Make many changes including package restructuring, returning time series, returning data frames, and code cleaning

Importantly, paradox_pe_sim is now paradox_pe.

The old paradox_sim and get_pe functions are now deleted. They have been replaced by the new paradox_sim function.

I have added documentation and examples to (the new) paradox_sim.

paradox_sim now has the option of returning the time series.

I have also added a function to make custom filled.contour plots (for multipanel plotting) called filled_contour.