If you are using R Markdown to create pdf presentations you are using the Latex document class Beamer. Unlike in – for example – LibreOffice Impress, the content on your slides is not positioned at the top but in the center of the slide in Beamer by default.
If you would like to change the default positioning to top alignment you can modify the Beamer output template. The first line in this template is something like this:
\documentclass[$if(fontsize)$$fontsize$,$endif$$if(lang)$$babel-lang$,$endif$$if(handout)$handout,$endif$$if(beamer)$ignorenonframetext,$endif$$for(classoption)$$classoption$$sep$,$endfor$]{$documentclass$}To change default positioning to top, simply change this line to
\documentclass[t,$if(fontsize)$$fontsize$,$endif$$if(lang)$$babel-lang$,$endif$$if(handout)$handout,$endif$$if(beamer)$ignorenonframetext,$endif$$for(classoption)$$classoption$$sep$,$endfor$]{$documentclass$}The added t inside the [ ] brackets does the trick (see http://tex.stackexchange.com/questions/9889/positioning-content-at-the-top-of-a-beamer-slide-by-default).