Introduction to the Toolkit

Dr. Mine Dogucu

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A headshot of a woman with curly, short, ear-length hair with green eyes and red lipstick.

Mine Dogucu
Assistant Professor of Teaching
Department of Statistics

M 10 - 11 am, F 3 - 4 pm
mdogucu@uci.edu
MineDogucu
mdogucu

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A headshot of a woman with long straight hair and glasses

Josie Jiang
PhD Student
Department of Statistics

xiwenj@uci.edu
XiwenJiang

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Goals

Introduction to the Course
Introduction to R and RStudio
Introduction to R Markdown
Introduction to Git and GitHub

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Introduction the Course

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By the end of this program you should be able to adopt reproducible computing workflows.

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By the end of this program you should be able to adopt reproducible computing workflows in R.

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By the end of this course you should be able to adopt reproducible computing workflows in R for all your scientific work (e.g. data management, analysis, dissemination).

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By the end of this course you should be able to adopt reproducible computing workflows in R for all your scientific work (e.g. data management, analysis, dissemination).

I may not teach you every single detail on the topic but you will gain enough foundations to tailor it to your future work.

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End ProductsPersonal website (will come as homework)
R package
Final project of your own choice
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Introduction to R

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R review

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Object assignment operator

birth_year <- 1950

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Object assignment operator

birth_year <- 1950

	Windows	Mac
Shortcut	Alt + -	Option + -

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R is case-sensitive

my_age <- 2020 - birth_year
My_age

Error in eval(expr, envir, enclos): object 'My_age' not found

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R is case-sensitive

my_age <- 2020 - birth_year
My_age

Error in eval(expr, envir, enclos): object 'My_age' not found

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If something comes in quotes, it is not defined in R.

ages <- c(25, my_age, 32)
names <- c("Menglin", "Mine", "Rafael")
data.frame(age = ages, name = names)

  age    name
1  25 Menglin
2  70    Mine
3  32  Rafael

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Vocabulary

do(something)

do() is a function;
something is the argument of the function.

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Vocabulary

do(something)

do() is a function;
something is the argument of the function.

do(something, colorful)

do() is a function;
something is the first argument of the function;
colorful is the second argument of the function.

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Getting Help

In order to get any help we can use ? followed by function (or object) name.

?c

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tidyverse_style_guide

canyoureadthissentence?

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tidyverse_style_guide

canyoureadthissentence?

age <- c(6, 9, 15)
data.frame(age_kid = age)

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tidyverse_style_guide

canyoureadthissentence?

age <- c(6, 9, 15)
data.frame(age_kid = age)

After function names do not leave any spaces.

Before and after operators (e.g. <-, =) leave spaces.

Put a space after a comma, not before.

Object names are all lower case, with words separated by an underscore.

The tidyverse style guide

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RStudio Setup
  
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Introduction to R Markdown

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markup languages

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LaTeX

$\frac{3}{5}$

\(\frac{3}{5}\)

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HTML (Hypertext Markup Language)

<a href = "http://minedogucu.com">
  Mine Dogucu</a>

Mine Dogucu

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markdown

[Mine Dogucu](http://minedogucu.com)

Mine Dogucu

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R Markdown

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R Markdown

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markdown

_Hello world_ 
__Hello world__
~~Hello world~~

Hello world

Hello world

~~Hello world~~

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= .R file

= .md file

+ = .Rmd file

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markdown document
  
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R Markdown document
  
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YAML (Yet Another Markup Language)
  
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More YAML

output:pdf_document

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More YAML

output:pdf_document

output:
  html_document:
    toc: true

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More YAML

output:pdf_document

output:
  html_document:
    toc: true

output:
  html_document:
    fig_width: 7
    fig_height: 6

Starting a New R Markdown document

File > New File > R Markdown

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Add Chunk

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Run the Current Chunk

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Knit

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Shortcuts


Windows
Mac


add chunk
Ctrl + Alt + I
Cmd + Option + I

run the current chunk
Ctrl + Alt + C
Cmd + Option + C

run current line/selection
Ctrl + Enter
Cmd + Return

knit
Ctrl + Shift + K
Cmd + Shift + K

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	Windows	Mac
add chunk	Ctrl + Alt + I	Cmd + Option + I
run the current chunk	Ctrl + Alt + C	Cmd + Option + C
run current line/selection	Ctrl + Enter	Cmd + Return
knit	Ctrl + Shift + K	Cmd + Shift + K

(some) Chunk Options

echo = FALSE
hides the code

message = FALSE
hides messages

warning = FALSE
hides warning

error = TRUE
renders despite errors and displays the error

eval = FALSE
code is not evaluated

 cache = TRUE
will not run if it has been run before and 
 the output from previous run would be used

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Slides

Slides that you are currently looking at are also written in R Markdown. You can take a look at them on GitHub repo for the course website. They are made with xaringan package which we will talk more about later.

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Introduction to Git and GitHub

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Who uses GitHub?

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Who uses GitHub?

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Version control

hw1

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Version control

hw1

hw1_final

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Version control

hw1

hw1_final

hw1_final2

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Version control

hw1

hw1_final

hw1_final2

hw1_final3

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Version control

hw1

hw1_final

hw1_final2

hw1_final3

hw1_finalwithfinalimages

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Version control

hw1

hw1_final

hw1_final2

hw1_final3

hw1_finalwithfinalimages

hw1_finalestfinal

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