For example,
ierr = PetscOptionsGetReal(PETSC_NULL,"-dt",&dt,PETSC_NULL);CHKERRQ(ierr);
ierr = TSSetInitialTimeStep(ts,0.0,dt);CHKERRQ(ierr);
since TSSetFromOptions() already has the option -ts_dt there is no reason for the examples to provide the option.
Etc Etc.
Thanks
Barry