You should already be familiar with the basic ideas of CJS, since it was the basis of our examples (e.g., Dippers) in the previous lessons. Briefly, CJS involves
Release of marked animals at a series of occasions. Releases may be stratified by groups (sex, initial age, etc.)
Re-encounters of marked animals at subsequent occasions via live recapture or resighting.
The resulting data can be described via individual encounter histories (100001 etc.) denoting capture (1) or not (0) at each occasion
A series of maximum likelihood models can be constructed using these data and used to estimate apparent survival (Phi) and recapture (p) probabilities. Specific models allow time- or group-specific variation in these parameters, modeling of cohort and age structure, and modeling parameter variation as function of individual or time-specific covariates.
Details of CJS analysis are covered in the preceding lessons, specifically:
As we will see, the general approaches for each of these components follows very closely for our other data structures (dead recovery and live-dead), with important differences that will be discussed.
Next: Dead recovery analysis