How to add Latex packages to markdown?

Welcome to TeX.SE. Don't use square brackets [] in your math expression. Use braces {} only. You wrote: $xrightarrow[text{sample text}]$. It should be: $xrightarrow{text{sample text}}$.

Edit: Updated to show the use of Bracket and Set from the braket package.

---
title: "Title"
author: "Me"
header-includes:
  - usepackage{array}
  - usepackage{booktabs}
  - usepackage{mathtools}
  - usepackage{braket}
output:
  pdf_document:
    keep_tex: true
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

hrule <!-- draw a horizontal line -->

We can _write_ in **markdown** and add content that uses ``LaTeX`` syntax and LaTeX packages to format our document.

## Using ``mathtools`` package

$xrightarrow{text{sample text}}$

<br> <!-- add space, like bigskip % - this is a comment -->

## Using ``array``, ``booktabs`` and ``braket`` packages

begingroup
renewcommand*{arraystretch}{1.7}
setlength{tabcolsep}{10pt}
begin{tabular}{@{}>{footnotesize}r>{$displaystyle}l<{$}@{}}
toprule 
  verb+Braket{ phi | frac{partial^2}{partial t^2} | psi }+ & Braket{ phi | frac{partial^2}{partial t^2} | psi } 
  verb+Set{ xinmathbf{R}^2 | 0<{|x|}<5 }+                     & Set{ xinmathbf{R}^2 | 0<{|x|}<5 }                    
bottomrule
end{tabular}
endgroup

## We can do math

```{r math}
result <- 1 + 2
result
```