help.txt

General Options
===============
-f parFile        Selects parameter file
-npsr             Set max number of pulsars that can be loaded
-nobs             Set max number of observations per pulsar
-tempo1           Run in 'tempo1 emulation mode' (i.e. default to tempo1)
-allParTim        grab all par and tim files from the current directory.
-clkdir {dir}     Add {dir} to the start of the clock search path.

Help, verbosity, debugging
==========================
-h                This help
-H                Print more help, including list of plugins 
-v                Print verson number.
-debug            Print debuging information and files (very verbose!).
-tcheck           Print execution time information for the fit
-displayVersion   Display detailed CVS version number of every file used.

Set parameters
==============
-set {parm} {val} Set a par file parameter to a value
-clock {clk}      Set CLK parameter for all input par files
-epoch centre     Centres the PEPOCH in the fit
-name             Set JNAME for each par file
-modify {file}    Modify flags. Input is file with lines like 
     "flag oldflagval start_mjd end_mjd newflagval"
-nojump           Disable all jumps in par files


Filtering ToAs
==============
-pass "{flags}"   Delete all ToAs without given flags
-filter "{flags}" Delete points that match given flag
-select {file}    Use a 'select file' to pass and reject based on ToA properties.
-del              Load delete file -- list of SATs to delete
-splug {plugin}   Loads a special plugin that selects/deletes ToAs

Fit options
===========
-nofit            Disable all fit parameters (note will still fit for mean)
-fit {param}      Enable fitting for this parameter
-global           Specify a global par file to use across all pulsars
-qrfit            Use QR decomposition instead of SVD (faster, more reliable)
-svdfit           Use SVD decomposition instead of QR (tried and true)
-dcf model        Enable Generalised Least Squares using given model file
-noaccel          Disable LAPACK/BLAS acceleration.
-allglitch        Fit for glitches even outside of START/FINISH.
-norescale        Do not rescale parameter uncertainties by the sqrt(red. chisq)

Output and plugin options
=========================
-gr name          Uses 'name' plugin for graphical interface
-output name      Uses 'name' plugin for output format
-outpar {name}    Write post-fit par file to '{name}'
-newpar           Write post-fit par file to 'new.par'
-writeres         Write out prefit/postfit and design matrix in fit.
-writetim         Save ToAs to out.tim after fitting
-allInfo          Prints out clock, Earth orientation and similar information
-list             Provides listing of clock corrections and residuals etc.
-residuals        Outputs the residuals to a file
-reminder         Saves the command line to T2command.input for future reference.

Predictors and polycos
======================
-polyco "args"    Creates a TEMPO1-style polyco file.
     args = "mjd1 mjd2 nspan ncoeff maxha sitename freq"
-polyco_file      Specify a leading string for file outputs.
-pred "args"      Creates a predictive 2D Chebyshev polynomial.
     args = "sitename mjd1 mjd2 freq1 freq2 ntimecoeff nfreqcoeff seg_length (s)"

Environment Variables
=====================
$TEMPO2            Path to T2Runtime directory for clocks, observatories, EOPs etc.
$TEMPO2_CLOCK_DIR  OPTIONAL Path to search for extra clock files
$TEMPO2_PLUG_PATH  OPTIONAL Path to search for extra plugins
$TEMPO2_ALIAS      OPTIONAL Set to 'tempo' to use tempo1 aliases for observatories.