use data.frames for plotting

[jeff-goldsmith]

In many existing functions, plots are made by converting a matrix to a data.frame and then plotting. Commit f86ad0b added a as_refundObj function to convert matrices to objects with class data.frame using a consistent naming scheme for the time index (index), the subject id (id), and the function value (value). In the future, it's hoped that this naming scheme will be used throughout refund.

Other plotting functions should be similarly modified.