setup.model: Defines model specific parameters (internal use)

Description Usage Arguments Details Value Author(s) See Also

View source: R/setup.model.R


Compares model, the name of the type of model (eg "CJS") to the list of acceptable models to determine if it is supported and then creates some global fields specific to that type of model that are used to modify the operation of the code.


setup.model(model, nocc, mixtures = 1)



name of model type (must be in vector valid.models)


length of capture history string


number of mixtures


In general, the structure of the different types of models (e.g., "CJS","Recovery",...etc) are very similar with some minor exceptions. This function is not intended to be called directly by the user but it is documented to enable other models to be added. This function is called by other functions to validate and setup model specific parameters. For example, for live/dead models, the length of the capture history is twice the number of capture occasions and the number of time intervals equals the number of capture occasions because the final interval is included with dead recoveries. Whereas, for recapture models, the length of the capture history is the number of capture occasions and the number of time intervals is 1 less than the number of occasions. This function validates that the model is valid and sets up some parameters specific to the model that are used in the code.


model.list - a list with following elements


encounter type string for MARK input; typically same as model


number of capture occasions


number of time intervals relative to number of occasions (0 or -1)


number of mixtures if any


logical; TRUE if model produces derived estimates


Jeff Laake

See Also

setup.parameters, valid.parameters

RMark documentation built on Aug. 8, 2017, 5:08 p.m.

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