kfigr

kfigr is a streamlined cross-referencing system for R markdown documents that integrates with the knitr package. It defines a hook for anchoring code chunks and tracks chunks for cross-referencing document elements like figures, tables and code blocks.

Update 2016-04-23

I recently found out about bookdown which provides advanced labeling and cross-referencing functionality with pandoc. I encourage you to try bookdown as kfigr does not always play nice with pandoc and doesn't support markdown-->PDF.

Update 2015-07-14

Version 1.2 submitted to CRAN! This version makes package attaching and detaching a bit cleaner. I have also converted all documentation from inlinedocs to Roxygen2. Package functionality remains unchanged.