Change background in R Markdown beamer presentation

I'm writing on a beamer presentation in rmarkdown and I have two types of frames which should differ by their background. So I wrote two functions like that in latex:

\newcommand{\settitlestyle}{
\setbeamertemplate{background canvas}{%
  \includegraphics[width = \paperwidth, height = \paperheight] 
{backgroundtitle.jpg}}
} 

\setmainstyle is exactly the same command but another jpg.

In the YAML I have already input a tex file that defines the functions and calls \settitlestyle. Works. But after the first slide I want to switch to the mainstyle. When I call \setmainstyle in the markdownfile nothing happens.

The problem with your \setmainstyle command is that it will be used inside a frame and thus be void.

To avoid this problem you could use the same strategy as in https://tex.stackexchange.com/questions/173201/beamer-template-with-different-style-options-for-frames to create a frame option which will change the background.

Unfortunately rmarkdown simply ignores user created frame options and only passes on a tiny list of predefined options. To trick rmarkdown one could repurpose a frame option which is normally not used by beamer, the standout frame option (it is only used by the moloch theme)

---
output: 
  beamer_presentation:
    keep_tex: true
header-includes: |
  \usepackage{etoolbox}

  \defbeamertemplate{background canvas}{mydefault}{%
    \includegraphics[width=\paperwidth,height=\paperheight]{example-image-duck}
  }
  \defbeamertemplate{background canvas}{standout}{%
    \includegraphics[width=\paperwidth,height=\paperheight,page=2]{example-image-duck}
  }

  \BeforeBeginEnvironment{frame}{%
    \setbeamertemplate{background canvas}[mydefault]%
  }

  \makeatletter
  \define@key{beamerframe}{standout}[true]{%
    \setbeamertemplate{background canvas}[standout]%
  }
  \makeatother

---

# frametitle 

test

# frametitle with different background {.standout}

test

# frametitle

test

or if you want to change the background for all following frames:

\usepackage{etoolbox}

\defbeamertemplate{background canvas}{mydefault}{%
  \includegraphics[height=\paperheight,page=2]{example-image-duck}
}
\defbeamertemplate{background canvas}{standout}{%
  \includegraphics[height=\paperheight]{example-image-duck}
}

\setbeamertemplate{background canvas}[mydefault]%

\makeatletter
\define@key{beamerframe}{standout}[true]{%
  \setbeamertemplate{background canvas}[standout]%
}
\makeatother

Update:

Pandoc now allows arbitrary frame options (https://github.com/jgm/pandoc/commit/7fbce82f2f7b69e88b23cf138ea6cd3a86786b91)

---
output: 
  beamer_presentation:
header-includes: |

  \defbeamertemplate{background canvas}{mydefault}{}
  \defbeamertemplate{background canvas}{special}{%
    \includegraphics[width=\paperwidth,height=\paperheight]{example-image-duck}
  }

  \BeforeBeginEnvironment{frame}{%
    \setbeamertemplate{background canvas}[mydefault]%
  }

  \makeatletter
  \define@key{beamerframe}{special}[true]{%
    \setbeamertemplate{background canvas}[special]%
  }
  \makeatother

---

# frametitle 

test

# Heading {frameoptions="special"}

test

# frametitle 

test