We examine the variability in the intrinsic absorption in the Seyfert 1 galaxy Mrk 279 using three epochs of observations from the Far Ultraviolet Spectroscopic Explorer and two epochs of observations with the Space Telescope Imaging Spectrograph on the Hubble Space Telescope. Rather than finding simple photoionization responses of the absorbing gas to changes in the underlying continuum, the observed changes in the absorption profiles can be understood more clearly if the effective covering fraction of the gas in all emission components, continuum, and broad and intermediate velocity width emission lines, is accounted for. While we do not uniquely solve for all of these separate covering fractions and the ionic column densities using the spectral data, we examine the parameter space using previously well-constrained solutions for continuum and single emission component covering fractions. Assuming full coverage of the continuum, we find that of the two velocity components of the Mrk 279 absorption most likely associated with its outflow, one likely has zero coverage of the intermediate-line region (ILR) while the other does not. For each component, however, the broad-line region is more fully covered than the ILR. Changes in the O VI column densities are unconstrained due to saturation, but we show that small changes in the nonsaturated C IV and N V column densities are consistent with the outflow gas having zero or partial covering of the ILR and an ionization parameter changing from ~0.01 to ~0.1 from 2002 to 2003 as the UV continuum flux increased by a factor of ~8. The absence of a change in the C III absorbing column density is attributed to this species arising outside the Mrk 279 outflow
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