The feed intake and marker content in the feed gives you the marker intake in grams. Similarly the amount of manure collected and the marker content in the manure gives you the grams collected. Then divide output by intake, multiply by 100 and you have percentage recovery.
meaning, If I'm calculating the recovery rate based on digesta samples, should I use the same equation? what's the preferred sample weight to run the analysis of the marker in the digesta?
The calculations are identical for excreta and intestinal samples.
Concerning sample size, two different types of samples are important. In both cases, the inherent non-homogenous composition of both feeds and intestinal content or excreta, makes it imperative to collect a sample as large as possible to minimize the possibility of aberrant results. These (large) samples should then be thoroughly mixed to a homogenous mass.
Often (freeze) drying and milling to a fine powder is the best way of obtaining a homogeneous material, which allows you to take a (smaller) representative sample for the analysis. The size of the analytical sample is determined by your analytical method.
You can only get reliable results if you give a lot of care and attention to obtain representative sample in the first phase. If not, then the rest of your work might be useless.