Partial denitrations are made practical by an SCR catalyst placed downstream of a NOx adsorber. The SCR catalyst permits partial denitrations to be extended to where a favorable fuel penalty rate presented by driving conditions can be utilized to a sufficient extent that the benefit of the favorable conditions is not offset by the increased start-up fuel penalty associated with conducting opportunistic partial denitrations. Regenerations, including both denitration and desulfations, can be initiated selectively based on a fuel penalty calculation. Examples of such calculations lead to methods in which opportunistic regenerations are based on low oxygen concentrations, condition existing while shifting gears, and throttling events for a diesel engine with a throttled air supply. The methods flexibly take advantage of driving conditions to reduce fuel penalties associated with regenerations. In one embodiment, driving conditions include future conditions predicted based on GPS and map data.