Module 02: Getting Started with Packages & Data

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.title[
# Module 02: Getting Started with Packages & Data
]
.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>
]

---

# Why Learn R?

* https://www.tiobe.com/tiobe-index/r/
* https://www.tiobe.com/tiobe-index/
* https://r4stats.com/articles/popularity/

### AND Rmarkdown...

* Seamless integration of DATA + CODE + DOCUMENTATION
* See examples [https://rmarkdown.rstudio.com/gallery.html](https://rmarkdown.rstudio.com/gallery.html)
* Many output formats [https://rmarkdown.rstudio.com/formats.html](https://rmarkdown.rstudio.com/formats.html)
* Learn more at [https://rmarkdown.rstudio.com/lesson-1.html](https://rmarkdown.rstudio.com/lesson-1.html)

---

# R vs Other Stats Software

.pull-left[
## R

* bare bones
* takes up very little memory
* powerful base packages
* FREE/Open Source
]

.pull-right[
## SPSS, SAS examples

* Have to buy base ($$)
* AND Almost always have to buy add-ons, gets expensive $$
* Have to know what you want ahead of time
* Sometimes end up with more than you need
]

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# My SAS License Includes:

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# My SPSS License Includes:

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# R - Base R Packages

.pull-left[

```r
sessionInfo()
```
]

.pull-right[
<img src="sessionInfo01.png" width="100%" />
]

.footnote[Add package(s) as you need them...]
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# To add functionality to R - install/load Packages

### FIRST INSTALL Package(s)

.pull-left[
<img src="install_packages01.png" width="60%" />
]

.pull-right[
<img src="install_packages02.png" width="90%" />
]

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# List Packages Installed on Your Computer

.pull-left[
<img src="packages_list_user.png" width="100%" />
]

.pull-right[
<img src="packages_list_system.png" width="100%" />
]

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### SECOND - LOAD Package(s) into Current R Session

.pull-left[

Before you can use the functions in the package installed on your computer, you must load it into your current "R session" - only loaded as needed...

```r
# load tidyverse
library(tidyverse)

# run sessionInfo() again
# now how many packages are "attached"
# under "other attached packages"
sessionInfo()
```
]

.pull-right[

<img src="sessionInfo02.png" width="100%" />
]

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# Where to get R Packages - CRAN

# Where to get R Packages - Bioconductor

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# Where to get R Packages - Github, Local, Others...
[https://github.com/search?l=R&q=packages&type=Repositories](https://github.com/search?l=R&q=packages&type=Repositories)

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# Do Your Research

* Always research your packages - like any other "tool"
    * has it be validated? 
    * has it been published? 
    * has is it been used/accepted in your research field or application?
    
--

* Check download stats: [https://hadley.shinyapps.io/cran-downloads/](https://hadley.shinyapps.io/cran-downloads/)

* Check CRAN: e.g. `tidyverse` [https://cran.r-project.org/web/packages/tidyverse/index.html](https://cran.r-project.org/web/packages/tidyverse/index.html):
    * check date last updated
    * how many versions
    * how long has it existed

* Check Github repo if exists, check issues:
    * `tidyverse` [https://github.com/tidyverse/tidyverse](https://github.com/tidyverse/tidyverse)

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# EXERCISE 01 - Reviewing R Packages - do together

### 1. Open "module02_Rscript.R"
### 2. Read instructions for EXERCISE 01

* Go to https://hadley.shinyapps.io/cran-downloads/
* How many downloads have there been (on average) recently:
    * for the `ggplot2` and `palmerpenguins` packages?
    * remove `ggplot2` and make plot again
    * compare downloads for `arsenal` and `gtsummary` packages
    
* Go to https://cran.r-project.org/ - click on packages:
    * how many Packages are on CRAN today?
    * list by name and find `ggplot2` package
    * when was it last updated?
    * go to github repo for ggplot2 - any open issues?
    
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# Interactive RStudio

### 1. Open RStudio
### 2. Open "module02_Rscript.R"
### 3. Go to "DATASETS"
###    - step through code steps to load data
###    - save "image" close and reopen project
### 4. If time - check out [OPTIONAL] SAVING and LOADING the "abalone" dataset