Programming in R
- Working with Vectors and Data Frames
- Reading and Plotting Data
- Creating and Using Functions
- Loops and Conditionals
- Using R from the Command Line
- Reference...
Geospatial Raster with Python
- Intro to Raster data with Python
- Raster Calculations with Python
Geospatial Raster with R
- Intro to Raster data with R
- Raster Calculations with R
Setup
To participate in a
Software Carpentry
workshop,
you will need access to the software described below.
In addition, you will need an up-to-date web browser.
We maintain a list of common issues that occur during installation as a reference for instructors
that may be useful on the
Configuration Problems and Solutions wiki page.
Install the videoconferencing client
For this workshop we'll be using both Google Meet & Microsoft Teams.
When you are registered for the workshop you will receive links for both
applications (Meet & Teams) for each day you have registered for the workshop.
Set up your workspace
Like other Carpentries workshops,
you will be learning by "coding along" with the Instructors.
To do this, you will need to have both the window for the tool
you will be learning about (a terminal, RStudio, your web browser, etc..)
and the window for the Zoom video conference client open.
In order to see both at once,
we recommend using one of the following set up options:
- Two monitors: If you have two monitors,
plan to have your terminal up on one monitor and
the video conferencing software on the other.
- Two devices: If you don't have two monitors,
do you have another device (tablet, smartphone) with a medium to large
sized screen? If so, try using the smaller device as your video
conference connection and your larger device (laptop or desktop)
to follow along with the tool you will be learning about.
- Divide your screen: If you only have one device
and one screen, practice having two windows
(the video conference program and one of the tools you will be using
at the workshop) open together.
How can you best fit both on your screen?
Will it work better for you to toggle between them
using a keyboard shortcut?
Try it out in advance to decide what will work best for you.
This
blog post includes detailed information on how to set up your screen to follow along during the workshop.
The Bash Shell
Bash is a commonly-used shell that gives you the power to do
tasks more quickly.
- Download the Git for Windows installer.
- Run the installer and follow the steps below:
-
Click on "Next" four times (two times if you've previously
installed Git). You don't need to change anything
in the Information, location, components, and start menu screens.
-
From the dropdown menu select "Use the nano editor by default" and click on "Next".
-
Ensure that "Git from the command line and also from 3rd-party software" is selected and
click on "Next". (If you don't do this Git Bash will not work properly, requiring you to
remove the Git Bash installation, re-run the installer and to select the "Git from the
command line and also from 3rd-party software" option.)
-
Ensure that "Use the native Windows Secure Channel library" is selected and click on "Next".
-
Ensure that "Checkout Windows-style, commit Unix-style line endings" is selected and click on "Next".
-
Ensure that "Use Windows' default console window" is selected and click on "Next".
-
Ensure that "Default (fast-forward or merge) is selected and click "Next"
-
Ensure that "Enable file system caching" and "Enable Git Credential Manager" are selected
and click on "Next".
- Click on "Install".
- Click on "Finish" or "Next".
-
If your "HOME" environment variable is not set (or you don't know what this is):
- Open command prompt (Open Start Menu then type
cmd and press Enter)
-
Type the following line into the command prompt window exactly as shown:
setx HOME "%USERPROFILE%"
- Press Enter, you should see
SUCCESS: Specified value was saved.
- Quit command prompt by typing
exit then pressing Enter
This will provide you with both Git and Bash in the Git Bash program.
Video Tutorial
The default shell in some versions of macOS is Bash, and
Bash is available in all versions, so no need to install anything.
You access Bash from the Terminal (found in
/Applications/Utilities).
See the Git installation video tutorial
for an example on how to open the Terminal.
You may want to keep Terminal in your dock for this workshop.
To see if your default shell is Bash type echo $SHELL
in Terminal and press the Return key. If the message
printed does not end with '/bash' then your default is something
else and you can run Bash by typing bash
If you want to change your default shell, see
this Apple Support article and follow the instructions on "How to change your default shell".
Video Tutorial
The default shell is usually Bash and there is usually no need to
install anything.
To see if your default shell is Bash type echo $SHELL in
a terminal and press the Enter key. If the message printed
does not end with '/bash' then your default is something else and you
can run Bash by typing bash.
Git
Git is a version control system that lets you track who made changes
to what when and has options for easily updating a shared or public
version of your code
on github.com. You will need a
supported
web browser.
You will need an account at github.com
for parts of the Git lesson. Basic GitHub accounts are free. We encourage
you to create a GitHub account if you don't have one already.
Please consider what personal information you'd like to reveal. For
example, you may want to review these
instructions
for keeping your email address private provided at GitHub.
Git should be installed on your computer as part of your Bash
install (see the
Shell installation instructions).
For macOS, install Git for Mac
by downloading and running the most recent "mavericks" installer from
this list.
Because this installer is not signed by the developer, you may have to
right click (control click) on the .pkg file, click Open, and click
Open on the pop up window.
After installing Git, there will not be anything in your /Applications folder,
as Git is a command line program.
For older versions of OS X (10.5-10.8) use the
most recent available installer labelled "snow-leopard"
available here.
Video Tutorial
If Git is not already available on your machine you can try to
install it via your distro's package manager. For Debian/Ubuntu run
sudo apt-get install git and for Fedora run
sudo dnf install git.
Text Editor
When you're writing code, it's nice to have a text editor that is
optimized for writing code, with features like automatic
color-coding of key words. The default text editor on macOS and
Linux is usually set to Vim, which is not famous for being
intuitive. If you accidentally find yourself stuck in it, hit
the Esc key, followed by :+Q+!
(colon, lower-case 'q', exclamation mark), then hitting Return to
return to the shell.
nano is a basic editor and the default that instructors use in the workshop.
It is installed along with Git.
Others editors that you can use are
Notepad++ or
Sublime Text.
Be aware that you must
add its installation directory to your system path.
Please ask your instructor to help you do this.
nano is a basic editor and the default that instructors use in the workshop.
See the Git installation video tutorial
for an example on how to open nano.
It should be pre-installed.
Video Tutorial
Others editors that you can use are
BBEdit or
Sublime Text.
nano is a basic editor and the default that instructors use in the workshop.
It should be pre-installed.
Others editors that you can use are
Gedit,
Kate or
Sublime Text.
R
R is a programming language
that is especially powerful for data exploration, visualization, and
statistical analysis. To interact with R, we use
RStudio.
Install R by downloading and running
this .exe file
from CRAN.
Also, please install the
RStudio IDE.
Note that if you have separate user and admin accounts, you should run the
installers as administrator (right-click on .exe file and select "Run as
administrator" instead of double-clicking). Otherwise problems may occur later,
for example when installing R packages.
Video Tutorial
Install R by downloading and running
this .pkg file
from CRAN.
Also, please install the
RStudio IDE.
Video Tutorial
You can download the binary files for your distribution
from CRAN. Or
you can use your package manager (e.g. for Debian/Ubuntu
run sudo apt-get install r-base and for Fedora run
sudo dnf install R). Also, please install the
RStudio IDE.
Python
Python is a popular language for
research computing, and great for general-purpose programming as
well. Installing all of its research packages individually can be
a bit difficult, so we recommend
Anaconda,
an all-in-one installer.
Regardless of how you choose to install it,
please make sure you install Python version 3.x
(e.g., 3.6 is fine).
We will teach Python using the Jupyter Notebook,
a programming environment that runs in a web browser (Jupyter Notebook will be installed by Anaconda). For this to work you will need a reasonably
up-to-date browser. The current versions of the Chrome, Safari and
Firefox browsers are all
supported
(some older browsers, including Internet Explorer version 9
and below, are not).
- Open https://www.anaconda.com/products/individual#download-section with your web browser.
- Download the Anaconda for Windows installer with Python 3. (If you are not sure which version to choose, you probably want the 64-bit Graphical Installer Anaconda3-...-Windows-x86_64.exe)
- Install Python 3 by running the Anaconda Installer, using all of the defaults for installation except make sure to check Add Anaconda to my PATH environment variable.
Video Tutorial
- Open https://www.anaconda.com/products/individual#download-section with your web browser.
- Download the Anaconda Installer with Python 3 for macOS (you can either use the Graphical or the Command Line Installer).
- Install Python 3 by running the Anaconda Installer using all of the defaults for installation.
Video Tutorial
- Open https://www.anaconda.com/products/individual#download-section with your web browser.
- Download the Anaconda Installer with Python 3 for Linux.
(The installation requires using the shell. If you aren't
comfortable doing the installation yourself
stop here and request help at the workshop.)
-
Open a terminal window and navigate to the directory where
the executable is downloaded (e.g., `cd ~/Downloads`).
-
Type
bash Anaconda3-
and then press
Tab to autocomplete the full file name. The name of
file you just downloaded should appear.
-
Press Enter
(or Return depending on your keyboard).
You will follow the text-only prompts.
To move through the text, press Spacebar.
Type
yes and press enter to approve the license.
Press Enter (or Return)
to approve the default location
for the files.
Type yes and press
Enter (or Return)
to prepend Anaconda to your PATH
(this makes the Anaconda distribution the default Python).
-
Close the terminal window.