KUBDatalab · chrbknudsen · Mar 7, 2025 · Mar 7, 2025 · Mar 7, 2025 · Mar 7, 2025
diff --git a/episodes/whats-next.Rmd b/episodes/whats-next.Rmd
@@ -21,7 +21,7 @@ knitr::opts_chunk$set(echo = TRUE)
 
 ## What should I do next?
 
-First of all: If you do not have data you want to visualize 
+First of all: If you do not have data you want to visualise 
 already. Find some!
 
 [Kaggle](https://www.kaggle.com/datasets) host competitions 
@@ -57,6 +57,12 @@ we are not going to participate ourselves. But! The collection
 of visualizations from 2022 is humongous, and a great place
 to find ideas.
 
+Sometimes you have a pretty good idea about what you want to visualise. But 
+you are uncertain about what graphs might be used for that. Or you know 
+what graph you want to make, but can't quite figure out how to write the code.
+[The R Graph Gallery](https://r-graph-gallery.com/) have a wide selection of
+chart types with code!
+
 
 ## Other online courses
 

diff --git a/index.md b/index.md
@@ -2,8 +2,45 @@
 site: sandpaper::sandpaper_site
 ---
 
-This is a new lesson built with [The Carpentries Workbench][workbench]. 
 
+In this course we will look at how to visualise data using the `ggplot2` package
+in R.
+
+We will cover the basics, and look at a selection of common graphs, how to 
+manipulate axes, scales and colours.
+
+
+::::::::::::::::::::::::::::::::::::::: discussion
+### This is not an introduction to R
+In this course we assume you have the knowledge equivalent to attending one of 
+our <a href="https://kubdatalab.github.io/R-intro/" target="_blank">introductory courses</a>
+
+:::::::::::::::::::::::::::::::::::::::::::::::::::
+
+:::::::::::::::: solution
+
+### List of required knowledge
+- <a href="https://kubdatalab.github.io/R-api_new/#software-setup" target="_blank">Have R and R-studio installed</a> 
+    - Alternatively run everything on rstudio.cloud
+- Know how to assign values to variables
+- Know what a function is, and how we pass input and parameters to it
+- Be familiar with the %>% operator
+- Know the basic verbs from dplyr of the tidyverse:
+    - select
+    - filter
+    - mutate
+    - arrange
+    - summarise
+- Be familiar with dataframes
+- Know how to install and load packages
+- Know how to comment your code
+- Know how to do math on variables
+- Get the concept of vectors
+- Subsetting vectors and dataframes
+    - Using logical tests
+- Use NA to encode missing values
+- Read in data from a csv/excel
+
+:::::::::::::::::::::::::
 
-[workbench]: https://carpentries.github.io/sandpaper-docs
 
diff --git a/learners/setup.md b/learners/setup.md
@@ -1,45 +1,104 @@
----
-title: Setup
----
+## Software Setup
 
-FIXME: Setup instructions live in this document. Please specify the tools and
-the data sets the Learner needs to have installed.
+::::::::::::::::::::::::: callout
 
-## Data Sets
+### Warning
 
-<!--
-FIXME: place any data you want learners to use in `episodes/data` and then use
-       a relative link ( [data zip file](data/lesson-data.zip) ) to provide a
-       link to it, replacing the example.com link.
--->
-Download the [data zip file](https://example.com/FIXME) and unzip it to your Desktop
+Please do NOT install R and RStudio on Onedrive or other clouddrives.
+R will work but you will not be able to install the extensions to R
+that you will need in this course!
 
-## Software Setup
+::::::::::::
 
 ::::::::::::::::::::::::::::::::::::::: discussion
 
-### Details
+### Installing R and RStudio
+
+**R** and **RStudio** are separate downloads and installations. R is the
+underlying statistical computing environment, but using R alone is no
+fun. RStudio is a graphical integrated development environment (IDE) that makes
+using R much easier and more interactive. You need to install R before you
+install RStudio. Once installed, because RStudio is an IDE, RStudio will run R in 
+the background.  You do not need to run it separately. 
+
 
-Setup for different systems can be presented in dropdown menus via a `solution`
-tag. They will join to this discussion block, so you can give a general overview
-of the software used in this lesson here and fill out the individual operating
-systems (and potentially add more, e.g. online setup) in the solutions blocks.
 
 :::::::::::::::::::::::::::::::::::::::::::::::::::
 
 :::::::::::::::: solution
 
+### Online
+Rather than installing R and RStudio on your personal computer, 
+[Posit Cloud](https://posit.cloud//) offers a free, online alternative,
+where you will be able to run R and RStudio in your browser. 
+Sign up with your Google/Gmail account if you have one, or with any other email.
+
+The free version of RStudio Cloud places limitations on the number of projects you
+can work on, and the amount of memory and processing power you can access. For the 
+purposes of following these lessons, RStudio Cloud is perfectly adequate, and what we
+recommend if you have any problems installing R and RStudio on your personal computer.
+
+:::::::::::::::::::::::::
+
+:::::::::::::::: solution
+
 ### Windows
 
-Use PuTTY
+#### If you already have R and RStudio installed
+
+* Open RStudio, and click on "Help" > "Check for updates". If a new version is
+	available, quit RStudio, and download the latest version for RStudio.
+* To check which version of R you are using, start RStudio and the first thing
+  that appears in the console indicates the version of R you are
+  running. Alternatively, you can type `sessionInfo()`, which will also display
+  which version of R you are running. Go on
+  the [CRAN website](https://cran.r-project.org/bin/windows/base/) and check
+  whether a more recent version is available. If so, please download and install
+  it. You can [check here](https://cran.r-project.org/bin/windows/base/rw-FAQ.html#How-do-I-UNinstall-R_003f) for
+  more information on how to remove old versions from your system if you wish to do so.
+
+#### If you don't have R and RStudio installed
+
+* Download R from
+  the [CRAN website](https://cran.r-project.org/bin/windows/base/release.htm).
+* Run the `.exe` file that was just downloaded.
+* Go to the [RStudio download page](https://www.rstudio.com/products/rstudio/download/#download).
+* Under *Installers* select **RStudio x.yy.zzz - Windows.
+  Vista/7/8/10** (where x, y, and z represent version numbers).
+* Double click the file to install it.
+* Once it's installed, open RStudio to make sure it works and you don't get any
+  error messages.
 
 :::::::::::::::::::::::::
 
 :::::::::::::::: solution
 
 ### MacOS
 
-Use Terminal.app
+#### If you already have R and RStudio installed
+
+* Open RStudio, and click on "Help" > "Check for updates". If a new version is
+	available, quit RStudio, and download the latest version for RStudio.
+* To check the version of R you are using, start RStudio and the first thing
+  that appears on the terminal indicates the version of R you are running. Alternatively, you can type `sessionInfo()`, which will also display which version of R you are running. Go on
+  the [CRAN website](https://cran.r-project.org/bin/macosx/) and check
+  whether a more recent version is available. If so, please download and install
+  it. In any case, make sure you have at least R 3.2.
+
+#### If you don't have R and RStudio installed
+
+* Download R from
+  the [CRAN website](https://cran.r-project.org/bin/macosx/).
+* Select the `.pkg` file for the latest R version.
+* Double click on the downloaded file to install R.
+* It is also a good idea to install [XQuartz](https://www.xquartz.org/) (needed
+  by some packages).
+* Go to the [RStudio download page](https://www.rstudio.com/products/rstudio/download/#download).
+* Under *Installers* select **RStudio x.yy.zzz - Mac OS X 10.6+ (64-bit)**
+  (where x, y, and z represent version numbers).
+* Double click the file to install RStudio.
+* Once it's installed, open RStudio to make sure it works and you don't get any
+  error messages.
 
 :::::::::::::::::::::::::
 
@@ -48,7 +107,19 @@ Use Terminal.app
 
 ### Linux
 
-Use Terminal
+* Follow the instructions for your distribution
+  from [CRAN](https://cloud.r-project.org/bin/linux), they provide information
+  to get the most recent version of R for common distributions. For most
+  distributions, you could use your package manager (e.g., for Debian/Ubuntu run
+  `sudo apt-get install r-base`, and for Fedora `sudo yum install R`), but we
+  don't recommend this approach as the versions provided by this approach are
+  usually out of date. In any case, make sure you have at least R 3.2.
+* Go to the
+  [RStudio download page](https://www.rstudio.com/products/rstudio/download/#download).
+* Under *Installers* select the version that matches your distribution, and
+  install it with your preferred method (e.g., with Debian/Ubuntu `sudo dpkg -i
+  rstudio-x.yy.zzz-amd64.deb` at the terminal).
+* Once it's installed, open RStudio to make sure it works and you don't get any
+  error messages.
 
 :::::::::::::::::::::::::
-