Reproducible Reporting

.leftcol30[
<center>
<img src="https://github.com/emse-p4a-gwu/emse-p4a-gwu.github.io/raw/master/images/p4a_hex_sticker.png" width=250>
</center>
]

### <svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:white;overflow:visible;position:relative;"><path d="M496 128v16a8 8 0 0 1-8 8h-24v12c0 6.627-5.373 12-12 12H60c-6.627 0-12-5.373-12-12v-12H24a8 8 0 0 1-8-8v-16a8 8 0 0 1 4.941-7.392l232-88a7.996 7.996 0 0 1 6.118 0l232 88A8 8 0 0 1 496 128zm-24 304H40c-13.255 0-24 10.745-24 24v16a8 8 0 0 0 8 8h464a8 8 0 0 0 8-8v-16c0-13.255-10.745-24-24-24zM96 192v192H60c-6.627 0-12 5.373-12 12v20h416v-20c0-6.627-5.373-12-12-12h-36V192h-64v192h-64V192h-64v192h-64V192H96z"/></svg> EMSE 4571: Intro to Programming for Analytics
### <svg aria-hidden="true" role="img" viewBox="0 0 448 512" style="height:1em;width:0.88em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:white;overflow:visible;position:relative;"><path d="M224 256c70.7 0 128-57.3 128-128S294.7 0 224 0 96 57.3 96 128s57.3 128 128 128zm89.6 32h-16.7c-22.2 10.2-46.9 16-72.9 16s-50.6-5.8-72.9-16h-16.7C60.2 288 0 348.2 0 422.4V464c0 26.5 21.5 48 48 48h352c26.5 0 48-21.5 48-48v-41.6c0-74.2-60.2-134.4-134.4-134.4z"/></svg> John Paul Helveston
### <svg aria-hidden="true" role="img" viewBox="0 0 448 512" style="height:1em;width:0.88em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:white;overflow:visible;position:relative;"><path d="M0 464c0 26.5 21.5 48 48 48h352c26.5 0 48-21.5 48-48V192H0v272zm320-196c0-6.6 5.4-12 12-12h40c6.6 0 12 5.4 12 12v40c0 6.6-5.4 12-12 12h-40c-6.6 0-12-5.4-12-12v-40zm0 128c0-6.6 5.4-12 12-12h40c6.6 0 12 5.4 12 12v40c0 6.6-5.4 12-12 12h-40c-6.6 0-12-5.4-12-12v-40zM192 268c0-6.6 5.4-12 12-12h40c6.6 0 12 5.4 12 12v40c0 6.6-5.4 12-12 12h-40c-6.6 0-12-5.4-12-12v-40zm0 128c0-6.6 5.4-12 12-12h40c6.6 0 12 5.4 12 12v40c0 6.6-5.4 12-12 12h-40c-6.6 0-12-5.4-12-12v-40zM64 268c0-6.6 5.4-12 12-12h40c6.6 0 12 5.4 12 12v40c0 6.6-5.4 12-12 12H76c-6.6 0-12-5.4-12-12v-40zm0 128c0-6.6 5.4-12 12-12h40c6.6 0 12 5.4 12 12v40c0 6.6-5.4 12-12 12H76c-6.6 0-12-5.4-12-12v-40zM400 64h-48V16c0-8.8-7.2-16-16-16h-32c-8.8 0-16 7.2-16 16v48H160V16c0-8.8-7.2-16-16-16h-32c-8.8 0-16 7.2-16 16v48H48C21.5 64 0 85.5 0 112v48h448v-48c0-26.5-21.5-48-48-48z"/></svg> April 14, 2022
]

---

# Quiz 7 (last one!)

## Go to `#class` channel in Slack for quiz link

## Open RStudio first!

## Rules:

- You may use your notes and RStudio
- You may **not** use any other resources (e.g. the internet, your classmates, etc.)

]

]

---

## A bunch of today's slides are adapted from the brilliant<br>[Alison Presmanes Hill](https://alison.rbind.io/)

### [<svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#007bff;overflow:visible;position:relative;"><path d="M459.37 151.716c.325 4.548.325 9.097.325 13.645 0 138.72-105.583 298.558-298.558 298.558-59.452 0-114.68-17.219-161.137-47.106 8.447.974 16.568 1.299 25.34 1.299 49.055 0 94.213-16.568 130.274-44.832-46.132-.975-84.792-31.188-98.112-72.772 6.498.974 12.995 1.624 19.818 1.624 9.421 0 18.843-1.3 27.614-3.573-48.081-9.747-84.143-51.98-84.143-102.985v-1.299c13.969 7.797 30.214 12.67 47.431 13.319-28.264-18.843-46.781-51.005-46.781-87.391 0-19.492 5.197-37.36 14.294-52.954 51.655 63.675 129.3 105.258 216.365 109.807-1.624-7.797-2.599-15.918-2.599-24.04 0-57.828 46.782-104.934 104.934-104.934 30.213 0 57.502 12.67 76.67 33.137 23.715-4.548 46.456-13.32 66.599-25.34-7.798 24.366-24.366 44.833-46.132 57.827 21.117-2.273 41.584-8.122 60.426-16.243-14.292 20.791-32.161 39.308-52.628 54.253z"/></svg> @apreshill](http://twitter.com/apreshill)

### Check out her [RMarkdown slide deck](https://apreshill.github.io/rmd4cdc/)

]

]]

---

# Week 12: .fancy[Reproducible Reporting]

### 1. Why RMarkdown?
### 2. Metadata and output formats

### BREAK

### 3. Text
### 4. Code chunks

---

# Week 12: .fancy[Reproducible Reporting]

### 1. .orange[Why RMarkdown?]
### 2. Metadata and output formats

### BREAK

### 3. Text
### 4. Code chunks

---

class:center

## The horrors of a non-reproducible workflow

---

class:center

## RMarkdown to the rescue!

---

# "Literate programming"

> ### Treat programs as a "literature" understandable to **human beings**

]]

[Donald E. Knuth](https://en.wikipedia.org/wiki/Donald_Knuth)

]]

---

# Week 12: .fancy[Reproducible Reporting]

### 1. Why RMarkdown?
### 2. .orange[Metadata and output formats]

### BREAK

### 3. Text
### 4. Code chunks

---

background-image: url(images/horst_monsters_rmarkdown.png)
background-size: contain
background-color: #FFFFFF

---

---

---

background-color: #FFFFFF

**Y**AML<br>
**A**in't<br>
**M**arkup<br>
**L**anguage

```yaml
---
key: value
---
```
]

]

---

# Output options

---

background-color: #FFFFFF

# Save output options in your YAML

```yaml
---
title: Your title here
author: Your name here
output: html_document
---
```

```yaml
---
title: Your title here
author: Your name here
output:
  html_document:
    toc: true
    toc_float: true
    theme: flatly
---
```
]

]

---

---

---

---

---

---

class: middle center
background-image: url(images/Single-knit1.png)
background-size: contain

???

Here is what we knit.

---

???

Using the `THEME:` key in our YAML, we changed our font and colors.

---

???

And we have this nice table of contents floating off to the side...

---

## Preview bootswatch themes

https://bootswatch.com/

---

## Quick check-in

(a)

```yaml
---
output: html_document()
---
```

(b)

```yaml
---
output: html_document
---
```

]

(a)

```yaml
---
output:
  html_document:
    toc: true
---
```

(b)

```yaml
---
output:
  html_document(toc=true)
---
```

]

---

# Output formats

---

https://rmarkdown.rstudio.com/docs/reference/index.html#section-output-formats

---

# 🧶 Knit to multiple outputs

```r
rmarkdown::render("notes.Rmd", output_format ="all")
```

]

```yaml
---
title: Your title here
author: Your name here
output:
  html_document:
    toc: true
    toc_float: true
    theme: flatly
  word_document: default
  pdf_document: default
---
```

]

???

This is a great way to "control" your knit button!

Notice that when you knit, it respects those output options in your YAML.

This way you "save" your output options

---

(a)

```yaml
---
output:
  html_document: default
  word_document: default
---
```

(b)

```yaml
---
output:
  html_document()
  word_document()
---
```

]]

(a)

```yaml
---
output:
  html_document:
    toc: true
  word_document: default
---
```

(b)

```yaml
---
output:
  html_document(toc=true)
  word_document(default)
---
```

]]

---

---

---

# Extension output formats

.cols3[
<img src="https://raw.githubusercontent.com/rstudio/hex-stickers/master/PNG/flexdashboard.png">
]

---

https://rstudio.github.io/distill/

---

```yaml
---
author: Your name here
title: Your title here
output: distill::distill_article
---
```

]

```yaml
---
author: Your name here
title: Your title here
output:
  distill::distill_article:
    toc: true
---
```

]

---

## Quick practice

Go to your `notes.Rmd` file and knit it to the following outputs:

- `html_document` with a table of contents
- `distill_article` with a table of contents
- `word_document`
- `pdf_document`

---

# Week 12: .fancy[Reproducible Reporting]

### 1. Why RMarkdown?
### 2. Metadata and output formats

### BREAK

### 3. .orange[Text]
### 4. Code chunks

---

---

---

---

# Right now, bookmark this! 👇

# https://commonmark.org/help/

<hr>

# (When you have 10 minutes, do this! 👇)

# https://commonmark.org/help/tutorial/

---

# .center[Headers]

```markdown
# HEADER 1

## HEADER 2

### HEADER 3

#### HEADER 4

##### HEADER 5

###### HEADER 6
```

]

# HEADER 1

## HEADER 2

### HEADER 3

#### HEADER 4

##### HEADER 5

###### HEADER 6

]

---

# .center[Text]

```markdown
Childhood **vaccines**
are one of the
_great triumphs_
of modern medicine.
```

]

Childhood **vaccines**<br>
are one of the<br>
_great triumphs_<br>
of modern medicine.

]

---

# .center[Text]

## Type this...

- `normal text`
- `*italic text*`
- `**bold text**`
- `***bold italic text***`
- `~~strikethrough~~`
- `` `code text` ``

]

## ..to get this

- normal text
- *italic text*
- **bold text**
- ***bold italic text***
- ~~strikethrough~~
- `code text`

]

---

# .center[Lists]

Bullet list:

```r
- first item
- second item
- third item
```

- first item
- second item
- third item

]

Numbered list:

```r
1. first item
2. second item
3. third item
```

1. first item
2. second item
3. third item

]

---

# .center[Links]

Simple **url link** to another site:

```r
[Download R](http://www.r-project.org/)
```

[Download R](http://www.r-project.org/)

---

# .center[Images]

```markdown
![](https://p4a.seas.gwu.edu/2022-Spring/images/helveston.jpg)
```

]]

![](https://p4a.seas.gwu.edu/2022-Spring/images/helveston.jpg)

]

---

# .center[Local images]

```markdown
![](images/p4a_hex_sticker.png)
```

]]

![](images/p4a_hex_sticker.png)

]

---

## Quick check-in

How do you add headers in Markdown?

a. `! Header`

b. `- Header`

c. `# Header`

d. `1. Header`

]

What about lists? Bulleted? Numbered?

a. `! Item 1`

b. `- Item 1`

c. `# Item 1`

d. `1. Item 1`

]

---

class: center
background-image: url(images/typewriter.jpg)
background-size: contain
background-color: #f6f6f6

# Markdown tables

---

# Markdown tables

```markdown

| Column 1   | Column 2  |
|------------| ----------|
| Cell 1, 1  | Cell 2, 1 |
| Cell 1, 2  | Cell 2, 2 |

```

]

## ...produces this

| Column 1   | Column 2  |
|------------| ----------|
| Cell 1, 1  | Cell 2, 1 |
| Cell 1, 2  | Cell 2, 2 |

]

---

# Markdown tables

## This...

```markdown
| Time          | Session | Topic     |
|:--------------|:-------:|----------:|
| _left_        | _center_| _right_   |
| 01:00 - 01:50 | 1       | Practice  |
| 01:50 - 02:00 |         | **Break** |
| 02:00 - 02:45 | 2       | Class     |
| 02:45 - 03:00 |         | **Break** |

```

]

## ...produces this

| Time          | Session | Topic     |
|:--------------|:-------:|----------:|
| _left_        | _center_| _right_   |
| 01:00 - 01:50 | 1       | Practice  |
| 01:50 - 02:00 |         | **Break** |
| 02:00 - 02:45 | 2       | Class     |
| 02:45 - 03:00 |         | **Break** |

]

---

# .fancy[Break]

---

# Week 12: .fancy[Reproducible Reporting]

### 1. Why RMarkdown?
### 2. Metadata and output formats

### BREAK

### 3. Text
### 4. .orange[Code chunks]

---

---

---

---

---

# R Code

## Inline code

```r
`r insert code here`
```

]]

## Code chunks

````markdown
```{r}
insert code here
insert more code here
```
````

]]

---

# Inline R code

Embed R code directly in a markdown

```r
`r <insert code here>`
```

For example:

```r
The sum of 3 and 4 is `r 3 + 4`
```

Produces this:

The sum of 3 and 4 is 7

---

# R Code chunks

````markdown
```{r}
bears %>%
  count(month)
```
````

What is the fate of this chunk?

]

```r
bears %>%
  count(month)
```

```
#> # A tibble: 12 × 2
#>    month     n
#>    <dbl> <int>
#>  1     1     3
#>  2     2     1
#>  3     3     1
#>  4     4     4
#>  5     5    18
#>  6     6    20
#>  7     7    27
#>  8     8    28
#>  9     9    25
#> 10    10    25
#> 11    11    12
#> 12    12     2
```

]

---

# Code chunks

````markdown
```{r}
monthlyCount <- bears %>%
  count(month)
```
````

What fate do you predict here?

]

```r
monthlyCount <- bears %>%
  count(month)
```

]

---

# Code chunks

````markdown
```{r}
monthlyCount <- bears %>%
  count(month)

monthlyCount
```
````

]

```r
monthlyCount <- bears %>%
  count(month)

monthlyCount
```

]]

---

# Chunk options

Control what chunks output using options inside `{r}`:

Example: `{r, echo=FALSE, message=FALSE}`

---

# Chunk options

By default, code chunks print **code** + **output**:

## This...

````markdown
```{r}
cat('hello world!')
```
````

]

## ...produces this

```r
cat('hello world!')
```

```
#> hello world!
```

]

---

# .center[Chunk output options]

````markdown
```{r, echo=FALSE}
cat('hello world!')
```
````

Prints only **output**<br>(doesn't show code)

**Output**:

```
#> hello world!
```
]

````markdown
```{r, eval=FALSE}
cat('hello world!')
```
````

Prints only **code**<br>(doesn't run the code)

**Output**:

```r
cat('hello world!')
```

]

````markdown
```{r, include=FALSE}
cat('hello world!')
```
````

Runs, but doesn't print anything

**Output**:

]

---

# message / warning

![](https://www.tidyverse.org/images/tidyverse_1.2.0/tidyverse_1-2-0_pkg_load.gif)

---

# message / warning

````markdown
```{r, message=FALSE, warning=FALSE}
library(tidyverse)
```
````

]

```r
library(tidyverse)
```

]

---

# Using chunk options

````markdown
```{r, message=FALSE, warning=FALSE}
library(tidyverse)
```
````

- Place between curly braces<br>`{r option=value}`
- Multiple options separated by commas<br>`{r option1=value, option2=value}`
- Careful! The `r` part is the **code engine** (other engines possible)

]

---

# Inserting a Python code chunk

Change `{r}` to `{python}` in the code chunk.

Example:

```python
'In Python, you can concatenate strings' + ' like this!'
```
```
'In Python, you can concatenate strings like this!'
```

---

# A global `setup` chunk 🌍

One chunk to rule them all!

````markdown
```{r setup, include = FALSE}
knitr::opts_chunk$set(
  warning = FALSE,
  message = FALSE,
  comment = "#>",
  fig.retina = 3,
  fig.path = "figs/"
)
```
````

]

- A special chunk label: `setup`
- Typically the first chunk
- All following chunks will use these options (i.e., sets global chunk options)
- **Tip**: set `include=FALSE`
- You can (and should) use individual chunk options too

]

---

## Your turn: Birds & Bears

2) Create a "setup" code chunk to load the `tidyverse` library and the `birds.csv` and `bears.csv` files.

3) Use text and code to find answers each of the following questions - show your code and results to justify each answer:

- Which months have the highest and lowest number of bird impacts with aircraft?
- Does the annual number of bird impacts appear to be changing over time?
- Which months have the highest frequency of bear killings?
- Who has been killed more often by bears: hunters or hikers?
- How do the the number of bear attacks on men vs women compare?
]

---

# Including plots

---

# Including plots

```r
bears %>%
  count(month) %>%
  ggplot() +
  geom_col(
    aes(x = as.factor(month), y=n)) +
  theme_minimal(base_size = 22) +
  labs(x = 'Month', y = 'Count')
```

Will this print?

]

]

---

# Including plots

```r
bearMonthPlot <- bears %>%
  count(month) %>%
  ggplot() +
  geom_col(
    aes(x = as.factor(month), y=n)) +
  theme_minimal(base_size = 22) +
  labs(x = 'Month', y = 'Count')
```

What about this?

]

---

# Including plots

```r
bearMonthPlot <- bears %>%
  count(month) %>%
  ggplot() +
  geom_col(
    aes(x = as.factor(month), y=n)) +
  theme_minimal(base_size = 22) +
  labs(x = 'Month', y = 'Count')

*bearMonthPlot
```

What about this?

]

]

???

so, how did we get a figure into R Markdown?

Answer: it has to print!

---

# Chunk options for plots

- fig size
- fig resolution

---

# `out.width`

````markdown
```{r, out.width="70%"}
bearMonthPlot
```
````

]

````markdown
```{r, out.width="20%"}
bearMonthPlot
```
````

]

---

# `fig.width` & `fig.height`

````markdown
```{r, fig.width=6, fig.height=4}
bearMonthPlot
```
````

]

````markdown
```{r, fig.width=3, fig.height=4}
bearMonthPlot
```
````

]

---

# `fig.path`

````markdown
```{r, fig.path="figs/", echo=FALSE}
bearMonthPlot
```
````

---

# `fig.path`

````markdown
```{r bear-month-plot, fig.path="figs/", echo=FALSE}
bearMonthPlot
```
````

---

# A good chunk label

**Think: kebabs, not snakes**

### Good

`my-plot`

`myplot`

`myplot1`

`myplot-1`

`MY-PLOT`

]

### Bad

`my_plot`

`my plot`

everything else!

]

---

### View default options

```r
str(knitr::opts_chunk$get())
```

```
#> List of 53
#>  $ eval         : logi TRUE
#>  $ echo         : logi TRUE
#>  $ results      : chr "markup"
#>  $ tidy         : logi FALSE
#>  $ tidy.opts    : NULL
#>  $ collapse     : logi FALSE
#>  $ prompt       : logi FALSE
#>  $ comment      : chr "#>"
#>  $ highlight    : logi TRUE
#>  $ size         : chr "normalsize"
#>  $ background   : chr "#F7F7F7"
#>  $ strip.white  : 'AsIs' logi TRUE
#>  $ cache        : logi FALSE
#>  $ cache.path   : chr "index_cache/html/"
#>  $ cache.vars   : NULL
#>  $ cache.lazy   : logi TRUE
#>  $ dependson    : NULL
#>  $ autodep      : logi FALSE
#>  $ cache.rebuild: logi FALSE
#>  $ fig.keep     : chr "high"
#>  $ fig.show     : chr "asis"
#>  $ fig.align    : chr "default"
#>  $ fig.path     : chr "figs/"
#>  $ dev          : chr "png"
#>  $ dev.args     : NULL
#>  $ dpi          : num 72
#>  $ fig.ext      : NULL
#>  $ fig.width    : num 7.25
#>  $ fig.height   : num 4
#>  $ fig.env      : chr "figure"
#>  $ fig.cap      : NULL
#>  $ fig.scap     : NULL
#>  $ fig.lp       : chr "fig:"
#>  $ fig.subcap   : NULL
#>  $ fig.pos      : chr ""
#>  $ out.width    : NULL
#>  $ out.height   : NULL
#>  $ out.extra    : NULL
#>  $ fig.retina   : num 3
#>  $ external     : logi TRUE
#>  $ sanitize     : logi FALSE
#>  $ interval     : num 1
#>  $ aniopts      : chr "controls,loop"
#>  $ warning      : logi FALSE
#>  $ error        : logi FALSE
#>  $ message      : logi FALSE
#>  $ render       : NULL
#>  $ ref.label    : NULL
#>  $ child        : NULL
#>  $ engine       : chr "R"
#>  $ split        : logi FALSE
#>  $ include      : logi TRUE
#>  $ purl         : logi TRUE
```

]

---

# Two more important chunks:

- ## Images
- ## Tables

---

# .center[Image chunks]

### Insert images with markdown

```markdown
![](images/p4a_hex_sticker.png)
```

### Insert images with chunks (so you can resize it)

````markdown
```{r, echo=FALSE, out.width="20%"}
knitr::include_graphics("images/p4a_hex_sticker.png")
```
````

---

# .center[Image chunks]

````markdown
```{r, echo=FALSE, out.width="20%"}
knitr::include_graphics("images/p4a_hex_sticker.png")
```
````

<img src="images/p4a_hex_sticker.png" width="20%" />
]

````markdown
```{r, echo=FALSE, out.width="50%"}
knitr::include_graphics("images/p4a_hex_sticker.png")
```
````

]

---

# Convert a data frame to a table with `kable()`

```r
bears %>%
  count(bearType, wildOrCaptive)
```

```
#> # A tibble: 6 × 3
#>   bearType wildOrCaptive     n
#>   <chr>    <chr>         <int>
#> 1 Black    Captive          16
#> 2 Black    Wild             60
#> 3 Brown    Captive           8
#> 4 Brown    Wild             72
#> 5 Polar    Captive           4
#> 6 Polar    Wild              6
```

]

```r
bears %>%
  count(bearType, wildOrCaptive) %>%
  kable()
```

<table>
 <thead>
  <tr>
   <th style="text-align:left;"> bearType </th>
   <th style="text-align:left;"> wildOrCaptive </th>
   <th style="text-align:right;"> n </th>
  </tr>
 </thead>
<tbody>
  <tr>
   <td style="text-align:left;"> Black </td>
   <td style="text-align:left;"> Captive </td>
   <td style="text-align:right;"> 16 </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Black </td>
   <td style="text-align:left;"> Wild </td>
   <td style="text-align:right;"> 60 </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Brown </td>
   <td style="text-align:left;"> Captive </td>
   <td style="text-align:right;"> 8 </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Brown </td>
   <td style="text-align:left;"> Wild </td>
   <td style="text-align:right;"> 72 </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Polar </td>
   <td style="text-align:left;"> Captive </td>
   <td style="text-align:right;"> 4 </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Polar </td>
   <td style="text-align:left;"> Wild </td>
   <td style="text-align:right;"> 6 </td>
  </tr>
</tbody>
</table>

]

---

## Your turn: College Majors

1) Create a new R Markdown file (`.Rmd`) in RStudio - title it _"College Majors Analysis"_

2) Create a "setup" code chunk to load the `tidyverse` library and the `recent_grads.csv` file.

3) Use text, code, and plots to find answers each of the following questions - show your code and results to justify each answer:

- What are the highest earning engineering majors?
- Within the engineering majors, which ones have better employment rates?
- Within the engineering majors, which ones have a better gender balance?

(Use good code chunk names for your figures!)

]