikimedia Commons

Roche DG, Lanfear R, Binning SA, Haff TM, Schwanz LE, et al. (2014), [CC BY 4.0](https://creativecommons.org/licenses/by/4.0), via Wikimedia Commons

Background images from my iNaturalists observations:
https://www.inaturalist.org/photos/268028588 and
https://www.inaturalist.org/photos/101251571

Other images attributed in the slide text or source code.

### *R* session info

```{r}
sessionInfo()
```
:::