Setting documentclass in Rmarkdown v2

Question

I would like to write my master thesis in RMarkdown v2 and I would be very glad if I could use a prepared LaTeX class.

Also I'd like to put some lines in the header and somehow add an abstract.

Can any1 knows how to do that?

Lines I'd be happy to have before \begin{document} are typically:

\usepackage[utf8]{inputenc}
\usepackage{polski}

\usepackage{amsfonts}
\usepackage{amsmath}
\usepackage{amssymb}
\usepackage{amsthm}

\usepackage{tikz}
\usepackage{float} %pakiet do obsługi obrazków
\usepackage{graphicx} %pakiet do dodawania obrazków
\usepackage{tabularx} %pakiet do utrzymywania szerokości tabel równo z szerokością tekstu
\usepackage[T1]{fontenc} %przełączamy sie na fonty EC
\usepackage{dsfont}
% \usepackage[latin2]{inputenc} %kodowania polskich znakow ISO-8859-2  - mamy utf wyzej
\usepackage{xcolor} %pakiet do nadawania kolorów w \definecolor
\usepackage{listings} %pakiet do robienia tła jak w programie R
\lstset{language=R,%    
  % numbers=left,%
   tabsize=3,%
   numberstyle=\footnotesize,%
   basicstyle=\ttfamily \footnotesize \color{black},%
   escapeinside={(*@}{@*)}}

\usepackage{longtable}


\definecolor{ListingBackground}{rgb}{0.95,0.95,0.95}
\definecolor{ListingRule}{rgb}{0.7,0.7,0.7}

\lstdefinestyle{incode}  %definiowanie stylu tła dla pisania kodu w R
{
basicstyle={\ttfamily\footnotesize},
backgroundcolor={\color{ListingBackground}},
frame={lr},
rulecolor={\color{ListingRule}},
framerule={2pt}
}


\usepackage{hyperref} %pakiet do dodawania hiperłącz
\hypersetup{colorlinks=true,
            linkcolor=blue,
            citecolor=blue,
            urlcolor=blue}


%------------------------------------------------------------------------------%
\title{ o }
\author{Marcin Kosiński}
\supervisor{prof. dr hab. Michał Nowak}
\type{magisters}
\discipline{matematyka}
\monthyear{lipiec 2015}
\date{\today}
\album{123456}

And if possible after \begin{document} .

\begin{abstract}

some text
\end{abstract}

\tableofcontents
\listoffigures 
\listoftables

Thanks for help in advance :) ! I'm aware I'll need to specify setting somehow in the begging of the Rmarkdown v2 document

---
title: "Magisterka"
author: "Marcin Kosiński"
date: "Tuesday, July 29, 2014"
output: pdf_document
documentclass: mini
includes:
      in_header: headerMgr.tex
---

EDIT:

The soultion is good YAML specification:

---
title: "Magisterka"
author: "Marcin Kosiński"
date: "Tuesday, July 29, 2014"
output:
  pdf_document:
    includes:
      in_header: header.tex
      before_body: doc_prefix.tex
---

Answer 1

Based on this http://rmarkdown.rstudio.com/pdf_document_format.html, you need to include those lines:

---
title: "Magisterka"
author: "Marcin Kosiński"
date: "Tuesday, July 29, 2014"
output:
  pdf_document:
    includes:
      in_header: header.tex
      before_body: doc_prefix.tex
---

You need to remember to put all of the files (.Rmd, and all of .tex) in the same folder.