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Merge pull request #43 from UtrechtUniversity/dorien-changes
first try at automation, content edits
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‎.gitignore

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.Rproj.user
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# Project-specific files that need to be ignored
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data/penguins_isotopes.csv
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datascience_solutions_files/
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docs/

‎LICENSE.md

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‎book/_quarto.yml

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project:
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type: book
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output-dir: ../docs
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pre-render:
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- "pre-rendering/zip-course-materials.R"
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- "pre-rendering/render-slides.R"
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book:
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title: "Introduction to R & Data"

‎book/data-structures.qmd

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<iframe class="slide-deck" src="slides/slides_introduction.html#data-structures" title="Data structures" width="100%" height="540"></iframe>
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```
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[Link to the slides](slides/slides_introduction.html#data-structures)
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911
## Video
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{{< video https://youtu.be/Ffk2Kxa_b_M >}}

‎book/data-visualization.qmd

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<iframe class="slide-deck" src="slides/slides_tidyverse.html#data-visualization" title="Data visualization with ggplot2" width="100%" height="540"></iframe>
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```
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[Link to the slides](slides/slides_tidyverse.html#data-visualization)
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## Video
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{{< video https://vimeo.com/470862707 >}}

‎book/functions.qmd

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<iframe class="slide-deck" src="slides/slides_introduction.html#programming-functions" title="Functions" width="100%" height="540"></iframe>
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```
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[Link to the slides](slides/slides_introduction.html#programming-functions)
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## Video
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{{< video https://youtu.be/P_qSXHyIUpQ >}}

‎book/if-statements.qmd

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<iframe class="slide-deck" src="slides/slides_introduction.html#programming-if-statements" title="If-statements" width="100%" height="540"></iframe>
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```
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[Link to the slides](slides/slides_introduction.html#programming-if-statements)
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## Video
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{{< video https://youtu.be/ASVKW4dyLZI >}}

‎book/importing-data.qmd

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<iframe class="slide-deck" src="slides/slides_tidyverse.html#importing-data" title="Importing data" width="100%" height="540"></iframe>
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```
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[Link to the slides](slides/slides_tidyverse.html#importing-data)
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## Video
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{{< video https://vimeo.com/470836273 >}}

‎book/indexing-dataframes.qmd

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<iframe class="slide-deck" src="slides/slides_introduction.html#indexing-a-data-frame" title="Indexing dataframes" width="100%" height="540"></iframe>
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```
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[Link to the slides](slides/slides_introduction.html#indexing-a-data-frame)
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## Video
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{{< video https://youtu.be/m15hbXG6I-Y >}}

‎book/indexing-vectors-and-lists.qmd

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<iframe class="slide-deck" src="slides/slides_introduction.html#indexing-vectors-lists" title="Indexing vectors and lists" width="100%" height="540"></iframe>
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```
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[Link to the slides](slides/slides_introduction.html#indexing-vectors-lists)
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## Video
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{{< video https://youtu.be/e10nO2swYIE >}}

‎book/introduction-tidyverse.qmd

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<iframe class="slide-deck" src="slides/slides_tidyverse.html" title="Introduction to the Tidyverse" width="100%" height="540"></iframe>
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```
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[Link to the slides](slides/slides_tidyverse.html)
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## Video
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{{< video https://vimeo.com/470831693 >}}

‎book/introduction.qmd

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<iframe class="slide-deck" src="slides/slides_introduction.html" title="Introduction to R and Rstudio" width="100%" height="540"></iframe>
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```
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[Link to the slides](slides/slides_introduction.html)
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## Video
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{{< video https://youtu.be/FFYSAUJ305o >}}

‎book/loops.qmd

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<iframe class="slide-deck" src="slides/slides_introduction.html#programming-loops" title="For-loops" width="100%" height="540"></iframe>
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```
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[Link to the slides](slides/slides_introduction.html#programming-loops)
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## Video
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{{< video https://youtu.be/K4KSjizSJFk >}}

‎book/missing-data.qmd

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<iframe class="slide-deck" src="slides/slides_introduction.html#missing-data" title="Missing data" width="100%" height="540"></iframe>
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```
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[Link to the slides](slides/slides_introduction.html#missing-data)
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## Video
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{{< video https://youtu.be/4gVvlg1Itzs >}}

‎book/piping.qmd

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<iframe class="slide-deck" src="slides/slides_tidyverse.html#piping-operations" title="Piping operations" width="100%" height="540"></iframe>
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```
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[Link to the slides](slides/slides_tidyverse.html#piping-operations)
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## Exercise 8
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Now try out exercise 8 in `datascience_exercises.Rmd`.

‎book/pre-rendering/render-slides.R

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library(quarto)
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print("Let's render the Morning slides first")
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quarto_render("slides/slides_introduction.qmd")
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print("Moving onto the Tidyverse slides")
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quarto_render("slides/slides_tidyverse.qmd")
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print("Done rendering the slides! Now onto the book itself...")

‎book/pre-rendering/zip-course-materials.R

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print("Zipping the course materials folder")
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zip(zipfile = "../course-materials.zip",
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files = "../course-materials")
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print("Course materials zipped!")

‎book/schedule.qmd

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| 12:40 | Recap & Questions |
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| **12:45** | **Lunch break** |
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| 13:30 | Introduction to Tidyverse, Importing data: _Exercises 0-3_ |
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| 14:15 | Selecting & filtering data, Piping operations: _Exercises 4-8_ |
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| 14:15 | Selecting, filtering, mutating and renaming data, Piping operations: _Exercises 4-8_ |
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| 14:55 | Recap & Questions |
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| **15:00** | **Coffee break** |
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| 15:15 | Tidy data, Summarizing & combining data: _Exercises 9-11_ |
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| 16:00 | Data visualization: _Exercise 12_ |
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| 16:00 | Data visualization: _Exercise 12-13_ |
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| 16:55 | Final recap and closing |

‎book/slides/slides_tidyverse.html

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‎book/slides/slides_tidyverse.qmd

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format:
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pagetitle: "The data science workflow with Tidyverse"
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theme: [default]
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theme: default
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css: custom.css
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embed-resources: true
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keep-md: false
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smaller: true
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gfm:
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mermaid-format: png
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---
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# {background-color=#FFCD00}
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A key tidyverse component that chains all data science steps together:
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`%>%`
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`%>%`[^1]
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. . .
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- no need to save intermediate R objects with `<-`
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- easily add and/or delete steps in your pipeline without breaking the code
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[^1]: Base R now also has a piping operator: `|>`
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which [works very similarly](https://www.tidyverse.org/blog/2023/04/base-vs-magrittr-pipe/) to the magrittr piping operator `%>%`
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## Pipe operator: how it works
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> Tidy data sets are all alike; but every messy data set is messy in its own way ([Wickham/Grolemund, 2017](https://r4ds.had.co.nz/tidy-data.html)]
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> Tidy data sets are all alike; but every messy data set is messy in its own way ([Wickham/Grolemund, 2017](https://r4ds.had.co.nz/tidy-data.html))
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1. Each variable must have its own column.
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2. Each observation must have its own row.
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3. Each value must have its own cell.
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![](https://d33wubrfki0l68.cloudfront.net/6f1ddb544fc5c69a2478e444ab8112fb0eea23f8/91adc/images/tidy-1.png "Visualization of the tidy data principles. Source: R 4 Data Science, https://r4ds.had.co.nz/tidy-data.html")
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## Our df - but extended
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**Wide!** Why is this not tidy?
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## Wide vs Long
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. . .
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- ggplot2 book: <https://ggplot2-book.org/>
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A scatterplot of Culmen_Length_mm against Flipper_Length_mm per Island.
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- Data Science in a Box: <https://datasciencebox.org/content>
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- Learning statistics with R: <https://learningstatisticswithr.com/book/>
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- Statistical Inference via Data Science: A ModernDive into R and the Tidyverse: <https://moderndive.com/>
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- Big Book of R: <https://www.bigbookofr.com/>
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- Better spreadsheets: <https://better-spreadsheets.netlify.app/>
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**See also the [What's next page](https://utrechtuniversity.github.io/workshop-introduction-to-R-and-data/what-next.html).**
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## Where to find us
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‎book/subsetting-and-mutating-data.qmd

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<iframe class="slide-deck" src="slides/slides_tidyverse.html#selecting-filtering-data" title="Selecting and filtering data" width="100%" height="540"></iframe>
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```
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[Link to the slides](slides/slides_tidyverse.html#selecting-filtering-data)
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## Video
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{{< video https://vimeo.com/470859983 >}}

‎book/summarizing-combining-data.qmd

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<iframe class="slide-deck" src="slides/slides_tidyverse.html#summarizing-and-combining-data" title="Summarizing and combining data" width="100%" height="540"></iframe>
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[Link to the slides](slides/slides_tidyverse.html#summarizing-and-combining-data)
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## Exercise 10-11
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‎book/summary.qmd

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‎book/syntax-and-data-types.qmd

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<iframe class="slide-deck" src="slides/slides_introduction.html#r-syntax-data-types" title="Syntax and data types" width="100%" height="540"></iframe>
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[Link to the slides](slides/slides_introduction.html#r-syntax-data-types)
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## Video
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{{< video https://youtu.be/S8zTmEvpYYk >}}

‎book/transformations-and-tidy-data.qmd

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<iframe class="slide-deck" src="slides/slides_tidyverse.html#tidy-data" title="Tidy data" width="100%" height="540"></iframe>
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[Link to the slides](slides/slides_tidyverse.html#tidy-data)
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‎book/vectors.qmd

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<iframe class="slide-deck" src="slides/slides_introduction.html#vectors-in-r" title="Vectors in R" width="100%" height="540"></iframe>
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[Link to the slides](slides/slides_introduction.html#vectors-in-r)
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## Video
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{{< video https://youtu.be/XMFjteCdHbQ >}}

‎book/what-next.qmd

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# What's next?
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Not finished learning? Feel free to check our website, [uu.nl/rdm](https://www.uu.nl/en/research/research-data-management/training-workshops/) for our other workshops and trainings.
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Not finished learning? Feel free to check our website, [uu.nl/rdm](https://www.uu.nl/en/research/research-data-management/training-workshops/) for our other workshops and trainings.
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### More R resources
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- R 4 Data Science: <https://r4ds.hadley.nz/>
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- Data Science in a Box: <https://datasciencebox.org/content>
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- Learning statistics with R: <https://learningstatisticswithr.com/book/>
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- Statistical Inference via Data Science: A ModernDive into R and the Tidyverse: <https://moderndive.com/>
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- Big Book of R: <https://www.bigbookofr.com/>
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- Better spreadsheets: <https://better-spreadsheets.netlify.app/>
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### Data visualization
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- Choose a visualization > Get example code: <https://www.data-to-viz.com/>
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- ggplot2 book: <https://ggplot2-book.org/>
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- ggplot flipbook: <https://evamaerey.github.io/ggplot_flipbook/ggplot_flipbook_xaringan.html>
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- Better plots: <https://better-plots.netlify.app/>
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### Get practice
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- Starting a data analysis project - Extra practice exercises: <https://tavareshugo.github.io/r-intro-tidyverse-gapminder/90-appendix-exercises/index.html>
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- Exercises data wrangling with the tidyverse: <https://data-se.netlify.app/2021/02/24/exercises-to-data-wrangling-with-the-tidyverse/>
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- Use real public data: <https://github.com/awesomedata/awesome-public-datasets>

‎course-materials.zip

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