UCSD Carpentries Bootcamp - R, Unix Shell, and Git (Oct 2022)

Workshop Details
Dates: October 10th - 13th, 2022
Days: Monday - Thursday
Time: 1pm - 4pm

Workshop Agenda:
https://ucsdlib.github.io/2022-10-10-UCSD/

Software Installation:
R Studio downloads: https://www.r-project.org/ - download the free version
Online/Cloud R Studio interface: https://rstudio.cloud/
This is an online interface that can be used when unable to download R Studio
Git software: https://git-scm.com/downloads

Lesson Data (download)
Gapminder data and Feline-data

Workshop Day 1

First name and Last Name/Organization/Dept./Email

Name (first & last)	Organization	Dept.	Email	Role
(example) Kimberly Thomas	UCSD	IT	[e-mail]	Staff
Eastern Kang (instructor)	UCSD	Peds	[e-mail]
Sarah Segall	UCSD	PSYC	[e-mail]
Tommaso Menara	UCSD	MAE	[e-mail]
Ece Bayram	UCSD	Neurosciences	[e-mail]
Zhaoning Wang	UCSD	CMM	[e-mail]
Shemp Wilkinson	UCSD	COGS	[e-mail]
Kalam Park	UCSD	COGS	[e-mail]
Kristy Hwang	UCSD	Neuroscience	[e-mail]
Jake Maurer	UCSD	Economics	[e-mail]
Taelor Getz	UCSD	Pediatrics	[e-mail]
Meyer Friedman	UCSD	MED	[e-mail]
Federica Klaus	UCSD	Psychiatry	[e-mail]
Sara Ramos	UCSD	Neurosciences	[e-mail]

Day 1 Questions:

Please enter any questions not answered during live session here:
1.

End Day 1

Workshop Day 2

First name and Last Name/Organization/Dept./Email

Name (first & last)	Organization	Dept.	Email
Melodi Frey	UCSD	CMM	[e-mail]
Sara Ramos	UCSD	Neuro.	[e-mail]
Tommaso Menara	UCSD	MAE	[e-mail]
Sarah Segall	UCSD	PSYC	[e-mail]
Jake Maurer	UCSD	ECON	[e-mail]
Federica Klaus	UCSD	Psychiatry	[e-mail]
Ece Bayram	UCSD	Neurosciences	[e-mail]
Kristy Hwang	UCSD	Neuroscience	[e-mail]
Shemp Wilkinson	UCSD	COGS	[e-mail]
Rukmini Ravi	UCSD	San Diego Supercomputer Center	[e-mail]
Kalam Park	UCSD	COGS	[e-mail]
Meyer Friedman	UCSD	MED	[e-mail]
Taelor Getz	UCSD	Pediatrics	👌😒
Zhaoning Wang	UCSD	CMM	[e-mail]

Quick recap:

The package dplyr provides easy tools for the most common data wrangling tasks. Some of the most common functions are:

• select(): subset columns
• filter(): subset rows on conditions
• mutate(): create a new column (variable) by using information from other columns
• group_by() and summarize(): create summary statistics on grouped data

Pipes (%>%)

What if you want to select and filter at the same time?
With multiple steps, it is easy to clutter up the workspace with lots of objects that you have name individually.

The pipes let y ou take the output of one function and send it directly to the next, which is useful when you need to do many things to the same dataset. It looks like %>%.

Day 2 Questions:

Please enter any questions not answered during live session here:

1. How can a variable that is a number with attributes (e.g. import from SPSS, numbers with titles) be converted to a factor to be used as x-label in plot? (Federica)

End Day 2

Workshop Day 3

First name and Last Name/Organization/Dept./Email

Name (first & last)	Organization	Dept.	Email
Shemp Wilkinson	UCSD	COGS	[e-mail]
Sarah Segall	UCSD	PSYC	[e-mail]
Kristy Hwang	UCSD	Neuroscience	[e-mail]
Zhaoning Wang	UCSD	CMM	[e-mail]
Jake Maurer	UCSD	ECON	[e-mail]
Kalam Park	UCSD	COGS	[e-mail]
Taelor Getz	UCSD	Pediatrics	[e-mail]
Federica Klaus	UCSD	Psychiatry	[e-mail]
Meyer Friedman	UCSD	MED	[e-mail]
Ece Bayram	UCSD	Neurosciences	[e-mail]
Rukmini Ravi	UCSD	San Diego Supercomputer Center	[e-mail]
Sara Ramos	UCSD	Neuro.	[e-mail]

Day 3 Questions:

Please enter any questions not answered during live session here:
1.

End Day 3

---

Workshop Day 4 - Git

download data:

https://librarycarpentry.org/lc-shell/data/shell-lesson.zip

First name and Last Name/Organization/Dept./Email

Name (first & last)	Organization	Dept.	Email
Jake Maurer	UCSD	ECON	[e-mail]
Kristy Hwang	UCSD	Neuroscience	[e-mail]
Shemp Wilkinson	UCSD	COGS	[e-mail]
Tommaso Menara	UCSD	MAE	[e-mail]
Ece Bayram	UCSD	Neurosciences	[e-mail]
Sarah Segall	UCSD	PSYC	[e-mail]
Kalam Park	UCSD	COGS	[e-mail]
Taelor Getz	UCSD	Pediatrics	[e-mail]
Meyer Friedman	UCSD	MED	[e-mail]
Sara Ramos	UCSD	Neuro.	[e-mail]
Rukmini Ravi	UCSD	San Diego Supercomputer Center	[e-mail]

Collaborative Lesson notes:

download data:
https://librarycarpentry.org/lc-shell/data/shell-lesson.zip

shell commands:

MacOS - run Terminal application

Windows - Gitbash application

pwd #print working directory show directory path 

ls #or "list" will display directory contents

ls -l #list detailed directory information `-l` is a flag that add additional commands

cd #change directory - move around the file system

cd .. #move up in the folder hierarchy
cd ../.. #moves high up in the folder hierarchy skipping directories


clear #move prompt to the top, clearing the terminal window

ls -F #will show folders using a `/`  

man ls # typing man and the command will display the help information about the command.  

mkdir #create new file directory

rmdir #permanently delete files *becareful with this*

cat #view contents in a file with out opening it

head #shows the first 10 lines at the begining of the file 

tail #shows the last 10 lines at the end of the file 


cp #rename files 

nano # built-in Shell text editor 

vim # advanced built-in text editor

Shell cheatsheet:

https://www.ifixit.com/Wiki/MacOS_Unix_Commands

---

Git lesson

initial git setup –global config you only have to do this once, unless your git and github account info is updated or changed.

#setup global config properties 
git config --global user.email
git config --global core.editor "nano -w"

git config --global init.defaultBranch main


git init #initialize folder for git version tracking.  note: make sure to init a single folder, do not init nested folders.  

git checkout -b # change branch to main branch


## git steps for adding and commiting
git status # get current status of file tracking changes

git add #adding changes to be tracked 

git status 

git commit -m "[enter breif note]"  # commit changes that were made to the file

git status 

git log #check the commit log information lists information about the commit 


git ignore #ignore file will not track listed content
git remote add origin [paste remote repository] #only needed for each new remote repository
git remote -v  # view remote url connection to Github 

git push origin main #push to github online branch repository

git pull origin main #if collaborating pull latest branch to your local machine 

git one time commands:
git init
git checkout
git ignore #ignore file will not track listed content

git remote commands:
git remote add origin [paste remote repository] #only needed for each new remote repository
git remote -v # view
git push origin main #push to github online branch
git pull origin main #if collaborating pull latest branch to your local machine

Here is the list of basic git commands to commit a file for version control:
git status
git add
git commit -m "[commit message]"
git status
git log
git diff

Day 4 Questions:

Please enter any questions not answered during live session here:
1.Will there be a quiz today?

CCR Quiz will be sent out with the workshop survey after the end of today.

End Day 4