Even though the S1R is weather sealed, I used one of these:
http://fotosharp.com/original_camera_rain_covers.html. It covered most of the camera, but not the lens when fully extended. Rain got on the extended parts of the lens and I was concerned as the zoomed lens retracted fearing that water would get trapped inside. Fortunately, everything was fine.

This was only my first time shooting with this camera / lens combo, and it did remarkably well. I really enjoyed the shooting experience, and it was without a doubt more fun to shoot with than either Sony or Nikon bodies. The only drawback is that it’s a big and heavy system, but with results like these, it’s a trade off worth making.