Output directory for knitr can only be set as function argument

[hlapp]

If we want the top-level .Rmd file to be rendered to the doc/paper directory, then this output directory needs to be configurable as an option. However, apparently it isn't; only the directory for figure output can be set. This means that rendering the Markdown, HTML, LaTeX, and PDF versions need to be executed as rmarkdown::render() so that the output path can be passed as an argument. That the "Knit HTML" button is not to be used is likely rather undesirable for practical use and teaching purposes.

[cboettig]

Very good point. I don't use the button that frequently and had forgotten this could only be done in function calls. Given the prevalence of the RStudio button the inability to set this as a configuration feels more like a knitr bug to me, see yihui/knitr#913