Module 01: Getting Started with R, RStudio, R Objects

.title[
# Module 01: Getting Started with R, RStudio, R Objects
]
.subtitle[
## Rollins COVID-19 Epidemiology Fellowship R Training: Nov 11, 2022
]
.author[
### <a href="https://melindahiggins.netlify.app/">Melinda Higgins</a>
]
.date[
### Director Biostatistics & Data Core </br> School of Nursing - Emory University </br>
]

---

# Overview - Website for Workshop

---

# R + RStudio

Old Fashioned "command line"

<img src="Rconsole.png" width="=100%" />
]

Integrated Development Environment

_NOTE: This is NOT a GUI_
]

---

background-size: 100%
background-image: url(rstudio_ide01.png)
background-position: 70% 70%
class: center, top

---

background-size: 100%
background-image: url(rstudio_ide02.png)
background-position: 70% 70%
class: center, top

---

background-size: 100%
background-image: url(rstudio_ide03.png)
background-position: 70% 70%
class: center, top

---

background-size: 100%
background-image: url(rstudio_ide04.png)
background-position: 70% 70%
class: center, top

---

background-size: 100%
background-image: url(rstudio_ide05.png)
background-position: 70% 70%
class: center, top

---

background-size: 100%
background-image: url(rstudio_ide06.png)
background-position: 70% 70%
class: center, top

---

# Let's get started!!
### 1. Open RStudio

---

# Create a new project
Go to File/New Project

---

# Create a new project
Choose New Directory

---

# Create a new project
Click New Project

---

# Create a new project
Type in folder name and choose parent directory

---

# What is a RStudio "Project"?

* A "container" or _aka_ a directory with all files for this RStudio Project

* Good Coding Practice!!

* The DEFAULT place RStudio looks for your files

---

# Your new `Rworkshop` project

---

# Get files for the Workshop

1. Go to [https://melindahiggins2000.github.io/Emory_RWorkshop_11Nov2022/](https://melindahiggins2000.github.io/Emory_RWorkshop_11Nov2022/)

2. Download `module01_Rscript.R` and put it into the new folder on your computer, _e.g._ `C:\Rworkshop`.

---

# Files in your `Rworkshop` folder on your computer

<img src="module01_Rworkshop02.png" width="=80%" />
---

# Files in your `Rworkshop` folder/RStudio project

---

# Basic commands done in Console

---

count: false
 
Code lines run in the console or from script window
.panel1-console1-auto[

```r
*4 + 4
```
]
 
.panel2-console1-auto[

```
[1] 8
```
]

---
count: false
 
Code lines run in the console or from script window
.panel1-console1-auto[

```r
4 + 4
*sqrt(25)
```
]
 
.panel2-console1-auto[

```
[1] 8
```

```
[1] 5
```
]

---
count: false
 
Code lines run in the console or from script window
.panel1-console1-auto[

```r
4 + 4
sqrt(25)
*pi
```
]
 
.panel2-console1-auto[

```
[1] 8
```

```
[1] 5
```

```
[1] 3.141593
```
]

---
count: false
 
Code lines run in the console or from script window
.panel1-console1-auto[

```r
4 + 4
sqrt(25)
pi
*seq(from=1, to=10, by=0.5)
```
]
 
.panel2-console1-auto[

```
[1] 8
```

```
[1] 5
```

```
[1] 3.141593
```

```
 [1]  1.0  1.5  2.0  2.5  3.0  3.5  4.0  4.5  5.0  5.5  6.0  6.5  7.0  7.5  8.0
[16]  8.5  9.0  9.5 10.0
```
]

---

# **ASSIGN** your results to an "object", use .big[**<-**]

We really don't want to keep typing one line at a time in the Console, so we need to save/store value(s) in an object. An object is a text string we use to retrieve the value (or elements) we saved. Let's save the results of `2+2` in an object `result`.

For this we will use the **ASSIGN** operator .big[**`<-`**].

```r
result <- 2+2
```
]

This is saved now in your "Global Environment". To retrieve this value, simply type the text string `result` to see the value `4`.

```r
result
```

```
[1] 4
```

]

---

# Your Turn

### 1. Start RStudio - Open "module01_Rscript.R"
### 2. Highlight Run Code for EXERCISE 01

---

# How to "run" code in an R script

<img src="module01_runExample01.png" width="=80%" />
---

```r
# save sequence of numbers in object x
*x <- seq(from=1, to=10, by=0.5)
```
]
 
.panel2-console2-auto[

]

---
count: false
 
Create Objects and Use Them
.panel1-console2-auto[

```r
# save sequence of numbers in object x
x <- seq(from=1, to=10, by=0.5)

# view the contents of x
*x 
```
]
 
.panel2-console2-auto[

```
 [1]  1.0  1.5  2.0  2.5  3.0  3.5  4.0  4.5  5.0  5.5  6.0  6.5  7.0  7.5  8.0
[16]  8.5  9.0  9.5 10.0
```
]

---
count: false
 
Create Objects and Use Them
.panel1-console2-auto[

```r
# save sequence of numbers in object x
x <- seq(from=1, to=10, by=0.5)

# view the contents of x
x

# use x to create new object y
*y <- x*x
```
]
 
.panel2-console2-auto[

```
 [1]  1.0  1.5  2.0  2.5  3.0  3.5  4.0  4.5  5.0  5.5  6.0  6.5  7.0  7.5  8.0
[16]  8.5  9.0  9.5 10.0
```
]

---
count: false
 
Create Objects and Use Them
.panel1-console2-auto[

```r
# save sequence of numbers in object x
x <- seq(from=1, to=10, by=0.5)

# view the contents of x
x

# use x to create new object y
y <- x*x
*y 
```
]
 
.panel2-console2-auto[

```
 [1]  1.0  1.5  2.0  2.5  3.0  3.5  4.0  4.5  5.0  5.5  6.0  6.5  7.0  7.5  8.0
[16]  8.5  9.0  9.5 10.0
```

```
 [1]   1.00   2.25   4.00   6.25   9.00  12.25  16.00  20.25  25.00  30.25
[11]  36.00  42.25  49.00  56.25  64.00  72.25  81.00  90.25 100.00
```
]

---
count: false
 
Create Objects and Use Them
.panel1-console2-auto[

```r
# save sequence of numbers in object x
x <- seq(from=1, to=10, by=0.5)

# view the contents of x
x

# use x to create new object y
y <- x*x
y

# plot x and y
*plot(x,y)
```
]
 
.panel2-console2-auto[

```
 [1]  1.0  1.5  2.0  2.5  3.0  3.5  4.0  4.5  5.0  5.5  6.0  6.5  7.0  7.5  8.0
[16]  8.5  9.0  9.5 10.0
```

```
 [1]   1.00   2.25   4.00   6.25   9.00  12.25  16.00  20.25  25.00  30.25
[11]  36.00  42.25  49.00  56.25  64.00  72.25  81.00  90.25 100.00
```

![](Rworkshop_11Nov2022_Module01_files/figure-html/console2_auto_05_output-1.png)
]

---

# Questions

1. How many objects are in your "Environment" [top right window]

2. What kind of object is `x`?

3. How many elements does `y` have in it?

4. Where do you see the plot?

]

---

# Questions

### Getting Help

To find out what the `seq()` function does, in the Console window [bottom left] at the prompt `>` type:

```r
seq(from=1, to=10, by=0.5)
```

```
 [1]  1.0  1.5  2.0  2.5  3.0  3.5  4.0  4.5  5.0  5.5  6.0  6.5  7.0  7.5  8.0
[16]  8.5  9.0  9.5 10.0
```

Notice that we used equals `=` inside the `()` to assign _values_ to the _arguments_ for the `seq()` function.

]

---

# Your Turn

### 1. Open "module01_Rscript.R"
### 2. Highlight Run Code for EXERCISE 02
### 3. Write Code to make plot for tangent of x
### 4. Write Code to make plot of log of x with log y