We extend the recently introduced Bayesian framework ‘ Generative Pulsar Timing Analysis ’ to incorporate both pulse jitter ( high frequency variation in the arrival time of the pulse ) and epoch to epoch stochasticity in the shape of the pulse profile .
This framework allows for a full timing analysis to be performed on the folded profile data , rather than the site arrival times as is typical in most timing studies .
We apply this extended framework both to simulations , and to an 11 yr , 10 cm data set for PSR J1909 - 3744 .
Using simulations , we show that temporal profile variation can induce timing noise in the residuals that when performing a standard timing analysis is highly covariant with the signal expected from a gravitational wave ( GW ) background .
When working in the profile domain , these variations are de-correlated from the expected GW signal , resulting in significant improvement in the obtained upper limits .
Using the PSR J1909 - 3744 data set from the Parkes Pulsar Timing Array project , we find significant evidence for systematic high-frequency profile variation resulting from non-Gaussian noise in the oldest observing system , but no evidence for either detectable pulse jitter , or low-frequency profile shape variation .
Using our profile domain framework we therefore obtain upper limits on a red noise process with a spectral index of \gamma = 13 / 3 of 1 \times 10 ^ { -15 } , consistent with previously published limits .