00_welcome.qmd

---
title: "Introduction & Welcome!" 
author: "Dr Anna Krystallli" 
subtitle: "Reproducible Research Data and Project Management in R" 
institute: R-RSE 
materials_url: https://acce-rrresearch.netlify.app/ 
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## :wave: Hello

### me: **Dr Anna Krystalli**

::: nonincremental
-   **Research Software Engineer**, [*`R-RSE`*](https://www.r-rse.eu/)

    -   mastodon annakrystalli\@fosstodon.org
    -   github \@annakrystalli
    -   email **r.rse.eu\[at\]gmail.com**

-   Background in **Marine Macroecology**

-   **Core Team:** [ReproHack](https://github.com/reprohack/reprohack-hq)
:::

## Ice Breaker

### Split into break out rooms

### Introduce yourselves

### Q: Why did you decide to join this course?

# Why are we here?

## The paper is the advertisement

> “an article about computational result is advertising, not scholarship. The actual scholarship is the **full software environment, code and data, that produced the result.**”

*John Claerbout paraphrased in [Buckheit and Donoho (1995)](https://statweb.stanford.edu/~wavelab/Wavelab_850/wavelab.pdf)*

. . .

### [The Scientific Paper Is Obsolete](https://www.theatlantic.com/science/archive/2018/04/the-scientific-paper-is-obsolete/556676/)

Here's what's next

<small>APR 5, 2018, The Atlantic</small>

<img src="assets/SciencePaperFlames-New.gif" height="100px" width="350px"/>

## Lessons from the Reproducibility/Replicability crisis

-   Many issues statistical and a results of broken Academic incentive systems.

-   Much can be tackled by transparency and better computational literacy.

<img src="assets/woes.png" width="450px"/>

## [Reproducible Research in Computational Science](http://science.sciencemag.org/content/334/6060/1226)

ROGER D. PENG, SCIENCE 02 DEC 2011 : 1226-1227

> Reproducibility has the potential to serve as a minimum standard for judging scientific claims when full independent replication of a study is not possible.

![](assets/repro-spectrum.jpg){width="550"}

## Reinventing discovery by open sourcing science

*Nielsen, Michael. Reinventing Discovery: The New Era of Networked Science. Princeton University Press, 2012. JSTOR, www.jstor.org/stable/j.ctt7s4vx.*

::: columns
::: {.column width="50%"}
-   Sharing resources

-   Collective intelligence

-   Mass collaboration
:::

::: {.column width="50%"}
<img src="assets/reinventing-innovation.png" height="300px"/>
:::
:::

## The internet was built for open science

### Key to next generation networked science

```{r, echo=FALSE, out.width="70%"}
knitr:::include_graphics("assets/www.jpg")
```

## **The grand vision**

### Hans Rosling on open data (and data science) back in 2006

```{r}
knitr::include_url("https://goo.gl/ry6AiG")
```

::: fragment
> So how far have we come?
:::

## [gapminder.org](https://www.gapminder.org/): today

#### Fighting global misconceptions with data

[![](assets/gapminder-org.png)](https://www.gapminder.org/)

## gapmider at our fingertips

```{r, fig.show = "animate", message=FALSE, warning=FALSE}
#| echo: true
library(ggplot2)

p <- ggplot(gapminder::gapminder, 
            aes(gdpPercap, lifeExp, size = pop, 
                color = continent, frame = year)) +
  geom_point() + scale_x_log10() + theme_bw()
```

```{r, message=FALSE, warning=FALSE, fig.height=4}
#| echo: true
plotly::ggplotly(p)
```

# How do we get there?

## **Research meta-responsibilities**

We need better digital curation of the workhorses of modern science: **code** & **data**

> **aim to create secure materials that are [FAIR](https://www.nature.com/articles/sdata201618)** *findable, accessible, interoperable, reusable*

![](assets/FAIRPrinciples.jpg){fig-align="center" width="700"}

## **Research meta-responsibilities**

::: columns
::: {.column width="50%"}
-   Think about traceability and provenance.

-   Follow community conventions.

-   Prepare it to share it.
:::

::: {.column width="50%"}
### We all need to do our bit!

```{r, echo=FALSE}
knitr::include_graphics("assets/CultureShift.jpg")
```
:::
:::

## **Drivers of better digital management**

-   **Funders**: value for money, impact, reputation

-   **Publishers**: many now require code and data.

    -   Specialist journals have emerged for:
        -   **software**: [Journal of Open Source Software](http://joss.theoj.org/), [MEE](https://besjournals.onlinelibrary.wiley.com/journal/2041210x)
        -   **data**: [Scientific Data](https://www.nature.com/sdata/))

-   **PIs, Supervisors and immediate research group**

-   Your **wider scientific community**

-   The **public**

## **Yourselves!**

**Be your own best friend:**

![](https://media.giphy.com/media/9Q249Qsl5cfLi/giphy.gif)

## **Ultimately it's about getting a handle on our research materials**

> "Agree on a community convention...then follow it""

![](assets/img/beer_messy_tidy.png)

## The concept of a Research Compendium

::: columns
::: {.column width="50%"}
> “ ...We introduce the **concept of a compendium** as both a **container** for the different **elements that make up the document and its computations** (i.e. text, code, data, ...), and as a **means for distributing, managing and updating the collection**."

[*Gentleman and Temple Lang, 2004*](https://biostats.bepress.com/bioconductor/paper2/)
:::

::: {.column width="50%"}
```{r, echo=FALSE}
knitr::include_graphics("assets/ResearchCompendium.jpg")
```
:::
:::

## Why Research Compendia?

[![Kartik Ram: rstudio::conf 2019 talk](assets/reproducible-data-analysis-02.png)](https://github.com/karthik/rstudio2019)

## Research Compendium Principles

[![Kartik Ram: rstudio::conf 2019 talk](assets/reproducible-data-analysis-04.png)](https://github.com/karthik/rstudio2019)

## R + Rstudio

### Next generation data science powerhouse

::: fragment
#### Backed by a diverse and active community of learners, users and developers

![](assets/logo-big.png){width="150"} ![](https://software-carpentry.org/files/2017/12/satrday-logo.png){width="150"} ![](assets/rladies-logo.png){width="150"} ![](https://forwards.github.io/images/forwards.svg){width="150"} ![](assets/ro-logo.png){width="150"}
:::

## Back to "Why are we here?"

-   To show you howto use R + Rstudio to perform reproducible data analyses.

. . .

-   To help you make the most of the real workhorses of your work, **YOUR CODE & DATA**!

. . .

-   To help you be empowered by modern tools & technologies rather than be overwhelmed by them.

. . .

-   To help you lead the culture change rather than be burdened by increased requirements.

. . .

-   Ultimately, to **change how science works for better for everyone**!

-   We'll do this by introducing you to **useful data and software tools and best practices**.

## Course Outline

::: columns
::: {.column width="30%"}
### Day 1

-   

    #### Basics

-   

    #### Project Management

-   

    #### Data Munging
:::

::: {.column width="30%"}
### Day 2

-   

    #### Metadata

-   

    #### Analysing & presenting data
:::

::: {.column width="30%"}
### Day 3

-   

    #### Version Control

-   

    #### Packaging Code

-   

    #### Research Compendia
:::
:::

**We'll take regular breaks and aim to break for lunch between 13:00 - 14:00 for an hour**

# Before we dive in

-   We'll exploring best practice in data and workflow management. I've tried to focus on concepts and tools that I wish I knew when I started.

. . .

-   We'll explore individual tools and concepts and show how they work nicely together.

. . .

-   We'll be coding together and working in Posit Cloud.

. . .

-   Feedback: After each day, let me know on the notepad:
    -   :green_book: : somethind you liked
    -   :red_circle: : somethind that could be improved

. . .

-   Please feel free to ask questions if I use jargon you don't understand or need some clarification. Questions are helpful for everyone! :sparkles:

## Working on Zoom

-   Have your mic on mute by default.

. . .

-   Please try to have your camera on as much as possible.

. . .

-   You can use the chat for questions but better to interrupt me.

. . .

-   Please try to help each other!

. . .

-   If you get lost, the materials and appendices are your friend!

. . .

-   Use status reaction emojis to communicate how it's going.

. . .

## A note about Posit Cloud Projects

-   Please also **do not share the link to Course Shared space on Posit Cloud**.
-   Posit Cloud projects **will be deleted after a week** of the course ending. Please \[**download any work you want to keep.**\]

# Let's go!

### Get back [{{< fa home >}}](index.qmd)