jrag-timing: joint radio and gamma-ray pulsar timing analysis

This python script performs a joint radio and gamma-ray pulsar timing analysis by using PINT and emcee. The result is a corner plot showing the posteriors and a parameter file giving the highest-likelihood result with uncertainty levels.
Note: The script can also work with only one type of data (radio or gamma rays).

Author:
Lars Nieder
Max Planck Institute for Gravitational Physics (Albert Einstein Institute), D-30167 Hannover, Germany
Leibniz University Hannover, D-30167 Hannover, Germany

Options:
   -h, --help            show this help message and exit

Basic input parameters.:
    Caution: Some of these are required.
    -p PARFILE, --parfile=PARFILE     Path to parameter file [REQUIRED].
    --newparfile=NEWPARFILE           Name of output parameter file.
    --resultsfile=RESULTSFILE         Name of output results file.
    -t TEMPFILE, --tempfile=TEMPFILE  Path to template file.
    --newtempfile=NEWTEMPFILE         Name of output template file.
    -l FT1FILE, --ft1file=FT1FILE     Path to FT1 file (LAT data).
    -f FT2FILE, --ft2file=FT2FILE     Path to FT2 file (satellite).
    -r TIMFILE, --timfile=TIMFILE     Path to tim file (radio).
    --weightfield=WEIGHTFIELD         Weightfield name in FT1 file.
    -d DEBUG, --debug=DEBUG           Level of debug messages.
    --plotonly=PLOTONLY               No MCMC run, only plotting from previous runs.

Timing options:
    Caution: Choose wisely!
    -n NPOINTS, --npoints=NPOINTS     Number of walkers. [default: 128]
    -x MAXITER, --maxiter=MAXITER     Number of iterations. [default: 100]
    -b BURNIN, --burnin=BURNIN        Number of burnins. [default: 100]
    --usetau=USETAU                   Use autocorrelation time (tau) for timing analysis. [default: 0]
    -s OFFSET, --offset=OFFSET        Fractional offset. [default: 0.01]
    -c PCUT, --pcut=PCUT              Minimum photon weight to be used. [default: 0.0]
    --eclipse=ECLIPSE                 Orbital phase radius in which radio TOAs are removed. [default: 0.0]
    --toacut=TOACUT                   Maximum error in radio TOAs (microsecs). [default: 1000.0]
    --compare=COMPARE                 Compare radio and gamma-ray posteriors. [default: 0]

Output files contain the stored chains, show convergence-analysis plots and the posteriors in different ways (red=radio, blue=gamma-ray, black=joint), and the parfiles reporting parameters returning the highest likelihood with the uncertainties computed from the posteriors.