I use the following sequence in spinning r scripts: (i) use knitr::spin on the script, (ii) open the md file, and (3) Use Preview > Preview PDF. In recent times, the last step has resulted in the figure subdirectory being deleted, after the output is created. I can avoid this by checking the Output option "Keep tex source file used to produce PDF" in the Advanced tab of the Preview settings. However, I have to do this every time I preview the md file, something that was unnecessary in the past (and which is not necessary on a colleague's machine).
Here is a reprex that causes the fault:
#'# A reprex for problem where figure directory gets deleted on render of md doc
#'## Running this script produces a plot that is saved in the figure subdirectory of the working directory
ggplot(mtcars, aes(x = mpg)) + geom_dotplot()
Saving this as a file and running knitr::spin on it as described above produces the fault.
I am running Windows 10, R 3.6.1 and RSTudio 1.2.1555.
Any help to return to a state where the default behaviour is the retention of the figure directory will be greatly appreciated. Chris