    MC-QUANTITIES:  Quantities from log files relating to Monte Carlo simulation.

    The quantities below relating to Markov chain Monte Carlo can be
    obtained from log files (eg, for use in xxx-plt).  Note that the
    generic quantities documented in quantities.doc will also be
    available, as will quantities specific to the particular Markov chain
    application being used.

        T   Temperature used (see xxx-mc.doc, NOT from the tempering schedule)
        E   Potential energy at end of iteration
        E0  Potential energy at end of iteration at inverse temperature of 0
        E1  Equal to E - E0
        K   Kinetic energy at end of iteration
        K0  Expected value of kinetic energy, equal to half the dimensionality
        H   Total energy at end of iteration (sum of E and K)
        D[n] Change in total energy for last state proposed (up to max of n)
             (for Metropolis, hybrid, and multivariate slice sampling operations)

        i   Inverse temperature being used (from the tempering schedule)
        I   Index of current inverse temperature value in schedule
        j   Direction of change for inverse temperature
        J   Higher temperature for attempted transition (meaningful only if
            last operation in iteration was sim-temp)
        Q[n] Importance weight, or log of importance weight (see below)
        F[n] Factor for estimating ratio of normalizing constants using
             tempered transitions (see below).

        d   Heatbath decay factor used in this iteration
        f   Stepsize factor used in this iteration
        r   Rejection rate for this iteration
        e   Average number of evaluations per slice sampling update this iteration
        k   Cumulative cpu usage in minutes.

        m   Point last moved to relative to starting point
        m0  Point moved to relative to lowest point for spiral and double-spiral
        m1  Starting point relative to lowest point for spiral and double-spiral
        m2  Switch point for double-spiral operations
        m3  Equal to m0-m2 (double-spiral only)
        m4  Equal to m1-m2 (double-spiral only)
        m5  Equal to |m3|-|m4|

        qn  Component n of position
        pn  Component n of momentum
        sn  Stepsize selected by application for component n

    None of these quantities can be used with a range; 'q', 'p', and 's'
    must have a modifier; 'D' and 'Q' may have a modifier; 'E' may only
    have a modifier of '0' or '1'; 'K' may only have a modifier of '0';
    the others may not have a modifier.

    The 'Q' quantity is the importance weight, which will always be one
    except during annealed importance sampling.  Note that these weights
    might sometimes be so extreme that this value overflows or underflows.
    If a modifier of 0 is given to 'Q', the value is the log of the
    importance weight, which is much less likely to be out of bounds.  If
    a modifier n greater than zero is given for 'Q', the value is the log
    of the importance weight unless that is less than -n, in which case
    the value is -n.

    The 'F' quantities are factors obtained from the last tempered
    transition in the iterations, which can be averaged to estimate the
    ratio of normalizing constants for the distribution at temperature one
    to that of the distribution at the highest temperature.  The 'F1'
    quantity is based on only the first half of the tempered transition.
    The 'F2' quantity is based on both halves if the tempered transition
    is accepted, and is otherwise based on just the first half.

    Momenta of zero are assumed if none exist.

                Copyright (c) 1995-2004 by Radford M. Neal