README

Southampton version of the JAVELIN code created by Ying Zu to measure time lags
between different bands/emission lines in Active Galactic Nuclei.

For the original, and instructions, go here:

http://www.astronomy.ohio-state.edu/~yingzu/codes.html#javelin

See below for a list of the changes in relation to the original, see below:

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lcmodel:
    show_hist - features added:

        lag_lims - define limits of lag plot
        lagbinsize - can now be not integer
        lagplotonly - allows only the lag distribution to be plotted
        fontsize - allows control of the plot font size
        xlabel,ylabel - allows control of lag plot labels
        prob_density - set to True to save probability density instead of no. 
                        models (for all plotted variables)

    save_hist_data - new function added:

        allows the data from a histrogram to be saved as a txt file. Requires no
        params, but some optional ones available. Includes lag_lims, lagbinsize,
         & bins, as with show_hist.

        filename - choose filename, instead of default 'javelin_hist.dat'
        plot - set to True to see the plot whose data was just saved
        prob_density - set to True to save probability density instead of no. models

    save_mod_data:

        allows all the output data from a model to be saved as a txt file,
        which can be binned and plotted at leisure. filename optional

        filename - set the filename to something other than the default
                    ('javelin_mod.dat')

    do_mcmc - improved:

        using 'fchain' to save the chain data now also adds a header containing
        the file route and file names of each of the lightcurves involved in the
        chain.

    load_chain - improved:

        if the user loads a chain into a model using lightcurves which have
        names different to those used to create the chain, or are saved in a
        different location to those originally used, a warning is given.

hist_tools - new module:

    plot_saved_mod:

        plots the data from a saved model file (saved with save_model_data),
        without requiring you to load chains and lightcurves. Uses the
        show_hist function, so has all the same parameters.

        filename - string, required
             Filename of the saved model data to plot

    show_hist_new:

        works in exactly the same way as Rmap_Model.show_hist, but is not 
        associated with a particular object and will work if provided with a 
        model as an argument, or if given the data directly in the form of an 
        array.

    plot_new:

        works in exactly the same way as Rmap_Model.plot, but is not associated
        with a particular object and will work if provided with a model
        as an argument.

zylc:
    plot - errors sorted:

        It is now possible to plot a single lightcurve without an error

    get_data - improved:

        If the file that the user is attempting to open is not in the current
        working directory/doesn't exist, the user will be warned and the
        operation cancelled, instead of just returning an error about strings.

        Adds the file route and filenames of each LC, for book keeping
        purposes

    Lightcurve (object) - features added:

        Lightcurve.fnames - contains the file route (0th element) and
        filenames of each of the files loaded into the object, as
        described above in get_data. Optional if creating an object
        directly, with the input parameter name 'fnames'.