Some improvements: 1) fixed non-appearing of plots in PDF report (don't use fig.align - use fig.caption instead: https://github.com/rstudio/rmarkdown/issues/148); 2) added knitr setting to use Cairo PDF device (for potential use in the future): https://github.com/yihui/knitr/issues/436; 3) added absolute path for generated figures via fig.path.