This code is my standard setup for rmarkdown in knitr.

knitr set up

```{r global_options, include=FALSE, cache=FALSE}
library(knitr)
  # Set basic options. You usually do not want your code, messages, warnings    etc.
  # to show in your actual manuscript however for the first run or two these will 
  # be set on.
opts_chunk$set(echo=FALSE, 
               warning=FALSE, 
               message=FALSE,
               cache = TRUE,
               include = FALSE,
               results = 'hide',
               error = TRUE)

# setup changes according to html or docx

output <- opts_knit$get("rmarkdown.pandoc.to")

if (output=="html") {
  
  opts_chunk$set(fig.width=11, 
                 fig.height=11)
  
  } # # end html `if` statement

## setting up the figure parameters for docx
if (output=="docx") {

    opts_chunk$set(dev = 'pdf',
                   fig.width = 6, 
                   fig.height = 6)
                     } # end docx `if` statement


```