Embed a pdf in a R Markdown file and adapt pagination

Question

I am finishing my PhD, and I need to embed some papers (in pdf format) in somewhere in the middle of my R Markdown text.

When converting the R Markdown into PDF, I would like those PDF papers to be embed in the conversion.

However, I would like those PDF papers to be also numbered according to the rest of the Markdown text.

How can I do it?

---

UPDATE: New error

By using \includepdf, I get this error:

output file: Tesis_doctoral_-_TEXTO.knit.md

! Undefined control sequence.
l.695 \includepdf
                 [pages=1-10, angle=90, pagecommand={}]{PDF/Paper1.pdf} 
Here is how much of TeX's memory you used:
 12157 strings out of 495028
 174654 string characters out of 6181498
 273892 words of memory out of 5000000
 15100 multiletter control sequences out of 15000+600000
 40930 words of font info for 89 fonts, out of 8000000 for 9000
 14 hyphenation exceptions out of 8191
 31i,4n,35p,247b,342s stack positions out of 5000i,500n,10000p,200000b,80000s

Error: Failed to compile Tesis_doctoral_-_TEXTO.tex. See Tesis_doctoral_-_TEXTO.log for more info.
Execution halted

---

EXAMPLE of the R Markdown code

---
title: Histología dental de los homininos de la Sierra de Atapuerca (Burgos, España)
  y patrón de estrategia de vida
author: "Mario Modesto-Mata"
date: "20 September 2018"
output:
  pdf_document:
    highlight: pygments
    number_sections: yes
    toc: yes
    toc_depth: 4
  word_document:
    toc: yes
    toc_depth: '4'
  html_document: default
csl: science.csl
bibliography: references.bib
header-includes:
- \usepackage{pdfpages}
---

```{r opciones_base_scripts, message=FALSE, warning=FALSE, include=FALSE, paged.print=FALSE}
library(captioner)
tabla_nums <- captioner(prefix = "Tabla")
figura_nums <- captioner(prefix = "Figura")
anx_tabla_nums <- captioner(prefix = "Anexo Tabla")
```

# Resumen

Los estudios de desarrollo dental en homínidos han sido sesgados involuntariamente en especies pre-Homo y algunos especímenes Homo tempranos, que representan la condición primitiva con tiempos de formación dental más rápidos, respetan a los Neandertales posteriores y a los humanos modernos, que comparativamente tienen tiempos de formación más lentos.

## PDF Article

\includepdf[pages=1-22, pagecommand={}]{PDF/Paper1.pdf}

## Bayes

El desarrollo dental relativo se evaluó empleando un enfoque estadístico bayesiano (31).

This is the link to download the PDF

---

NEW IMAGE

Answer 1

I had to remove a few things from your example, but after that it worked without problems:

---
title: Histología dental de los homininos de la Sierra de Atapuerca (Burgos, España)
  y patrón de estrategia de vida
author: "Mario Modesto-Mata"
date: "20 September 2018"
output:
  pdf_document:
    highlight: pygments
    number_sections: yes
    toc: yes
    toc_depth: 4
    keep_tex: yes
  word_document:
    toc: yes
    toc_depth: '4'
  html_document: default
header-includes:
- \usepackage{pdfpages}
---


# Resumen

Los estudios de desarrollo dental en homínidos han sido sesgados involuntariamente en especies pre-Homo y algunos especímenes Homo tempranos, que representan la condición primitiva con tiempos de formación dental más rápidos, respetan a los Neandertales posteriores y a los humanos modernos, que comparativamente tienen tiempos de formación más lentos.

## PDF Article

\includepdf[pages=1-22, pagecommand={}, scale = 0.9]{Paper1.pdf}

## Bayes

El desarrollo dental relativo se evaluó empleando un enfoque estadístico bayesiano (31).

Result:

BTW, for something like a thesis I would use bookdown, since this gives you cross-referencing etc.

If that does not work for you, I suggest first looking at plain LaTeX, i.e. does the following LaTeX document work for you:

\documentclass{article}
\usepackage{pdfpages}
\begin{document}
foo

\includepdf[pages=1-22, pagecommand={}, scale = 0.9]{Paper1.pdf}

bar
\end{document}