Flow Accumulation in R

You should also take a look at TauDEM (http://hydrology.usu.edu/taudem/taudem5/index.html)

It's a set of command-line .exe files (you run them in the Windows Command Prompt) for calculating flow direction, flow accumulation, and stream thresholds. The input and output of each command is a GeoTiff raster file. TauDEM can be installed stand-alone without ArcGIS.

In R, you can quite easily call third-party command-line executables from your R script with the system() function. There is an example how to use TauDEM in R on their website: http://hydrology.usu.edu/taudem/taudem5/TauDEMRScript.txt