updated and simplified installation instructions, and moved the moving files from JupyterHub to an appendix

Author: ttimbers

_bookdown.yml

@@ -3,4 +3,4 @@ language:
   ui:
     chapter_name: "Chapter "
 delete_merged_file: true
-rmd_files: ["index.Rmd", "intro.Rmd", "reading.Rmd", "wrangling.Rmd", "viz.Rmd", "classification1.Rmd", "classification2.Rmd", "regression1.Rmd", "regression2.Rmd", "clustering.Rmd", "inference.Rmd", "jupyter.Rmd", "version-control.Rmd", "setup.Rmd", "references.Rmd"]
+rmd_files: ["index.Rmd", "intro.Rmd", "reading.Rmd", "wrangling.Rmd", "viz.Rmd", "classification1.Rmd", "classification2.Rmd", "regression1.Rmd", "regression2.Rmd", "clustering.Rmd", "inference.Rmd", "jupyter.Rmd", "version-control.Rmd", "setup.Rmd", "references.Rmd", "appendixA.Rmd"]

appendixA.Rmd

@@ -0,0 +1,27 @@
+\cleardoublepage
+
+```{r echo=FALSE, results='asis'}
+if(!knitr::is_latex_output()){
+  cat("# (APPENDIX) Appendix {-}")
+} else {
+  cat("\\appendix")
+}
+```
+
+# Download files from a JupyterHub for later local use {#appendixA}
+
+This section will help you
+save your work from the JupyterHub web-based platform to your own computer. 
+
+First, in JupyterHub, open a terminal by clicking "terminal" in the Launcher tab. 
+Next, type the following in the terminal to create a 
+compressed `.zip` archive for the work you are interested in downloading:
+
+```
+zip -r hub_folder.zip your_folder
+```
+
+After the compressing process is complete, right-click on `hub_folder.zip`
+in the JupyterHub file browser
+and click "Download". You should be able to use your computer's software to unzip
+the compressed folder by double-clicking on it. 

setup.Rmd

@@ -2,19 +2,15 @@
 
 ## Overview
 
-Throughout this book, we have assumed that you are working on a web-based platform, 
-such as JupyterHub, which already has Jupyter, R, several R packages, and Git set up and ready to use. 
-In this chapter, you'll learn how to install all of that software on your own computer in case
-you don't have a preconfigured JupyterHub available to you.
+In this chapter, you'll learn how to install all of that software 
+needed to do this data science covered in this book on your own computer.
 
 ## Chapter learning objectives
 
 By the end of the chapter, readers will be able to:
 
-- install Git and the miniconda Python distribution
+- install the Git version control software
 - install and launch a local instance of JupyterLab with the R kernel
-- download files from a JupyterHub for later local use
-
 
 ## Installing software on your own computer
 
@@ -25,41 +21,33 @@ we have created instructions for multiple operating systems.
 In particular, the installation instructions below have been verified to work
 on a computer that:
 
-- runs one of the following operating systems: MacOS 10.15.X (Catalina); Ubuntu 20.04; Windows 10, version 2004.
+- runs one of the following operating systems: Ubuntu 20.04, macOS Big Sur (version 11.4.x or 11.5.x), Windows 10 Professional, Enterprise or Education (version 2004, 20H2, or 21H1).
 - can connect to networks via a wireless connection
 - uses a 64-bit CPU
 - uses English as the default language
 
-**For macOS users only:** Apple recently changed the default shell in the terminal to Zsh.
-However, the programs we need work better with the Bash shell. Thus, we recommend you change 
-the default shell to Bash by opening the terminal 
-([how-to video](https://youtu.be/5AJbWEWwnbY)) and typing:
-
-```
-chsh -s /bin/bash
-```
-
-You will have to quit all instances of open terminals and then restart the 
-terminal for this to take effect.
-
 ### Git
 
-As shown in Chapter \@ref(Getting-started-with-version-control), Git is a very useful tool for version
-controlling your projects, as well as sharing your work with others. Here's how to install Git on 
+As shown in Chapter \@ref(Getting-started-with-version-control), 
+Git is a very useful tool for version controlling your projects, 
+as well as sharing your work with others. Here's how to install Git on 
 the following operating systems: 
 
 **Windows:** To install
 Git on Windows, go to <https://git-scm.com/download/win> and download the Windows 
 version of Git. Once the download has finished, run the installer and accept 
 the default configuration for all pages.
 
-**MacOS:** To install Git on Mac OS, open the terminal and type the following command:
+**MacOS:** To install Git on Mac OS, 
+open the terminal ([how-to video](https://youtu.be/5AJbWEWwnbY)) 
+and type the following command:
 
 ```
 xcode-select --install
 ```
 
-**Ubuntu:** To install Git on Ubuntu, open the terminal and type the following commands:
+**Ubuntu:** To install Git on Ubuntu, open the terminal 
+and type the following commands:
 
 ```
 sudo apt update
@@ -69,33 +57,37 @@ sudo apt install git
 
 ### Miniconda
 
-To run Jupyter notebooks on our computers, we will need to install the web-based platform JupyterLab. 
+To run Jupyter notebooks on our computers, 
+we will need to install the web-based platform JupyterLab. 
 But JupyterLab relies on Python; we can install this via
 the [miniconda Python package distribution](https://docs.conda.io/en/latest/miniconda.html).
 
 **Windows:** To install miniconda on Windows, download 
-the [Python 3.8 64-bit version from here](https://repo.anaconda.com/miniconda/Miniconda3-latest-Windows-x86_64.exe). 
-Once the download has finished, run the installer and accept the default 
-configuration for all pages. After installation, you can open the Anaconda Prompt
+the [latest Python 64-bit version from here](https://repo.anaconda.com/miniconda/Miniconda3-latest-Windows-x86_64.exe). 
+Once the download has finished, run the installer 
+and accept the default configuration for all pages. 
+After installation, you can open the Anaconda Prompt
 by opening the Start Menu and searching for the program called 
-"Anaconda Prompt (miniconda3)". When this opens, you will see a prompt similar to 
+"Anaconda Prompt (miniconda3)". 
+When this opens, you will see a prompt similar to 
 `(base) C:\Users\your_name`. 
 
 **MacOS:** To install miniconda on MacOS, download 
-the [Python 3.8 64-bit version from here](https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.pkg). 
+the [latest Python 64-bit version from here](https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.pkg). 
 After the download has finished, run the installer and accept the default 
 configuration for all pages.
 
 **Ubuntu:** To install miniconda on Ubuntu, we first download
-the [Python 3.8 64-bit version from here](https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh). 
+the [latest Python 64-bit version from here](https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh). 
 After the download has finished, open the terminal and execute the following 
 commands:
 
 ```
 bash path/to/Miniconda3-latest-Linux-x86_64.sh
 ```
 
-> Note: most often, this file is downloaded to the Downloads directory, and thus the command will look like this:
+> Note: most often, this file is downloaded to the Downloads directory, 
+and thus the command will look like this:
 > ```
 > bash Downloads/Miniconda3-latest-Linux-x86_64.sh
 > ```
@@ -117,42 +109,45 @@ Type the following into the Anaconda Prompt (Windows) or the terminal (MacOS and
 
 ```
 conda install -c conda-forge -y jupyterlab
-conda install -y nodejs=10.*
+conda install -y nodejs
 pip install --upgrade jupyterlab-git
-jupyter lab build
 ```
 
 To test that your JupyterLab installation is functional, you can type 
-`jupyter lab` into the Anaconda Prompt (Windows) or terminal (MacOS and Ubuntu) and press enter. This should open a new 
+`jupyter lab` into the Anaconda Prompt (Windows) 
+or terminal (MacOS and Ubuntu) and press enter. This should open a new 
 tab in your default browser with the JupyterLab interface. To exit out of 
 JupyterLab you can click `File -> Shutdown`, or go to the terminal from which 
-you launched JupyterLab, hold `Ctrl`, and press `c` twice.
+you launched JupyterLab, hold `Ctrl`, and press `C` twice.
 
 ### R and the IRkernel
 
-To have R available to you in JupyterLab, you will need to install the R programming language and the IRkernel. 
+To have R available to you in JupyterLab, 
+you will need to install the R programming language and the IRkernel R package. 
 To install these, type the following into 
 the Anaconda Prompt (Windows) or terminal (MacOS and Ubuntu):
 
 ```
-conda install -c conda-forge -y r-base
+conda install -c conda-forge -y r-base">=4.1.1"
 conda install -c conda-forge -y r-irkernel
 ```
 
 To improve the experience of using R in JupyterLab, we will add an extension 
 that allows us to setup keyboard shortcuts for inserting text.
-By default, this extension creates shortcuts for inserting two of the most common R 
+By default, 
+this extension creates shortcuts for inserting two of the most common R 
 operators: `<-` and `|>`. Type the following in the Anaconda Prompt (Windows)
 or terminal (MacOS and Ubuntu) and press  enter:
 
 ```
 jupyter labextension install @techrah/text-shortcuts
-jupyter lab build
 ```
 
 ### R packages
 
-To install the packages used in this book, type the following in the Anaconda Prompt (Windows) or terminal (MacOS and Ubuntu) and press enter:
+To install the packages used in this book, 
+type the following in the Anaconda Prompt (Windows) 
+or terminal (MacOS and Ubuntu) and press enter:
 
 ```
 conda install -c conda-forge -y \
@@ -166,6 +161,7 @@ conda install -c conda-forge -y \
   r-rsqlite \
   r-testthat \
   r-tidymodels \
+  r-tidyverse \
   r-tinytex \
   unixodbc
 ```
@@ -175,10 +171,23 @@ conda install -c conda-forge -y \
 To be able to render `.ipynb` files to `.pdf` you need to install a LaTeX 
 distribution. These can be quite large, so we will opt to use `tinytex`, a 
 light-weight cross-platform, portable, and easy-to-maintain LaTeX distribution 
-based on TeX Live. To install it open JupyterLab by typing `jupyter lab` 
+based on TeX Live. 
+
+**MacOS:** To install `tinytex` 
+we need to make sure that `/usr/local/bin` is writable. 
+To do this, type the following in the terminal:
+
+```
+sudo chown -R $(whoami):admin /usr/local/bin
+```
+
+> *Note: You might be asked to enter your password during installation.*
+
+**All operating systems:** 
+To install LaTeX open JupyterLab by typing `jupyter lab` 
 in the Anaconda Prompt (Windows) or terminal (MacOS and Ubuntu) and press enter.
 Then from JupyterLab open an R console and type the commands listed below and 
-press Shift + enter to install `tinytex`:
+press `Shift` + `enter` to install `tinytex`:
 
 ```
 tinytex::install_tinytex()
@@ -203,19 +212,24 @@ tinytex::tlmgr_install(c("eurosym",
                          "upquote"))
 ```
 
-## Moving files to your computer
-This section will help you
-save your work from the JupyterHub web-based platform to your own computer. 
-
-First, in JupyterHub, open a terminal by clicking "terminal" in the Launcher tab. 
-Next, type the following in the terminal to create a 
-compressed `.zip` archive for the work you are interested in downloading:
+**Ubuntu:** 
+To append the TinyTex executables to our `PATH` we need to edit our `.bashrc file`. 
+The TinyTex executables are usually installed in `~/bin`. 
+Thus, add the lines below to the bottom of your `.bashrc` file 
+(which you can open by `nano ~/.bashrc` and save the file:
 
 ```
-zip -r hub_folder.zip your_folder
+# Append TinyTex executables to the path
+export PATH="$PATH:~/bin"
 ```
 
-After the compressing process is complete, right-click on `hub_folder.zip`
-in the JupyterHub file browser
-and click "Download". You should be able to use your computer's software to unzip
-the compressed folder by double-clicking on it. 
+> Note: If you used `nano` to open your `.bashrc` file, 
+follow the keyboard shortcuts at the bottom of the nano text editor 
+to save and close the file.
+
+## Finishing up installation
+
+It is good practice to restart all the programs you used when installing this
+software stack before you proceed to doing your data analysis.
+This will ensure all the software and settings you put in place are 
+correctly sourced. This includes JupyterLab, terminal or Anaconda Prompt.