Here We Go!

class: center, middle, inverse, title-slide

.title[
# Here We Go!
]
.subtitle[
## Starting Module 1
]
.author[
### Dr. Christopher Kenaley
]
.institute[
### Boston College
]
.date[
### 2025/8/27
]

---

class: inverse, top
# Hello!

<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.14.0/css/all.min.css">

.pull-left[
Today we'll ....

- Get R and RStudio installed

- Perform some basic operations in R

- Peak under the hood of Module Project 1

- Set up git on RStudio

]

.pull-right[
![](https://www.analyticsvidhya.com/wp-content/uploads/2016/02/rstudio.jpg)
]

---
class: inverse, top

# Announcements

## TTD ASAP

- Set up GitHub account (now if you haven't yet, ahum Reid, Neale)
- Accept invite to join our class team
- Check out discussion (first post = group assignments )
- Reach out to group members
- Accept invite to join repository for Module 1 Project (e.g., "Module1_Team1")

---
class: inverse, top

# On tap today

-How R works

``` r
any_function() #this is a comment: the "()" identify a function

left_value <- rigth_value #storing a value in an object using " <- "
```

-Some simple operations in R

``` r
foo <- 1:10

mean(foo)
```

```
## [1] 5.5
```

- Basic object classes

``` r
class(foo)
```

```
## [1] "integer"
```

---
class: inverse, top

# On tap today

-Installing and loading packages

``` r
install.packages("tidyverse")
library(tidyverse)
```

- Get help

``` r
?log
```

---
class: inverse, top

# GitHub

- Accept my invite to our team ("orgbiof25")
- Watch our team repo:
  - https://github.com/bcorgbio/orgbiof25
  - enables notifications re discussion

---
class: inverse, top

# GitHub

### The git worflow with GitHub
 .pull-left[
 
 Clone = copy the entire contents of a GitHub repository to your local computer (done once)
 
 Commit = move a changed local file to your local staging area (step 2)
 
 Pull = get file(s) from the cloud to your local computer – opposite of a “push” (step 3)
 
 Push = move file(s) to the cloud from your local computer – opposite of a “pull” (step 4)
 
]

.pull-right[
<center>
<img src="https://pages.github.nceas.ucsb.edu/lter/github-workshop/images/git-workflow.png" alt="drawing" width="400"/>
]

---
class: inverse, top

# GitHub

### Most MacOS users won't have git installed

### Xcode Command Line Tools (Recommended for basic Git usage):

+ Open your Terminal application.
  + Run: `xcode-select --install`
  + Follow the prompts

### Using Homebrew

+ Install Homebrew 
    - Open Terminal and paste the installation script from the official Homebrew website ([brew.sh](https://brew.sh/)).
    - `/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)`
  + Install Git: in terminal app, run: `brew install git`

---
class: inverse, top

# GitHub

## Generating a GitHub personal access token (PAT)
  + Go to your GitHub profile settings.
  + Go to Developer settings.
  + Select Personal access tokens.
  + Choose  Tokens (classic) 
  + Click Generate new token.
  + Provide a name for the token, set an expiration date, and select the desired scopes/permissions.
  + Generate the token and copy it immediately---it will not be displayed again after you leave the page.
  + Save as text file somewhere safe and accessible

---
class: inverse, top

# GitHub and RStudio

### Start a New Project in RStudio:
  + Open RStudio.
  + Go to File -> New Project....
  + Choose Version Control:
  + In the "New Project" dialog, select "Version Control".
  + Then, choose "Git" as the version control system.
  + Paste Repository URL and Configure Project:
  + In the "Clone Git Repository" dialog, paste the copied repository URL into the "Repository URL" field.
  + Give repo a name.
  + Browse and select the "Create project as a subdirectory of" location on your local machine where you want the cloned repository to reside.
  + Click "Create Project".