RobotAndDOFPtr rad(
                   new RobotAndDOF(robot, vector<int>(), 11, OR::Vector(0, 0, 1)));

1. 11 stands for the enum OpenRAVE::DOFAffine value, the doc is found at OpenRAVE::DOFAffine. However, the author use a magic number here, by checking the souce code, I found that 11 stands for DOF_X|DOF_Y|DOF_RotationAxis, which means the robot can move in the x and y direction, and can rotate around an axis.
2. The fourth argument OR::Vector(0, 0, 1) is the rotation axis of the robot.

This is a typedef of openrave type RaveTransform

typedef RaveTransform<dReal> Transform;

In RaveTransform class, the public attributes rot is a quaternion, as pointed out here.

The function RaveGetTransformFromAffineDOFValues converts affine dof values into a transform, with the doc here.

set the transform of the first link (the rest of the links are computed based on the joint values). The doc is here.