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session04.qmd
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session04.qmd
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# Data Management, Reproducibility & Integrity
*Session Presenter*
![](images/Presenters4.png)
## *Required packages*
```{r, warning=FALSE, message=FALSE}
library(tidyverse)
library(palmerpenguins)
library(webexercises)
data("penguins")
```
## Reproducible research
::: callout-tip
## Goal
*Our goal is to make reproducible* research, and *data management* and *integrity* are the necessary steps to achieve this goal
:::
::: panel-tabset
##### Question
![](images/task.png){.class width="48" height="48"} Have you ever had problems reproducing your own or someone else’s research?
```{r}
#| echo: false
#| results: asis
# Define the questions
q1 <- "Have you ever had problems reproducing your own or someone else’s research?"
# Define the answer choices
q1_choices <- c(answer = "My own research", answer = "Someone else's",answer= "Both",answer= "I have never had problems reproducing r...")
cat(q1,longmcq(q1_choices))
```
##### Answer
![](images/repro4.png)
Check out <https://www.repro4everyone.org/>
:::
### Things to consider when it comes to research
We will go through some of the practical steps for reproducible research:
![](images/reproducibility.png)
## Quarto for Reproducibility
### Meet Quarto
Quarto enables you to weave together content and executable code into a finished document. To learn more about Quarto see <https://quarto.org>.
### Meet the penguins
![](https://raw.githubusercontent.com/quarto-dev/quarto-web/main/docs/get-started/hello/rstudio/lter_penguins.png){style="float:right;" fig-alt="Illustration of three species of Palmer Archipelago penguins: Chinstrap, Gentoo, and Adelie. Artwork by @allison_horst." width="401"}
The `penguins` data from the [**palmerpenguins**](https://allisonhorst.github.io/palmerpenguins "palmerpenguins R package") package contains size measurements for `{r} nrow(penguins)` penguins from three species observed on three islands in the Palmer Archipelago, Antarctica.
The plot below shows the relationship between flipper and bill lengths of these penguins.
```{r}
#| label: plot-penguins
#| warning: false
#| echo: false
ggplot(penguins,
aes(x = flipper_length_mm, y = bill_length_mm)) +
geom_point(aes(color = species, shape = species)) +
scale_color_manual(values = c("darkorange","purple","cyan4")) +
labs(
title = "Flipper and bill length",
subtitle = "Dimensions for penguins at Palmer Station LTER",
x = "Flipper length (mm)", y = "Bill length (mm)",
color = "Penguin species", shape = "Penguin species"
) +
theme_minimal()
```
### Quarto file
::: callout-note
## Exercise
![](images/task.png){#id .class width="48" height="48"} Download an example quarto file and try running it on your own.
```{css}
#| echo: false
.btn-default,
.btn-default:hover,
.btn-default:active {
font-size: 20px;
color: Grey;
background-color: lightblue;
border-color: black;
}
.btn-default:hover {
color: grey;
transition: 0.2s;
}
```
```{r, echo=FALSE, warning=FALSE}
library(downloadthis)
download_file(path = './session04.qmd',
output_name = "hello",
output_extension = ".qmd",
button_label = "Download hello.qmd",
button_type = "default",
has_icon = TRUE,
icon = "fa fa-file-csv"
)
```
:::
## *Further Study*
Check out the information life cycle <https://data.uq.edu.au/data-essentials/information-lifecycle>
Check out the push for open research, research that is reproducible and accessible <https://www.repro4everyone.org/>
### Meta data:
How to write metadata?
Stanford Libraries – [Create metadata for your research project](https://guides.library.stanford.edu/research-metadata)
The Carpentries Incubator – [Introduction to metadata](https://carpentries-incubator.github.io/fair-bio-practice/05-intro-to-metadata/index.html)
ARDC – [Metadata guide](https://ardc.edu.au/resource/metadata-guide/)
### Data Planning
links:
<https://mynotebook.labarchives.com/login>
<https://dmptool.org/>