Lab 06: Building reports in R

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# Lab 06: Building reports in R

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<span>
Dr. Lucy D'Agostino McGowan
</span>
</div>

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# Agenda

* **Knitting a pdf document**
* **Creating tables in R**
* **Lab 06:** on your own

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## Knitting a pdf document

* Currently your yaml at the top of your `.Rmd` files looks something like this:

```yaml
---
title: "The title of your document"
name: "Your name"
output: html_document
---
```
---

## Knitting a pdf document

.question[
What do you think you would change to render this as a **pdf** document instead of **html**?
]

* Currently your yaml at the top of your `.Rmd` files looks something like this:

```yaml
---
title: "The title of your document"
name: "Your name"
output: html_document
---
```
---

## Knitting a pdf document

.question[
What do you think you would change to render this as a **pdf** document instead of **html**?
]

* Currently your yaml at the top of your `.Rmd` files looks something like this:

```yaml
---
title: "The title of your document"
name: "Your name"
*output: pdf_document
---
```

* For this lab and your final project I want you to create .pdf files.

---

## Making pretty tables

* We've been using the `tidy()` and `glance()` functions to print tables of our model output.
* These kind of look like "code" in our final reports
* We can make these prettier with the **knitr** package

```r
lm(wt ~ am, data = mtcars) %>%
  tidy()
```

```
## # A tibble: 2 x 5
##   term        estimate std.error statistic  p.value
##   <chr>          <dbl>     <dbl>     <dbl>    <dbl>
## 1 (Intercept)     3.77     0.165     22.9  1.49e-20
## 2 am             -1.36     0.258     -5.26 1.13e- 5
```

---

## Making pretty tables

--
* Load the **knitr** package with `library(knitr)`
* Use the `kable()` function to output a pretty table

```r
*library(knitr)
lm(wt ~ am, data = mtcars) %>%
  tidy() %>%
* kable()
```

<table>
 <thead>
  <tr>
   <th style="text-align:left;"> term </th>
   <th style="text-align:right;"> estimate </th>
   <th style="text-align:right;"> std.error </th>
   <th style="text-align:right;"> statistic </th>
   <th style="text-align:right;"> p.value </th>
  </tr>
 </thead>
<tbody>
  <tr>
   <td style="text-align:left;"> (Intercept) </td>
   <td style="text-align:right;"> 3.768895 </td>
   <td style="text-align:right;"> 0.1646171 </td>
   <td style="text-align:right;"> 22.894914 </td>
   <td style="text-align:right;"> 0.00e+00 </td>
  </tr>
  <tr>
   <td style="text-align:left;"> am </td>
   <td style="text-align:right;"> -1.357895 </td>
   <td style="text-align:right;"> 0.2582726 </td>
   <td style="text-align:right;"> -5.257603 </td>
   <td style="text-align:right;"> 1.13e-05 </td>
  </tr>
</tbody>
</table>
---

## Putting all the R code at the end

* For these fancy reports, we want to see the R code, but we don't want it intersperced throughout the document. 
* You can "hide" an R chunk by adding `echo = FALSE` to each of your chunks.

````
```{r, echo = FALSE}
```
````
* You can "hide" all of your chunks by adding this to the top of your .Rmd file

```eval
library(knitr)
opts_chunk$set(echo = FALSE)
```

* **THEN** at the end of you document (in the Appendix) you can add

````
```{r ref.label=knitr::all_labels(), echo = TRUE, eval = FALSE}
```
````

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## Open `Lab 06: Building Reports` in RStudio