2.1.1 Tables

Bookdown Reference: https://bookdown.org/yihui/bookdown/tables.html#tables

You’ll find that packages knitr (and knitrExtra) or xtable are useful to help make presentable tables (especially to pdf). Moreover broom can help compress lots of models in R into data frames that can then be passed into these functions (ex. broom::tidy). And the pander package also can convert summary data of models pretty well.

To reference a table we need a few things. First we need to have an R block with a name. In the following example we name our code block “table-name” (and the code in the box would produces a basic table). Section A.2 provides more details on parameters that can be used in R code blocks

```{r table-name}
knitr::kable(
  data.frame(`model id` = 1:5,
             `score` = c(1,1.1,3,.5,2)))
```

Now that we have a table with a name we can use \@ref(tab:table-name) to reference the table (note the differences between the \(\LaTeX\) approach which would be \ref{tab:table-name}). Note that the underlying pandoc and bookdown code knows that this is a table, so it will index the table we made above differently than figures we might also have. Additionally note that bookdown::pdf_document2 won’t allow for underscores (_) in the names of the table - so we use dashes (-).

```{r table-name2}
data.frame(`model id` = 1:5,
           `score` = c(1,1.1,3,.5,2)) %>%
  knitr::kable(format = "latex", caption = "Model Scores") %>%
  kableExtra::kable_styling(latex_options = "HOLD_position")
```

2.1.2 Figures

Bookdown reference: https://bookdown.org/yihui/bookdown/figures.html#figures

In R referencing figures is similar to referencing tables, but the creation of the names and captions are different. Below we demonstrate creating some code with a figure (with the name figure-name for the code block)

```{r figure-name}
library(ggplot2)
data.frame(`model id` = 1:5,
           `score` = c(1,1.1,3,.5,2))) %>%
  ggplot() + geom_bar(aes(x = `model id`, y = score))
```

We can use the same referencing idea from the tables, i.e. we use \@ref(fig:figure-name) to reference the figure (again, note the differences between the \(\LaTeX\) approach which would be \ref{fig:figure-name}).

```{r figure-name2, fig.cap = "Model Scores", fig.align="center", fig.width=5, fig.asp=1, fig.pos="H"}
library(ggplot2)
data.frame(`model id` = 1:5,
           `score` = c(1,1.1,3,.5,2))) %>%
  ggplot() + geom_bar(aes(x = `model id`, y = score))
```

```{r figure-name3, fig.cap = "Model Scores (like Table \\ref{tab:table-name3})", fig.align="center", fig.width=5, fig.asp=1, fig.pos="H"}
library(ggplot2)
data.frame(`model id` = 1:5,
           `score` = c(1,1.1,3,.5,2))) %>%
  ggplot() + geom_bar(aes(x = `model id`, y = score))
```

```{r table-name3}
data.frame(`model id` = 1:5,
           `score` = c(1,1.1,3,.5,2)) %>%
  knitr::kable(format = "latex", 
               caption = "Model Scores (like Figure \\ref{fig:figure-name3})"
               ) %>%
  kableExtra::kable_styling(latex_options = "HOLD_position")
```

2.1.3. Non-code based Figures

Suppose you’d like to include a figure already created or saved online. In order to work with it in the Figure referencing, there are a few approaches that can be used.

```{r figure-name5, fig.cap = "Go Tartans!", fig.align="center", fig.width=5, fig.asp=1, fig.pos="H"}
knitr::include_graphics("locally/saved/image/file/SCOTTY.png")
```

```{r fig-webimage, fig.cap = "Random image from the web.", echo=F, message=F, warning=F, fig.align="center", out.width = "100%"}
url <- "https://raw.githubusercontent.com/benjaminleroy/36-350-summer-data/master/Week5/percolation1.png"
library(png)
library(RCurl)
url_cont <- getURLContent(url)
img <- readPNG(url_cont)
rimg <- as.raster(img) # raster multilayer object
r <- nrow(rimg) / ncol(rimg) # image ratio
plot(rimg)
```

3.1.1 Special Bibliography in the yaml (aka “inline references”)

The “most basic” but least easy to maintain approach to creating a bibliography is to do so in the yaml header (and example of which can be seen below). Rmarkdown gives useful help with the approach here need references to all field options.

---
title: "All of Statistics"
author: "Larry Wasserman"
output: bookdown:pdf_document2
references:
- id: wassserman2013
  title: All of statistics: a concise course in statistical inference
  author:
  - family: Wasserman
    given: Larry
  publisher: Springer Science & Business Media
  type: book
  issued:
    year: 2013
- id: lopezpintado2011
  title: A half-region depth for functional data
  author:
  - family: L{\'o}pez-Pintado
    given: Sara 
  - family: Romo
    given: Juan
  container-title: Computational Statistics \& Data Analysis,
  volume: 55
  issue: 4
  page: 1679-1695
  year: 2011
  publisher: Elsevier
  tyle: article-journal
---

3.1.2 Using external files to store your bibliography

As mentioend above it’s pretty common to use an external file to store your bibliography. There are many options of files that you can use (see Rmarkdown’s cite for the list), but we will be showing the .bib BibLaTeX approach (which we think is the most common in Statistics).

To link an external style to be used we change the yaml from above to:

---
title: "A half-region depth for functional data"
author: "Sara Lopez-Pintado and Juan Romo"
output: bookdown:pdf_document2
bibliography: "my_bibliography.bib"
---

With the understanding that in the same folder as your .Rmd file you also have a my_bibliography.bib file, that looks something like:

@book{wasserman2013,
  title={All of statistics: a concise course in statistical inference},
  author={Wasserman, Larry},
  year={2013},
  publisher={Springer Science \& Business Media}
}

@article{lopezpintado2011,
  title={A half-region depth for functional data},
  author={L{\'o}pez-Pintado, Sara and Romo, Juan},
  journal={Computational Statistics \& Data Analysis},
  volume={55},
  number={4},
  pages={1679--1695},
  year={2011},
  publisher={Elsevier}
}

You can find more about the potential fields and types of things you can reference in lots of places including the wikipedia page.

3.2.1 Which tool shall we use?

Now that we have a group of documents to reference, how do we reference them? The answer is that we have a lot of options, and that the options mirror our options in \(LaTeX\) where we can choose to use the build into biblatex referencing or use the \usepackage{natbib}. There are lots of discussion about the differences (one of which on slackexchange can be found here. To get a clear visual understanding I recommend the detailed commentary on each from overleaf: biblatex, natbib).

3.2.1.1 Introduction to Biblatex (the default)

To use biblatex as your biliography tool, in the yaml top of the file we want to change it to:

---
title: "Distribution-free prediction sets"
author: "Jing Lei, James Robins, and Larry Wasserman"
output: 
  bookdown:pdf_document2:
    citation_package: biblatex
bibliography: "our_bibliography.bib"
---

Provide image and code of basic document (maybe copy overleaf a bit?)

3.2.1.2 Introduction to Natbib (my preferred)

---
title: "The functional mean-shift algorithm for mode hunting and clustering in infinite dimensions"
author: "Mattia Ciollaro, Christopher Genovese, Jing Lei, and Larry Wasserman"
output: 
  bookdown:pdf_document2:
    citation_package: natbib
bibliography: "hopefully_a_bibliography.bib"
---

Provide image and code of basic document (maybe copy overleaf a bit?)

Other references: http://merkel.texture.rocks/Latex/natbib.php

3.2.1.3 More on Styling

Even after you’ve decided on biblatex vs natbib there are still a lot of different styles that can be used. The most basic change is setting a style of the references and table using a yaml parameter biblio-style demostrated in the following example:

---
title: "The functional mean-shift algorithm for mode hunting and clustering in infinite dimensions"
author: "Mattia Ciollaro, Christopher Genovese, Jing Lei, and Larry Wasserman"
output: 
  bookdown:pdf_document2:
    citation_package: natbib
bibliography: "hopefully_a_bibliography.bib"
biblio-style: plainnat.bst
---

The options are presented well in a document from Reed college, but note that natbib and biblatex don’t call the styles the same thing. Additionally, if you find that some the biblio-style isn’t working as expected you can either do:

---
title: "The functional mean-shift algorithm for mode hunting and clustering in infinite dimensions"
author: "Mattia Ciollaro, Christopher Genovese, Jing Lei, and Larry Wasserman"
output: 
  bookdown:pdf_document2:
    citation_package: natbib
bibliography: "hopefully_a_bibliography.bib" 
header-includes:
  - \bibliographystyle{plainnat.bst}
---

where style is the style you want to use OR you can use a can include a style guide in the form of a .csl file. This github repository provides a lot of options to look over. An example is shown below (and you can also store the .csl locally). This Rmarkdown) page also has more comments about where to find .csl files.

---
title: "The functional mean-shift algorithm for mode hunting and clustering in infinite dimensions"
author: "Mattia Ciollaro, Christopher Genovese, Jing Lei, and Larry Wasserman"
output: 
  bookdown:pdf_document2:
    citation_package: natbib
bibliography: "hopefully_a_bibliography.bib" 
csl: "https://github.com/citation-style-language/styles/blob/master/american-statistical-association.csl"
---

extra Pandoc resource: https://pandoc.org/demo/example19/Extension-citations.html

3.2.2 Let’s ACTUALLY Reference something

To use the reference tools in bookdown’s .Rmd files we can do

• [@wasserman2013] to get a parenthesis based reference (e.g. natbib: [Wasserman, 2013] and biblatex: [1])

• @wasserman2013 to get an inline text presentation (e.g. natbib: Wasserman [2013], doesn’t work for biblatex)

• -@wasserman2013 removes author mention (e.g. natbib: [2013], doesn’t work for biblatex)