There's a single decoder/encoder which reads/converts to both DNxHD and DNxHR.
You have to set the correct profile switch. Available options are
dnxhd E..V....
dnxhr_444 E..V....
dnxhr_hqx E..V....
dnxhr_hq E..V....
dnxhr_sq E..V....
dnxhr_lb E..V....
Basic minimal syntax would be
ffmpeg -i in.mp4 -c:v dnxhd -profile:v dnxhr_hq out.mov
The Avid codecs package has no interaction with ffmpeg.
[19-1-2017] At this time, the encoder does not support 444 or HQX profiles.
[4-2-2017] Now, it does.