Git/GitHub and Basic Interactivity

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## .base_color[Git/GitHub]

## .base_color[and]

## .base_color[Basic Interactivity with `plotly`]

#### .navy[Kelly McConville]

#### .navy[ Stat 108 | Week 3 | Spring 2023]

]

---

## Announcements

* All P-Sets are now due at **10pm** instead of **5pm** on Wednesdays so that you have time to finish up/process the help given during the Wednesday afternoon OHs.
    + **Important note**: The teaching team will NOT be actively watching the Slack #q-and-a channel from 5-10pm.

************************

## Week 3 Goals

**Mon Lecture**

* Animation with `gganimate`
* Data wrangling with `dplyr`

]

**Wed Lecture**

* GitHub/git
* RStudio Projects
* Basic interactivity with `plotly`
    + More advanced interactivity to come later on.

]

---

## But First: A Few Student Questions

---

## How do I save an animation?

```r
library(gganimate)
anim_save("p_aleutian_an.gif", p_aleutian_an)
```

---

## Inheriting `aes` from `ggplot()`

```r
ggplot(data = Births2015, 
       mapping = aes(x = date, y = births,
                     color = wday)) + 
  geom_point() +
  geom_point(data = holidays, size = 3,
             color = "black")
```

* What `aes`thetics did the second `geom_point()` inherit?  What didn't it inherit?

]

]

---

```r
glimpse(Births2015)
```

```
## Rows: 365
## Columns: 8
## $ date <date> 2015-01-01, 2015-01-02, 2015-01-03, 2015-01-04, 2015-01-…
## $ births <dbl> 8068, 10850, 8328, 7065, 11892, 12425, 12141, 12094, 1186…
## $ wday <ord> Thu, Fri, Sat, Sun, Mon, Tue, Wed, Thu, Fri, Sat, Sun, Mo…
## $ year <dbl> 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 201…
## $ month <dbl> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, …
## $ day_of_year <int> 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17…
## $ day_of_month <dbl> 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17…
## $ day_of_week <dbl> 5, 6, 7, 1, 2, 3, 4, 5, 6, 7, 1, 2, 3, 4, 5, 6, 7, 1, 2, …
```

```r
glimpse(holidays)
```

```
## Rows: 7
## Columns: 9
## $ date <date> 2015-01-01, 2015-05-25, 2015-07-04, 2015-12-25, 2015-11-…
## $ occasion <chr> "New Year", "Memorial Day", "Independence Day", "Christma…
## $ births <dbl> 8068, 7746, 7944, 6515, 7332, 8714, 8127
## $ wday <ord> Thu, Mon, Sat, Fri, Thu, Thu, Mon
## $ year <dbl> 2015, 2015, 2015, 2015, 2015, 2015, 2015
## $ month <dbl> 1, 5, 7, 12, 11, 12, 9
## $ day_of_year <int> 1, 145, 185, 359, 330, 358, 250
## $ day_of_month <dbl> 1, 25, 4, 25, 26, 24, 7
## $ day_of_week <dbl> 5, 2, 7, 6, 5, 5, 2
```

---

## Inheriting `aes` from `ggplot()`

* What `aes`thetics did the second `geom_point()` inherit?  What didn't it inherit?

```r
holidays <- rename(holidays, Dates = date)

ggplot(data = Births2015, 
       mapping = aes(x = date, y = births,
                     color = wday)) + 
  geom_point() +
  geom_point(data = holidays, size = 3,
             color = "black")
```

```
## Error in `geom_point()`:
## ! Problem while computing aesthetics.
## ℹ Error occurred in the 2nd layer.
## Caused by error in `compute_aesthetics()`:
## ! Aesthetics are not valid data columns.
## ✖ The following aesthetics are invalid:
## ✖ `x = date`
## ℹ Did you mistype the name of a data column or forget to add `after_stat()`?
```

---

## Inheriting `aes` from `ggplot()`

```r
ggplot(data = Births2015, 
       mapping = aes(x = date, y = births,
                     color = wday)) + 
  geom_point() +
  geom_point(data = holidays, size = 3,
             color = "black", 
             mapping = aes(x = Dates))
```

* What `aes`thetics did the second `geom_point()` inherit?  What didn't it inherit?

]

]

---

## Inheriting `aes` from `ggplot()`

```r
ggplot(data = Births2015, 
       mapping = aes(x = date, y = births,
                     color = wday)) + 
  geom_point() +
  geom_point(data = holidays, size = 3,
             color = "black", 
             mapping = aes(x = Dates),
             inherit.aes = FALSE)
```

```
## Error in `geom_point()`:
## ! Problem while setting up geom.
## ℹ Error occurred in the 2nd layer.
## Caused by error in `compute_geom_1()`:
## ! `geom_point()` requires the following missing aesthetics: y
```

* What `aes`thetics did the second `geom_point()` inherit?  What didn't it inherit?

]

]

---

## Inheriting `aes` from `ggplot()`

```r
ggplot(data = Births2015, 
       mapping = aes(x = date, y = births,
                     color = wday)) + 
  geom_point() +
  geom_point(data = holidays, size = 3,
             color = "black", 
             mapping = aes(x = Dates,
                           y = births),
             inherit.aes = FALSE)
```

* What `aes`thetics did the second `geom_point()` inherit?  What didn't it inherit?

]

]

---

## Inheriting `aes` from `ggplot()`

```r
#Add a box around Thanksgiving to Christmas
holidays_season <- 
 data.frame(start = as_date("2015-11-26"), 
 end = as_date("2015-12-24"))

ggplot(data = Births2015, 
       mapping = aes(x = date, y = births,
                     color = wday)) +
  geom_rect(data = holidays_season,
            mapping = aes(xmin = start,
                          xmax = end,
                          ymin = 6000,
                          ymax = 14000)) + 
  geom_point()
```

```
## Error in `geom_rect()`:
## ! Problem while computing aesthetics.
## ℹ Error occurred in the 1st layer.
## Caused by error in `FUN()`:
## ! object 'births' not found
```

* Problem: non-matching `aes` arguments

]

]

---

## Inheriting `aes` from `ggplot()`

```r
ggplot(data = Births2015, 
       mapping = aes(x = date, y = births,
                     color = wday)) +
  geom_rect(data = holidays_season,
            mapping = aes(xmin = start,
                          xmax = end,
                          ymin = 6000,
                          ymax = 14000),
             inherit.aes = FALSE) + 
  geom_point()
```

* Problem: non-matching `aes` arguments

]

]

---

## Safe Play: Put the mappings in the individual `geoms`

```r
ggplot(data = Births2015) +
  geom_rect(data = holidays_season,
            mapping = aes(xmin = start,
                          xmax = end,
                          ymin = 6000,
                          ymax = 14000),
             inherit.aes = FALSE) + 
  geom_point(mapping = aes(x = date,
                           y = births,
                           color = wday))
```

* Problem: non-matching `aes` arguments

]

]

---

## Simple Interactivity with `ggplotly`

* We can use the `plotly` package to convert a static `ggplot` to an interactive plot.

```r
p <- ggplot(data = Births2015, 
 mapping = aes(x = date, y = births,
 color = wday)) + 
 geom_point()
p
```

]

]

---

## Simple Interactivity with `ggplotly`

* We can use the `plotly` package to convert a static `ggplot` to an interactive plot.

```r
library(plotly)
ggplotly(p)
```

* Conversion isn't always perfect.
    + May need to spend more time tweaking `theme()` beforehand.

* Can also create graphs with `plot_ly()`

]

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]

---

## Simple Interactivity with `ggplotly`

```r
ggplotly(p, dynamicTicks = TRUE) %>%
  rangeslider() %>%
  layout(hovermode = "x")
```

* Add a slider and make tick marks dynamic with zooming
* Change the comparisons made when you hover

]

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2015-01-03 births: 8328 wday: Sat","date: 2015-01-10 births: 8014 wday: Sat","date: 2015-01-17 births: 8280 wday: Sat","date: 2015-01-24 births: 8235 wday: Sat","date: 2015-01-31 births: 7987 wday: Sat","date: 2015-02-07 births: 8285 wday: Sat","date: 2015-02-14 births: 8390 wday: Sat","date: 2015-02-21 births: 8343 wday: Sat","date: 2015-02-28 births: 7989 wday: Sat","date: 2015-03-07 births: 7980 wday: Sat","date: 2015-03-14 births: 8217 wday: Sat","date: 2015-03-21 births: 8080 wday: Sat","date: 2015-03-28 births: 8071 wday: Sat","date: 2015-04-04 births: 7981 wday: Sat","date: 2015-04-11 births: 8092 wday: Sat","date: 2015-04-18 births: 8028 wday: Sat","date: 2015-04-25 births: 8101 wday: Sat","date: 2015-05-02 births: 8075 wday: Sat","date: 2015-05-09 births: 8216 wday: Sat","date: 2015-05-16 births: 8337 wday: Sat","date: 2015-05-23 births: 8267 wday: Sat","date: 2015-05-30 births: 8431 wday: Sat","date: 2015-06-06 births: 8313 wday: Sat","date: 2015-06-13 births: 8104 wday: Sat","date: 2015-06-20 births: 8451 wday: Sat","date: 2015-06-27 births: 8652 wday: Sat","date: 2015-07-04 births: 7944 wday: Sat","date: 2015-07-11 births: 8769 wday: Sat","date: 2015-07-18 births: 8546 wday: Sat","date: 2015-07-25 births: 8748 wday: Sat","date: 2015-08-01 births: 8851 wday: Sat","date: 2015-08-08 births: 8956 wday: Sat","date: 2015-08-15 births: 8938 wday: Sat","date: 2015-08-22 births: 9153 wday: Sat","date: 2015-08-29 births: 8772 wday: Sat","date: 2015-09-05 births: 8950 wday: Sat","date: 2015-09-12 births: 9062 wday: Sat","date: 2015-09-19 births: 9195 wday: Sat","date: 2015-09-26 births: 8927 wday: Sat","date: 2015-10-03 births: 8579 wday: Sat","date: 2015-10-10 births: 8550 wday: Sat","date: 2015-10-17 births: 8233 wday: Sat","date: 2015-10-24 births: 8239 wday: Sat","date: 2015-10-31 births: 8049 wday: Sat","date: 2015-11-07 births: 8517 wday: Sat","date: 2015-11-14 births: 8221 wday: Sat","date: 2015-11-21 births: 8392 wday: Sat","date: 2015-11-28 births: 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2016"],"tickvals":[16436,16526,16617,16709,16801],"categoryorder":"array","categoryarray":["Jan 2015","Apr 2015","Jul 2015","Oct 2015","Jan 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]

---

## Simple Interactivity with `ggplotly`

```r
p <- ggplot(data = holidays, 
 mapping = aes(text = occasion)) + 
 geom_point(data = Births2015,
 mapping = aes(x = date,
 y = births,
 color = wday),
 inherit.aes = FALSE) +
 geom_point(data = holidays, size = 3,
 color = "black", 
 mapping = aes(x = Dates,
 y = births))
ggplotly(p, tooltip = "text")
```

]

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]

---

## Shift from

]

## To

]

---

## R Projects

.pull-left[
    
* Where does your analysis live?
    + Working directory
        + Where `R` looks for files you ask it to load.
        + Where `R` puts files you ask it to save.

]

]

```r
getwd()
```

```
## [1] "/n/academic_homes/g117625/u428252g117625/stat108s23/slides"
```

* For a given project, your analyses should live in the folder where you store the files associated with the project.
    + In other words, **working directory = project folder**.

* Common default: Working directory = home directory

* Can change the working directory with `setwd()` but instead we will use RStudio Projects.
    
---

## RStudio Projects

**RStudio Projects**: RStudio feature that helps you organize your work.

* We will create a Stat 108 project shortly. 
    + Will store course related RMarkdown documents, script files, data, figures, etc there.
    
--

* For RStudio Projects, the working directory is the home directory of the project.

* **Question**: My RStudio Project is `stat108s23`. Why does the file path end there when I run the following?

```r
getwd()
```

```
## [1] "/n/academic_homes/g117625/u428252g117625/stat108s23/slides"
```

---

## RStudio Projects

* To access the project, you can do either of the following:
    + Go to the upper right and select "Open Project"
    + Click on the `___.Rproj`

* Notice that when I open the project, all the files and command history are still there.

---

## RStudio Projects

* To access files in this project, I use relative paths:

```r
knitr::include_graphics("img/STAT108Logo_Sharing.png")
```

---

## Projects and Workflow

* Create an RStudio project for each analysis project.
    + We will have three RStudio projects for this course:
        + An individual coursework related RStudio project
        + An RStudio project for project 1
        + An RStudio project for project 2

* Keep data files that you need for the project in a `data` folder.

* Keep your `Rmd`s and script files there.

* Save outputs there.

* Use relative paths whenever possible.

---

background-image: url("img/octocat.001.jpeg")
background-position: left
background-size: 50%

## git and GitHub

* **git**: Version control system
    + Think fancier type of *Track Changes*.

]

* **GitHub**: Hosting service for git projects (which are called repositories)
    + Think fancier type of *DropBox* or *Google Drive*.

* Useful resource when getting started: [https://happygitwithr.com/](https://happygitwithr.com/)

]

---

## Manual Version Control

* But I already do version control...
    + draft.Rmd, draft2.Rmd, final.Rmd, realFinal.Rmd, REALLYVERYREALFinal.Rmd...

* Issues with this version of version control:
    + Hard to know how these files relate.
    + Hard to extend this approach to working with others.

]

]
    
---

## Git Real

* Git is a *decentralized* version control system.
    + Each collaborator has a complete version of the repo.
    + Everyone can work offline and simultaneously.
    + GitHub holds the master copy.

* git is not friendly and can be frustrating.
      + BUT, the version control and collaborative rewards are big!
      
--

* [GitHub.com](GitHub.com) is a great place to develop an online presence.
    + In Stat 108, we will default to keeping the work private.
    
--

* If you end up with a mess of errors, then don't worry but come see one of the instructors for help.
    + It happens to [everyone](https://xkcd.com/1597/).

---

## Github Repo = `RStudio` Project

* A **repo**, short for repository, is the folder that contains all of the files for the project on [GitHub.com](GitHub.com).
 
* Under the **harvard-stat108s23** GitHub Organization you currently have 1 repo:
    + `work-username`: Just you and the Stat 108 teaching team can access

* For each repo, you should create an `RStudio` Project (with version control).
    + We will all do this together in a moment.

---

## Steps to Get Started

**Once-Per-Computer/Server:**

* Install git on your computer.
    + Already done on the Server.

* Get your local git talking to GitHub.

**Once-Per-Project:**

* Create a repo on GitHub. 
    + I did this step for us.

* Create a version controlled RStudio Project that is synced with the GitHub repo.

---

## Let's try to set this up **twice**:

### First on the FAS OnDemand RStudio **Server**

### Second on **your own computer** (if you have a local installation of R/RStudio)

---

## First on the FAS OnDemand RStudio Server

* Sign-in to GitHub.com.

* Sign into the Stat 108 RStudio Server.

* Let's **git** your RStudio synced with your GitHub account and then make a change to your personal repo!
    + Make sure you accepted the repo request sent to your email.

---

## Check if git is install on the RStudio Server

In **Terminal**, type

```r
which git
```

```r
git --version
```

* If you receive an answer, then git is already install! 🎉

* If the reply is `git: command not found` (or similar), then
    + Windows: Visit [https://gitforwindows.org/](https://gitforwindows.org/)
    + Macs: In the Terminal type

```r
xcode-select --install    
```

* If you had to install git, restart your RStudio Session.

---

## Introduce Yourself to Git

* Install the package `usethis`.

* In your R console, modify and run the following code to introduce yourself to git

```r
library(usethis)
use_git_config(user.name = "mcconvil", 
               user.email = "kmcconville@fas.harvard.edu")
```

---

## Personal Access Token Time

* To interact with GitHub, you need to include credentials.
    + Personal Access Token (PAT)

* In your R console, run

```r
usethis::create_github_token()
```

* Should take you to GitHub.

* Select "repo", "user", and "workflow" for the scopes.

* Click "Generate token".

* Copy the PAT to your clipboard and store it by running:

```r
library(usethis)
edit_r_environ()
```

---

## Personal Access Token Time

* Add the following to the `.Renviron` file:

```r
GITHUB_PAT=PasteYourTokenHere
```

* Also run the following the console and when prompted for your password, provide your PAT:

```r
library(credentials)
credential_helper_set("store", global = TRUE)
git_credential_ask('https://github.com')
```

* Also store the PAT somewhere safe in case you need it again!

---

## Sync GitHub.com repo and an RStudio Project

**In your repo on GitHub.com**:

* Click on the green clone or download button.
* Copy the given url for "Clone with HTTPS".

**In RStudio**:

* In the upper left, go to File > New Project > Version Control.
* Select Git.
* Paste in the url.  It should automatically give it a name. Select where you want the project to live in your home directory. Then click okay.

---

## Let's now do this for our local installation of RStudio!

---

## Check if git is install on your computer

In **Terminal**, type

```r
which git
```

```r
git --version
```

* If you receive an answer, then git is already install! 🎉

* If the reply is `git: command not found` (or similar), then
    + Windows: Visit [https://gitforwindows.org/](https://gitforwindows.org/)
    + Macs: In the Terminal type

```r
xcode-select --install    
```

* If you had to install git, restart your RStudio Session.

---

## Introduce Yourself to Git

* Install the package `usethis`.

* In your R console, modify and run the following code to introduce yourself to git

```r
library(usethis)
use_git_config(user.name = "mcconvil", 
               user.email = "kmcconville@fas.harvard.edu")
```

---

## Personal Access Token Time

* Copy your PAT (that you stored in a safe place).
    + You can also generate a new one if you want.

* Store it by running:

```r
gitcreds::gitcreds_set()
```

---

## Sync GitHub.com repo and an RStudio Project

**In your repo on GitHub.com**:

* Click on the green clone or download button.
* Copy the given url for "Clone with HTTPS".

**In RStudio**:

---

## Feel free to use EITHER the RStudio Server and/or your local RStudio.

---

## Workflow

Once your GitHub repo and RStudio project are synced, here's your workflow:

* **Pull** the most recent version of the repo from GitHub to your RStudio project.

* Do some work on your project in RStudio.

* **Commit** that work.
    + Committing takes a snapshot of all the files in the project.
    + Look over the **Diff**: which shows what has changed since your last update.
    + Include a quick note, **Commit Message** to summarize the motivation for the changes.

* **Push** your commit to GitHub from RStudio.

---

## Workflow Demo

---

## Ignoring Files

* There are several files that we want to **NOT** push to GitHub.

* These include:
    + `.gitignore`
    + `.DS_Store`

* Add these files to the `.gitignore`.

---

## Test the waters: Let's go through the workflow.

* Pull. (Yes, there is nothing to pull yet but it is always good practice to start here.)
* Click on the ReadMe.
* Add something to the ReadMe.
* Click on the git tab.  Check the box next to the ReadMe.md. Hit commit.
* Put in a commit message.  Look over the diff.  
* Push.

**Look for updates in the ReadMe on GitHub.com.**

---

## Git Collaboration: Merge conflicts

* What if my collaborators and I both make changes? 
    + Scenario: Your collaborator makes changes to a file, commits, and pushes to GitHub. You also modify that file, commit and push.  
    + Result: Your push will fail because there's a commit on GitHub that you don't have.  
    + Usual Solution: Pull and *usually* git will merge their work nicely with yours.  Then push.  If that doesn't work, you have a **merge conflict**.  Let's cross that bridge when we get there.  
    
* How to avoid merge conflicts?
    + Always pull when you are going to work on your project.
    + Always commit and push when you are done even if you made small changes.

---

## Collaboration: Git Style

* **Projects**: Can use to create to do lists and stay organized.

* **Issues**: Useful method to communicate with your group members.

---

### Reminders