class: center, middle, inverse, title-slide

.title[
# Tools
]
.subtitle[
## Introduction to Data Science (BIOL7800)
<a href="https://introdatasci.dlilab.com/" class="uri">https://introdatasci.dlilab.com/</a>
]
.author[
### Daijiang Li
]
.institute[
### LSU
]
.date[
### 2023/08/29
]

---

# Tools going to use

.font200[
- R
- git 
- bash (terminal)
- RStudio
- GitHub
- Make
- TinyTex (generate pdf using Rmarkdown)
]

---

# R (https://www.r-project.org)

.font200[
- A programming language

- First appeared: August 1993; 28 years ago

- \> 18,000 packages and counting

- Download and Installation (https://mirrors.nics.utk.edu/cran/)
]

--

# Tour of R

---

class: middle, inverse

## If you are using Windows 10, you should [enable and install Bash on Ubuntu on Windows](https://docs.microsoft.com/en-us/windows/wsl/install-win10). You can try to do this after class.

---

# Git (https://git-scm.com)

.pull-left[
.font200[
- Version control system
    - `which git` (Mac, Linux) or `where git` (Windows)

- [Download and Installation](https://carpentries-incubator.github.io/git-novice-branch-pr/setup/)

- [Setting up Git](https://carpentries-incubator.github.io/git-novice-branch-pr/02-setup/)
]
]

.pull-right[
![final doc](https://carpentries-incubator.github.io/git-novice-branch-pr/fig/phd101212s.png)
]

---

# RStudio (https://www.rstudio.com)

.font200[
- Integrated Development Environment (IDE)

- Public Benefit Co.

- [Download](https://www.rstudio.com/products/rstudio/download/#download) and Installation
]

--

# Tour of RStudio

.font150[
- Check Terminal in RStudio
- Check git panel
- `Alt + Shift + k` to show all shortcuts
- [Cheatsheet](https://raw.githubusercontent.com/rstudio/cheatsheets/main/rstudio-ide.pdf)
]

---

# GitHub (https://github.com)

.font200[
- Online platform to share code

- Collaborative coding
]

---

# Make (https://www.gnu.org/software/make/)

.font200[
- `make --version` to check whether you have it already
- [Windows version](http://gnuwin32.sourceforge.net/packages/make.htm)
]

---

# LaTex and TinyTex (https://yihui.org/tinytex/)

```r
# Open RStudio
install.packages('tinytex')
tinytex::install_tinytex()
```

### Create an Rmarkdown file and give it a try to generate a PDF file.

---

# macOS & linux (optional but highly recommended)

```bash
# macOS only
xcode-select --install
# Installing Homebrew for pkg management
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
```

### [Homebrew: The Missing Package Manager for macOS (or Linux)](https://brew.sh/)

---

# Useful links

.font200[
- [Happy Git and GitHub for the useR](https://happygitwithr.com)

- [R related Cheatsheets](https://www.rstudio.com/resources/cheatsheets/)

- [Software carpentry](http://software-carpentry.org/)

- [Data capentry](https://datacarpentry.org)

- [Minimal Make tutorial](https://kbroman.org/minimal_make/)
]

Notes for current slide

Notes for next slide

Tools

Introduction to Data Science (BIOL7800)

https://introdatasci.dlilab.com/

Daijiang Li

LSU

2023/08/29

1 / 11

Tools going to useR
git 
bash (terminal)
RStudio
GitHub
Make
TinyTex (generate pdf using Rmarkdown)

2 / 11

R (https://www.r-project.org)

A programming language
First appeared: August 1993; 28 years ago
> 18,000 packages and counting
Download and Installation (https://mirrors.nics.utk.edu/cran/)

3 / 11

R (https://www.r-project.org)

A programming language
First appeared: August 1993; 28 years ago
> 18,000 packages and counting
Download and Installation (https://mirrors.nics.utk.edu/cran/)

Tour of R

3 / 11

If you are using Windows 10, you should enable and install Bash on Ubuntu on Windows. You can try to do this after class.

4 / 11

Git (https://git-scm.com)

Version control system
- which git (Mac, Linux) or where git (Windows)
Download and Installation
Setting up Git

final doc

5 / 11

RStudio (https://www.rstudio.com)

Integrated Development Environment (IDE)
Public Benefit Co.
Download and Installation

6 / 11

RStudio (https://www.rstudio.com)

Integrated Development Environment (IDE)
Public Benefit Co.
Download and Installation

Tour of RStudio

Check Terminal in RStudio
Check git panel
Alt + Shift + k to show all shortcuts
Cheatsheet

6 / 11

GitHub (https://github.com)

Online platform to share code
Collaborative coding

7 / 11

Make (https://www.gnu.org/software/make/)

make --version to check whether you have it already
Windows version

8 / 11

LaTex and TinyTex (https://yihui.org/tinytex/)

# Open RStudio
install.packages('tinytex')
tinytex::install_tinytex()

Create an Rmarkdown file and give it a try to generate a PDF file.

9 / 11

macOS & linux (optional but highly recommended)

# macOS only
xcode-select --install
# Installing Homebrew for pkg management
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

Homebrew: The Missing Package Manager for macOS (or Linux)

10 / 11

Useful links

11 / 11

Tools going to useR
git 
bash (terminal)
RStudio
GitHub
Make
TinyTex (generate pdf using Rmarkdown)

2 / 11

Paused

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