Building Reports in R Markdown

# Building Reports in R Markdown
### Dr. D’Agostino McGowan

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<div class="my-footer">
<span>
Dr. Lucy D'Agostino McGowan
</span>
</div>

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## Harnessing the power of RMarkdown!

* Code chunk options
* Tables
* Inline code
* Output Formats

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## Code chunk options

* All chunk options can be found on [Yihui's website](http://yihui.name/knitr/options/)
--

* ````{r}`
--

* ````{r, echo = FALSE}`
--

* ````{r, eval = FALSE}`
--

* ````{r, message = FALSE, warning = FALSE}`
--

* ````{r, fig.cap = "PUT CAPTION HERE"}`

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## Code Chunks

* For these fancy reports, we want to see the R code, but we don't want it interspersed throughout the document. 
* You can "hide" all of your chunks by adding this to the top of your .Rmd file

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

class: inverse 
## <svg style="height:0.8em;top:.04em;position:relative;" viewBox="0 0 640 512"><path d="M624 416H381.54c-.74 19.81-14.71 32-32.74 32H288c-18.69 0-33.02-17.47-32.77-32H16c-8.8 0-16 7.2-16 16v16c0 35.2 28.8 64 64 64h512c35.2 0 64-28.8 64-64v-16c0-8.8-7.2-16-16-16zM576 48c0-26.4-21.6-48-48-48H112C85.6 0 64 21.6 64 48v336h512V48zm-64 272H128V64h384v256z"/></svg> `Application Exercise`

* Choose one of your analyses from the last Lab and copy it into a new R Markdown file
* Edit the chunks so that:
  * no messages or warnings are printed
  * All figures have appropriate captions
  * The code all is printed at the end of the document
---

## Tables

* There are several packages for making pretty tables in RMarkdown
--

* [knitr]((https://cran.r-project.org/web/packages/knitr/)
* [xtable](https://cran.r-project.org/web/packages/xtable/)
* [stargazer](https://cran.r-project.org/web/packages/stargazer/)
* [pander](http://rapporter.github.io/pander/)
* [tables](https://cran.r-project.org/web/packages/tables/)
* [ascii](http://eusebe.github.io/ascii/)
---

## Tables with knitr

```r
library(knitr)
kable(mtcars[1:4, ], caption = "Look at all those cars!")
```

Table: Look at all those cars!

|               |  mpg| cyl| disp|  hp| drat|    wt|  qsec| vs| am| gear| carb|
|:--------------|----:|---:|----:|---:|----:|-----:|-----:|--:|--:|----:|----:|
|Mazda RX4      | 21.0|   6|  160| 110| 3.90| 2.620| 16.46|  0|  1|    4|    4|
|Mazda RX4 Wag  | 21.0|   6|  160| 110| 3.90| 2.875| 17.02|  0|  1|    4|    4|
|Datsun 710     | 22.8|   4|  108|  93| 3.85| 2.320| 18.61|  1|  1|    4|    1|
|Hornet 4 Drive | 21.4|   6|  258| 110| 3.08| 3.215| 19.44|  1|  0|    3|    1|

---

## broom

* Helps create "tidy" tables from your `lm` output

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

```
## 
## Call:
## lm(formula = wt ~ am, data = mtcars)
## 
## Coefficients:
## (Intercept)           am  
##       3.769       -1.358
```
]
]

```r
library(broom)
m <- lm(wt ~ am, data = mtcars)
tidy(m)
```

```
## # 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
```
]

]

---

## kable + broom

* Use the `kable()` function to output a pretty table

```r
*library(knitr)
m <- lm(wt ~ am, data = mtcars)
kable(tidy(m))
```
]
.small[
<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>
]
---

## <svg style="height:0.8em;top:.04em;position:relative;" viewBox="0 0 640 512"><path d="M624 416H381.54c-.74 19.81-14.71 32-32.74 32H288c-18.69 0-33.02-17.47-32.77-32H16c-8.8 0-16 7.2-16 16v16c0 35.2 28.8 64 64 64h512c35.2 0 64-28.8 64-64v-16c0-8.8-7.2-16-16-16zM576 48c0-26.4-21.6-48-48-48H112C85.6 0 64 21.6 64 48v336h512V48zm-64 272H128V64h384v256z"/></svg> `Application Exercise`

* Using the same document as the previous application exercise, update all model output to be in "nicely" formatted tables using `tidy` and `kable` (or a different table package of your choosing)

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## Inline code

* You can include _inline_ by using `r` 
--

* This is especially useful if you want to reference a numeric value.

---

* Using the same document as the previous application exercise, update all references to numeric values using inline code. _Be sure to round numbers_.

---

## Output formats

## Updating your `yaml`

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

---

## Output formats

## Updating your `yaml`

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

---

* Using the same document as the previous application exercise, update your file to output a word document.