Introduction to R for Applied Epidemiology

class: center, middle, inverse, title-slide

# Introduction to R for Applied Epidemiology

### Pivoting data

contact@appliedepi.org
---

# Restructuring data

*pivoting, reshaping, melting, casting, transforming...* dataframes

---

# What is pivoting?

* *Excel pivot tables* are a way of summarizing and aggregating data

* In R, **pivoting** a dataframe has a **different meaning**

* Think of it as *restructuring*, or *reshaping* the dataframe

* We will use the `pivot_wider()` and `pivot_longer()` functions from the {tidyr} package

* You will often see examples using alternative functions from other packages: 
     * `melt()` and `cast()` from {reshape2}
     * `gather()` and `spread()` ancestors of the {tidyr} `pivot_()` functions  
     * `melt()` and `dcast()` from {data.table}

---
# Tidy data

Do you remember the 3 principles of "tidy data"?

1. Each **value** must have its own **cell**

2. Each **variable** must have its own **column**

3. Each **observation** must have its own **row**

---

# Terminology

Structurally, "data frames" in R consist of **columns** and **rows**.

However, **"variables"** and **"observations"** are more *abstract* concepts:

* **Variables** measure one *underlying attribute* (age, outcome, or date of onset)  
* **Observations** relate to a *unit of analysis*

Ideally, they align: **columns = variables** and **rows = observations**

.footnote[Image source: [R for Data Science](https://r4ds.had.co.nz/tidy-data.html)]

---
# Pivot longer 
.pull-left[
Data entry is often in “wide” format 
<table>
 <thead>
 <tr>
 <th style="text-align:left;"> country </th>
 <th style="text-align:right;"> 1999 </th>
 <th style="text-align:right;"> 2000 </th>
 <th style="text-align:right;"> 2001 </th>
 <th style="text-align:right;"> 2002 </th>
 </tr>
 </thead>
<tbody>
 <tr>
 <td style="text-align:left;"> Nigeria </td>
 <td style="text-align:right;"> 8000 </td>
 <td style="text-align:right;"> 7500 </td>
 <td style="text-align:right;"> 9250 </td>
 <td style="text-align:right;"> 10200 </td>
 </tr>
 <tr>
 <td style="text-align:left;"> India </td>
 <td style="text-align:right;"> 20100 </td>
 <td style="text-align:right;"> 25650 </td>
 <td style="text-align:right;"> 26800 </td>
 <td style="text-align:right;"> 27255 </td>
 </tr>
 <tr>
 <td style="text-align:left;"> Brazil </td>
 <td style="text-align:right;"> 4500 </td>
 <td style="text-align:right;"> 5120 </td>
 <td style="text-align:right;"> 5100 </td>
 <td style="text-align:right;"> 5860 </td>
 </tr>
</tbody>
</table>

* A subject’s characteristics are stored in a single row  
* Useful for presentation  
* **Not** ideal for some types of analysis.
]

--
.pull-right[
**Easier to analyse in "long" format** 
<table>
 <thead>
 <tr>
 <th style="text-align:left;"> country </th>
 <th style="text-align:left;"> year </th>
 <th style="text-align:right;"> cases </th>
 </tr>
 </thead>
<tbody>
 <tr>
 <td style="text-align:left;"> Nigeria </td>
 <td style="text-align:left;"> 1999 </td>
 <td style="text-align:right;"> 8000 </td>
 </tr>
 <tr>
 <td style="text-align:left;"> Nigeria </td>
 <td style="text-align:left;"> 2000 </td>
 <td style="text-align:right;"> 7500 </td>
 </tr>
 <tr>
 <td style="text-align:left;"> Nigeria </td>
 <td style="text-align:left;"> 2001 </td>
 <td style="text-align:right;"> 9250 </td>
 </tr>
 <tr>
 <td style="text-align:left;"> Nigeria </td>
 <td style="text-align:left;"> 2002 </td>
 <td style="text-align:right;"> 10200 </td>
 </tr>
 <tr>
 <td style="text-align:left;"> India </td>
 <td style="text-align:left;"> 1999 </td>
 <td style="text-align:right;"> 20100 </td>
 </tr>
 <tr>
 <td style="text-align:left;"> India </td>
 <td style="text-align:left;"> 2000 </td>
 <td style="text-align:right;"> 25650 </td>
 </tr>
 <tr>
 <td style="text-align:left;"> India </td>
 <td style="text-align:left;"> 2001 </td>
 <td style="text-align:right;"> 26800 </td>
 </tr>
 <tr>
 <td style="text-align:left;"> India </td>
 <td style="text-align:left;"> 2002 </td>
 <td style="text-align:right;"> 27255 </td>
 </tr>
 <tr>
 <td style="text-align:left;"> Brazil </td>
 <td style="text-align:left;"> 1999 </td>
 <td style="text-align:right;"> 4500 </td>
 </tr>
 <tr>
 <td style="text-align:left;"> Brazil </td>
 <td style="text-align:left;"> 2000 </td>
 <td style="text-align:right;"> 5120 </td>
 </tr>
 <tr>
 <td style="text-align:left;"> Brazil </td>
 <td style="text-align:left;"> 2001 </td>
 <td style="text-align:right;"> 5100 </td>
 </tr>
 <tr>
 <td style="text-align:left;"> Brazil </td>
 <td style="text-align:left;"> 2002 </td>
 <td style="text-align:right;"> 5860 </td>
 </tr>
</tbody>
</table>

]

---
# {ggplot2} example

How to plot cases over time for the three countries?

<table>
 <thead>
 <tr>
 <th style="text-align:left;"> country </th>
 <th style="text-align:right;"> 1999 </th>
 <th style="text-align:right;"> 2000 </th>
 <th style="text-align:right;"> 2001 </th>
 <th style="text-align:right;"> 2002 </th>
 </tr>
 </thead>
<tbody>
 <tr>
 <td style="text-align:left;"> Nigeria </td>
 <td style="text-align:right;"> 8000 </td>
 <td style="text-align:right;"> 7500 </td>
 <td style="text-align:right;"> 9250 </td>
 <td style="text-align:right;"> 10200 </td>
 </tr>
 <tr>
 <td style="text-align:left;"> India </td>
 <td style="text-align:right;"> 20100 </td>
 <td style="text-align:right;"> 25650 </td>
 <td style="text-align:right;"> 26800 </td>
 <td style="text-align:right;"> 27255 </td>
 </tr>
 <tr>
 <td style="text-align:left;"> Brazil </td>
 <td style="text-align:right;"> 4500 </td>
 <td style="text-align:right;"> 5120 </td>
 <td style="text-align:right;"> 5100 </td>
 <td style="text-align:right;"> 5860 </td>
 </tr>
</tbody>
</table>

```r
ggplot(data = example,
       mapping = aes(x = ???, y = ???))+
     geom_line()
```

---
# Pivot longer

.pull-left[
<div class="tabwid"><style>.cl-12c7d1f4{}.cl-12b2186e{font-family:'Arial';font-size:11pt;font-weight:normal;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-12b8888e{margin:0;text-align:left;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);padding-bottom:5pt;padding-top:5pt;padding-left:5pt;padding-right:5pt;line-height: 1;background-color:transparent;}.cl-12b88898{margin:0;text-align:right;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);padding-bottom:5pt;padding-top:5pt;padding-left:5pt;padding-right:5pt;line-height: 1;background-color:transparent;}.cl-12b8ae04{width:0.786in;background-color:rgba(255, 255, 255, 1.00);vertical-align: middle;border-bottom: 1.5pt solid rgba(102, 102, 102, 1.00);border-top: 1.5pt solid rgba(102, 102, 102, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-12b8ae0e{width:0.752in;background-color:rgba(255, 165, 0, 1.00);vertical-align: middle;border-bottom: 1.5pt solid rgba(102, 102, 102, 1.00);border-top: 1.5pt solid rgba(102, 102, 102, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-12b8ae18{width:0.786in;background-color:transparent;vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-12b8ae19{width:0.752in;background-color:transparent;vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-12b8ae22{width:0.786in;background-color:transparent;vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-12b8ae2c{width:0.752in;background-color:transparent;vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-12b8ae36{width:0.786in;background-color:transparent;vertical-align: middle;border-bottom: 1.5pt solid rgba(102, 102, 102, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-12b8ae37{width:0.752in;background-color:transparent;vertical-align: middle;border-bottom: 1.5pt solid rgba(102, 102, 102, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}</style><table data-quarto-disable-processing='true' class='cl-12c7d1f4'><thead><tr style="overflow-wrap:break-word;"><th class="cl-12b8ae04">country</th><th class="cl-12b8ae0e">1999</th><th class="cl-12b8ae0e">2000</th><th class="cl-12b8ae0e">2001</th><th class="cl-12b8ae0e">2002</th></tr></thead><tbody><tr style="overflow-wrap:break-word;"><td class="cl-12b8ae18">Nigeria</td><td class="cl-12b8ae19">8,000</td><td class="cl-12b8ae19">7,500</td><td class="cl-12b8ae19">9,250</td><td class="cl-12b8ae19">10,200</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-12b8ae22">India</td><td class="cl-12b8ae2c">20,100</td><td class="cl-12b8ae2c">25,650</td><td class="cl-12b8ae2c">26,800</td><td class="cl-12b8ae2c">27,255</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-12b8ae36">Brazil</td><td class="cl-12b8ae37">4,500</td><td class="cl-12b8ae37">5,120</td><td class="cl-12b8ae37">5,100</td><td class="cl-12b8ae37">5,860</td></tr></tbody></table></div>

* These **column names will be pivoted**

]

---
# Pivot longer

.pull-left[
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* These **values will be re-arranged**

]

---
# Pivot longer

.pull-left[
<div class="tabwid"><style>.cl-13430432{}.cl-133557e2{font-family:'Arial';font-size:11pt;font-weight:normal;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-133b2f5a{margin:0;text-align:left;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);padding-bottom:5pt;padding-top:5pt;padding-left:5pt;padding-right:5pt;line-height: 1;background-color:transparent;}.cl-133b2f6e{margin:0;text-align:right;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);padding-bottom:5pt;padding-top:5pt;padding-left:5pt;padding-right:5pt;line-height: 1;background-color:transparent;}.cl-133b5156{width:0.786in;background-color:rgba(255, 255, 255, 1.00);vertical-align: middle;border-bottom: 1.5pt solid rgba(102, 102, 102, 1.00);border-top: 1.5pt solid rgba(102, 102, 102, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-133b5160{width:0.752in;background-color:rgba(255, 165, 0, 1.00);vertical-align: middle;border-bottom: 1.5pt solid rgba(102, 102, 102, 1.00);border-top: 1.5pt solid rgba(102, 102, 102, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-133b516a{width:0.786in;background-color:rgba(173, 216, 230, 1.00);vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-133b5174{width:0.752in;background-color:rgba(49, 163, 84, 1.00);vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-133b5175{width:0.786in;background-color:rgba(173, 216, 230, 1.00);vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-133b517e{width:0.752in;background-color:rgba(49, 163, 84, 1.00);vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-133b517f{width:0.786in;background-color:rgba(173, 216, 230, 1.00);vertical-align: middle;border-bottom: 1.5pt solid rgba(102, 102, 102, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-133b5188{width:0.752in;background-color:rgba(49, 163, 84, 1.00);vertical-align: middle;border-bottom: 1.5pt solid rgba(102, 102, 102, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}</style><table data-quarto-disable-processing='true' class='cl-13430432'><thead><tr style="overflow-wrap:break-word;"><th class="cl-133b5156">country</th><th class="cl-133b5160">1999</th><th class="cl-133b5160">2000</th><th class="cl-133b5160">2001</th><th class="cl-133b5160">2002</th></tr></thead><tbody><tr style="overflow-wrap:break-word;"><td class="cl-133b516a">Nigeria</td><td class="cl-133b5174">8,000</td><td class="cl-133b5174">7,500</td><td class="cl-133b5174">9,250</td><td class="cl-133b5174">10,200</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-133b5175">India</td><td class="cl-133b517e">20,100</td><td class="cl-133b517e">25,650</td><td class="cl-133b517e">26,800</td><td class="cl-133b517e">27,255</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-133b517f">Brazil</td><td class="cl-133b5188">4,500</td><td class="cl-133b5188">5,120</td><td class="cl-133b5188">5,100</td><td class="cl-133b5188">5,860</td></tr></tbody></table></div>

* These **identifiers will be replicated**

]

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# Pivot longer

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<div class="tabwid"><style>.cl-137d19d8{}.cl-136ca58a{font-family:'Arial';font-size:11pt;font-weight:normal;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-13735bc8{margin:0;text-align:left;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);padding-bottom:5pt;padding-top:5pt;padding-left:5pt;padding-right:5pt;line-height: 1;background-color:transparent;}.cl-13735bdc{margin:0;text-align:right;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);padding-bottom:5pt;padding-top:5pt;padding-left:5pt;padding-right:5pt;line-height: 1;background-color:transparent;}.cl-13743b6a{width:0.786in;background-color:rgba(255, 255, 255, 1.00);vertical-align: middle;border-bottom: 1.5pt solid rgba(102, 102, 102, 1.00);border-top: 1.5pt solid rgba(102, 102, 102, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-13743b88{width:0.752in;background-color:rgba(255, 165, 0, 1.00);vertical-align: middle;border-bottom: 1.5pt solid rgba(102, 102, 102, 1.00);border-top: 1.5pt solid rgba(102, 102, 102, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-13743b89{width:0.786in;background-color:rgba(173, 216, 230, 1.00);vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-13743b92{width:0.752in;background-color:rgba(49, 163, 84, 1.00);vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-13743b9c{width:0.786in;background-color:rgba(173, 216, 230, 1.00);vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-13743ba6{width:0.752in;background-color:rgba(49, 163, 84, 1.00);vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-13743bb0{width:0.786in;background-color:rgba(173, 216, 230, 1.00);vertical-align: middle;border-bottom: 1.5pt solid rgba(102, 102, 102, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-13743bb1{width:0.752in;background-color:rgba(49, 163, 84, 1.00);vertical-align: middle;border-bottom: 1.5pt solid rgba(102, 102, 102, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}</style><table data-quarto-disable-processing='true' class='cl-137d19d8'><thead><tr style="overflow-wrap:break-word;"><th class="cl-13743b6a">country</th><th class="cl-13743b88">1999</th><th class="cl-13743b88">2000</th><th class="cl-13743b88">2001</th><th class="cl-13743b88">2002</th></tr></thead><tbody><tr style="overflow-wrap:break-word;"><td class="cl-13743b89">Nigeria</td><td class="cl-13743b92">8,000</td><td class="cl-13743b92">7,500</td><td class="cl-13743b92">9,250</td><td class="cl-13743b92">10,200</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-13743b9c">India</td><td class="cl-13743ba6">20,100</td><td class="cl-13743ba6">25,650</td><td class="cl-13743ba6">26,800</td><td class="cl-13743ba6">27,255</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-13743bb0">Brazil</td><td class="cl-13743bb1">4,500</td><td class="cl-13743bb1">5,120</td><td class="cl-13743bb1">5,100</td><td class="cl-13743bb1">5,860</td></tr></tbody></table></div>

* List the columns to pivot  
* Provide 2 **new column names**

]

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<div class="tabwid"><style>.cl-13bfd55c{}.cl-13b1424e{font-family:'Arial';font-size:11pt;font-weight:normal;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-13b784b0{margin:0;text-align:left;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);padding-bottom:5pt;padding-top:5pt;padding-left:5pt;padding-right:5pt;line-height: 1;background-color:transparent;}.cl-13b784c4{margin:0;text-align:right;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);padding-bottom:5pt;padding-top:5pt;padding-left:5pt;padding-right:5pt;line-height: 1;background-color:transparent;}.cl-13b7a774{width:0.786in;background-color:rgba(255, 255, 255, 1.00);vertical-align: middle;border-bottom: 1.5pt solid rgba(102, 102, 102, 1.00);border-top: 1.5pt solid rgba(102, 102, 102, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-13b7a77e{width:0.625in;background-color:rgba(255, 255, 0, 1.00);vertical-align: middle;border-bottom: 1.5pt solid rgba(102, 102, 102, 1.00);border-top: 1.5pt solid rgba(102, 102, 102, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-13b7a788{width:0.752in;background-color:rgba(203, 195, 227, 1.00);vertical-align: middle;border-bottom: 1.5pt solid rgba(102, 102, 102, 1.00);border-top: 1.5pt solid rgba(102, 102, 102, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-13b7a792{width:0.786in;background-color:rgba(173, 216, 230, 1.00);vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-13b7a793{width:0.625in;background-color:rgba(255, 165, 0, 1.00);vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-13b7a79c{width:0.752in;background-color:rgba(49, 163, 84, 1.00);vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-13b7a79d{width:0.786in;background-color:rgba(173, 216, 230, 1.00);vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-13b7a7a6{width:0.625in;background-color:rgba(255, 165, 0, 1.00);vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-13b7a7a7{width:0.752in;background-color:rgba(49, 163, 84, 1.00);vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-13b7a7a8{width:0.786in;background-color:rgba(173, 216, 230, 1.00);vertical-align: middle;border-bottom: 1.5pt solid rgba(102, 102, 102, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-13b7a7b0{width:0.625in;background-color:rgba(255, 165, 0, 1.00);vertical-align: middle;border-bottom: 1.5pt solid rgba(102, 102, 102, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-13b7a7ba{width:0.752in;background-color:rgba(49, 163, 84, 1.00);vertical-align: middle;border-bottom: 1.5pt solid rgba(102, 102, 102, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}</style><table data-quarto-disable-processing='true' class='cl-13bfd55c'><thead><tr style="overflow-wrap:break-word;"><th class="cl-13b7a774">country</th><th class="cl-13b7a77e">year</th><th class="cl-13b7a788">cases</th></tr></thead><tbody><tr style="overflow-wrap:break-word;"><td class="cl-13b7a792">Nigeria</td><td class="cl-13b7a793">1999</td><td class="cl-13b7a79c">8,000</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-13b7a792">Nigeria</td><td class="cl-13b7a793">2000</td><td class="cl-13b7a79c">7,500</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-13b7a792">Nigeria</td><td class="cl-13b7a793">2001</td><td class="cl-13b7a79c">9,250</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-13b7a792">Nigeria</td><td class="cl-13b7a793">2002</td><td class="cl-13b7a79c">10,200</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-13b7a79d">India</td><td class="cl-13b7a7a6">1999</td><td class="cl-13b7a7a7">20,100</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-13b7a79d">India</td><td class="cl-13b7a7a6">2000</td><td class="cl-13b7a7a7">25,650</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-13b7a79d">India</td><td class="cl-13b7a7a6">2001</td><td class="cl-13b7a7a7">26,800</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-13b7a79d">India</td><td class="cl-13b7a7a6">2002</td><td class="cl-13b7a7a7">27,255</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-13b7a79d">Brazil</td><td class="cl-13b7a7a6">1999</td><td class="cl-13b7a7a7">4,500</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-13b7a79d">Brazil</td><td class="cl-13b7a7a6">2000</td><td class="cl-13b7a7a7">5,120</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-13b7a79d">Brazil</td><td class="cl-13b7a7a6">2001</td><td class="cl-13b7a7a7">5,100</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-13b7a7a8">Brazil</td><td class="cl-13b7a7b0">2002</td><td class="cl-13b7a7ba">5,860</td></tr></tbody></table></div>
]

---
# ggplot command

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```r
example %>%
  pivot_longer(
       cols = `1999`:`2002`,
       names_to = "year",
       values_to = "cases") %>%
     
  ggplot(mapping = aes(
*           x = year,
*           y = cases,
*           color = country,
*           group = country))+
  geom_line()
```

**Note** this example is included in your course folder as an R script entitled "example_pivot.R" in the "ebola/scripts/examples" subfolder.

]

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]

---
# Pivoting wider

We won't cover pivoting wider in this course, because it is not as frequently used.

You can explore several examples in these Epi R Handbook chapters:

* [Pivoting data](https://epirhandbook.com/en/new_pages/pivoting.html)  
* [Descriptive tables with {dplyr}](https://epirhandbook.com/en/new_pages/tables_descriptive.html)

---
class: inverse, center, middle

# Exercise!

Go to the course website  
Open the exercise for Module 8 part 2, and login  
Follow the instructions to return to your "ebola" R project and continue coding in your RMD script
Let an instructor know if you are unsure what to do