With one R markdown file, I would like to create different possible output pdf documents, where the output file name should be defined within the document. Is there any way
Following up on what @ilya wrote, this webpage has a great example demonstrating what they are describing, which is how to create multiple, reproducible reports from the same .Rmd document:
http://www.reed.edu/data-at-reed/software/R/markdown_multiple_reports.html
The webpage uses two scripts, one R script and one Rmarkdown script to create multiple reports. I have used it as a template for my own work and found it very useful.