knitr setup chunk

```{knitr_setup, include=FALSE}

#=================
# Load packages (load all the packages here at the beginning)
#=================
  library(xtable) ## for making awesome tables
  library(psych) ## for the pca package 'principal'.
  library(ggplot2) ## for plotting
  library(mclust) ## for MClust.

# Don't set knitr options outside knitr
if ("package:knitr" %in% search()) {

  # Set some 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(warning=TRUE,
                message=TRUE,
                echo=TRUE,
                cache = FALSE,
                tidy = FALSE, ## remove the auto-formatting
                error=TRUE)   

    ## extra options that can be set within :                
                   ## dpi=96,
                        # Default figure widths
                   #fig.width=4, fig.height=4, 
                   # dev="tikz", 
                   #dev.args=list(type="cairo"), 
                   # The png device
                   # Change to dev="postscript" if you want the EPS-files
                   # for submitting. Also remove the dev.args() as the postscript
                   # doesn't accept the type="cairo" argument.
                 
  }
  # close if-statement
  
  # Evaluate the figure caption after the plot
  #opts_knit$set(eval.after='fig.cap')
  
  # Avoid including base64_images - this only
  # works with the .RProfile setup
 # options(base64_images = "none")

```