Warning: It is quite likely that this will be called within an Rmd file implying a recursive call to knit(). This will generate "duplicate label" errors for unlabelled chunks. To avoid this, all code chunks in your Rmd file should be named. Supposedly this error can also be avoided by setting the following option: options(knitr.duplicate.label = 'allow'). I tried this but it didn't seem to help.

knit_report(input_filename, output_filename, ...)

Arguments

input_filename Rmd file. Markdown or HTML output file. An HTML file is specified using the .htm, .html, .HTM or .HTML file extension. When html is specified, a similarly named markdown file is also generated. All output files including cache and figures will appear in the same folder as output_filename. Arguments to be passed to knitr::knit