how to add a (multipage) pdf to rmarkdown?

One can use pdfpages to include multiple pages from a PDF file at once. However, these are included on separate pages. While it is possible to add page numbers, you cannot easily put these images into a figure environment. Fortunately, \includegraphics has an option to use individual pages from a PDF. Unfortunately, knitr::include_graphics does not allow passing additional arguments to \includegraphics.

Here both possibilities:

---
title: "crazy test"
output:
  pdf_document
header-includes:
  - \usepackage{pdfpages}
---

```{r global_options, include=FALSE}
knitr::opts_chunk$set(echo = TRUE, fig.pos = 'h')
```


```{r, include=FALSE}
library(dplyr)
library(ggplot2)
library(tidyr)
library(purrr)

mydata <- data_frame(group = c('a', 'a', 'a', 'b', 'b', 'b'),
                     x = c(1,2,3,5,6,7),
                     y = c(3,5,6,4,3,2))

mydata2 <- mydata %>% group_by(group) %>% 
  nest() %>% 
  mutate(myplot = map(data, ~ggplot(data = .x, aes(x = x, y = x)) + geom_point()))

pdf("mychart.pdf")
print(mydata2$myplot)
dev.off()
```


## this is a test!!

Only first page

```{r label, out.width = "85%", fig.cap = "caption"}
knitr::include_graphics(path = "mychart.pdf")
```

All pages but w/o caption and taking a full page

\includepdf[pages=-,nup=2,pagecommand={}]{mychart.pdf}

Alternative, using explicit LaTeX commands.

\begin{figure}
\includegraphics[page=1,width=0.5\linewidth]{mychart.pdf}
\includegraphics[page=2,width=0.5\linewidth]{mychart.pdf}
\caption{\label{fig:test} Test.}
\end{figure}

One could also put these into a R chunk with cat() and result = 'asis'. However, the options for setting caption etc. are still not used.

Here's the Rmd solution with staplr. Please be advised that you need to install pdftk for split_pdf to work

---
title: "crazy test"
output:
  pdf_document
---

```{r global_options, include=FALSE}
knitr::opts_chunk$set(echo = TRUE, fig.pos = 'h')
```

## Split pdf

```{r}
staplr::split_pdf("mychart.pdf", output_directory = ".", prefix = "mychart_")
```

## Add pdfs

```{r label, out.width = "85%", fig.cap = c("caption 1", "caption 2"), echo = FALSE}
flist <- list.files()
mychart_files <- flist[grep("mychart_", flist)]
knitr::include_graphics(mychart_files)
```

Also, include graphics doesn't work in a loop. But it accepts multiple paths, so that works out well.

knitr has a specific chunk option called out.extra that allows to pass options to the \includegraphics command. See about this option in knitr doc.

This means it can be used to page the option page. Using the example above, you could do

---
title: "crazy test"
output:
  pdf_document:
    keep_tex: TRUE
---

```{r global_options, include=FALSE}
knitr::opts_chunk$set(echo = TRUE, fig.pos = 'h')
```


```{r, include=FALSE}
library(dplyr)
library(ggplot2)
library(tidyr)
library(purrr)

mydata <- tibble(group = c('a', 'a', 'a', 'b', 'b', 'b'),
                     x = c(1,2,3,5,6,7),
                     y = c(3,5,6,4,3,2))

mydata2 <- mydata %>% group_by(group) %>% 
  nest() %>% 
  mutate(myplot = map(data, ~ggplot(data = .x, aes(x = x, y = x)) + geom_point()))

pdf("mychart.pdf")
print(mydata2$myplot)
dev.off()
```

Only first page

```{r label, out.width = "85%", fig.cap = "caption"}
knitr::include_graphics(path = "mychart.pdf")
```

second page

```{r label2, out.width = "85%", fig.cap = "caption", out.extra="page=2"}
knitr::include_graphics(path = "mychart.pdf")
```