update vignettes to v 0.6.5

Author: bmansfeld

vignettes/QTLseqr.Rmd

@@ -15,13 +15,15 @@ header-includes: \usepackage{graphicx}
 ---
 
 ```{r setup, echo=FALSE, results="hide"}
-knitr::opts_chunk$set(tidy=FALSE, cache=FALSE,
+knitr::opts_chunk$set(tidy=FALSE, cache=TRUE,
                       dev="png",
                       message=FALSE, error=FALSE, warning=TRUE)
 ```	
 # Current version: Development - `r packageVersion("QTLseqr")` 
 
-# Standard workflow
+# Introduction
+
+## Citations
 
 **If you use QTLseqr in published research, please cite:**
 
@@ -48,8 +50,6 @@ G prime method:
 Here are the basic steps required to run and plot QTLseq and $G'$ analysis
 
 ```{r quickStart, eval=FALSE}
-
-
 #load the package
 library("QTLseqr")
 
@@ -118,6 +118,7 @@ getQTLTable(
 )
 ```
 
+# Standard workflow
 
 ## Input data