Some R packages which use our methods...
ctmcd contains routines for fitting discretely observed Markov jump processes based on Bladt & Sørensen (2005,2009).
sde contains a routine for simple diffusion bridge simulation. Related to M. Bladt & M. Sørensen (2013).
PhaseType contains a routine for fitting phase--type distributions via MCMC based on M. Bladt, A. González & S. L. Lauritzen (2003).
Matrixdist is a packages containing an object oriented implementation of various phase-type techniques, including fitting to PH and IPH.