Institute for Modeling Collaboration and Innovation @ The University of Idaho
Online
Apr 20-29, 2021
T/Th 2-5pm
Instructors:
Erich Seamon, Li Huang
Helpers:
Travis Seaborn, Lukas Grossfurthner
General Information
Data Carpentry develops and teaches workshops on the fundamental data skills needed to conduct
research. Its target audience is researchers who have little to no prior computational experience,
and its lessons are domain specific, building on learners' existing knowledge to enable them to quickly
apply skills learned to their own research.
Participants will be encouraged to help one another
and to apply what they have learned to their own research problems.
Who:
The course is aimed at graduate students and other researchers.
You don't need to have any previous knowledge of the tools
that will be presented at the workshop.
Where: This training will take place online.
The instructors will provide you with the information you will need to connect to this meeting.
Requirements:
Participants must have access to a computer with a
Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on.
They should have a few specific software packages installed (listed below).
Accessibility:
We are dedicated to providing a positive and accessible learning environment for all. Please
notify the instructors in advance of the workshop if you require any accommodations or if there is
anything we can do to make this workshop more accessible to you.
Roles:
To learn more about the roles at the workshop (who will be doing what),
refer to our Workshop FAQ.
Code of Conduct
Everyone who participates in Carpentries activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.
Collaborative Notes
We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.
Surveys
Please be sure to complete these surveys before and after the workshop.
To participate in a
Data Carpentry
workshop,
you will need access to the software described below.
In addition, you will need an up-to-date web browser.
If you haven't used Zoom before, go to the
official website
to download and install the Zoom client for your computer.
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 the tool you are learing 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 setup instructions for the Data Carpentry Geospatial workshop can be found at the workshop overview site.
The Bash Shell
Bash is a commonly-used shell that gives you the power to do
tasks more quickly.
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" (NOTE: you will need to scroll up to find it) and click on "Next".
On the page that says "Adjusting the name of the initial branch in new repositories", ensure that
"Let Git decide" is selected. This will ensure the highest level of compatibility for our lessons.
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 "Git Credential Manager Core" is selected and click on "Next".
Ensure that "Enable file system caching" is 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.
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.
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.
Code Access
We have created a streamlined github repository for each lesson’s code. The purpose of this repository is to give you a simple way of getting the code for each lesson, in a basic R file that can be used later. So, please feel free to clone this repo and use in any way you’d like. While we want to following along during the lesson and engaging, we also dont want you to worry that you have to type everything down, in order to preserve a file for your use later. Just clone the repo in advance of the workshop. https://github.com/erichseamon/BCB503_advanced_geospatial_workshop
Video Conference Access
This zoom conference information will be used for all classes.
A few other zoom/video conferencing housekeeping issues:
If you can use a dual monitor setup, this will greatly assist you.
If possible, make sure you have a webcam ergonomically set up level with your face, with your microphone close to you.
Please leave your webcam on while interfacing with the workshop. This is not a requirement. We realize that you may have additional family or work/class committments that may require you to step away. However, while you are engaged in the workshop, try to have your webcam on! It will be more fun and engaging! (If you can consider R and geospatial analysis fun!)
We will try to leverage zoom as much as possible. We are not going to use any other software, other than Rstudio and zoom. However, we will be lecturing using the materials referenced above. So - following along via your browser with the lesson we are going over will be helpful. That means: Rstudio + zoom + web browser. You can see why two monitors will be helpful if possible.
Zoom Access: password required - password is: idaho_geo
Topic: BCB503 Advanced Geospatial Analysis Workshop
Time: Apr 20, 2021 02:00 PM Pacific Time (US and Canada)
Every day, until Apr 21, 2021, 2 occurrence(s)
Apr 20, 2021 02:00 PM
Apr 21, 2021 02:00 PM
Please download and import the following iCalendar (.ics) files to your calendar system.
Daily: https://uidaho.zoom.us/meeting/tZEqd-Crpz8oH9ENLdiYDU1asxY5LNaqJI_i/ics?icsToken=98tyKuGtqTsjGd2RshyCRpwMB4igXenxmClBgvp4sjPhChl3V1L3Jfp7Z55REcn6
Meeting ID: 857 0939 4255
Passcode: idaho_geo
One tap mobile
+12532158782,,85709394255# US (Tacoma)
+13462487799,,85709394255# US (Houston)
Dial by your location
+1 253 215 8782 US (Tacoma)
+1 346 248 7799 US (Houston)
+1 669 900 6833 US (San Jose)
+1 301 715 8592 US (Washington DC)
+1 312 626 6799 US (Chicago)
+1 646 876 9923 US (New York)
Meeting ID: 857 0939 4255
Find your local number: https://uidaho.zoom.us/u/kdFOf5rvgD