Dtag S4 object

S4 class that organizes the various data inputs for the MARS model. MARSdata simply inherits the slots from 6 component classes: Dmodel, Dstock, Dfishery, Dsurvey DCKMR, and Dtag, where the D- prefix denotes an object for model data.

Details

For convenience, most arrays and matrices have the associated dimensions in the variable name. For example, Cobs_ymfr represents observed catch with the dimension following the underscore, following this template:

y	Year
m	Season
a	Age
r	Region
f	Fishery
i	Index
s	Stock

Slots inherited from Dtag

tag_ymarrs

Array. Number of tags that move between regions. Informs movement matrices of stocks between time steps.

tag_ymars

Array. Number of tags distributed among regions. Informs stock distribution (within time step).

tag_yy

Boolean matrix that aggregates years for the tag data. Only used for the tag movement array tag_ymarrs.

tag_aa

Boolean matrix that aggregates ages for the tag data.

tag_like

Character. Likelihood for the tagging data, either the vector of proportions by region of origin for tag_ymarrs, or by region of stock distribution for tag_ymars. See type argument of like_comp() for options

tagN_ymars

Array. Sample size of the tag movement vectors if using the multinomial or Dirichlet-multinomial likelihoods.

tagN_ymas

Array. Sample size of the tag distribution vectors if using the multinomial or Dirichlet-multinomial likelihoods.

tagtheta_s

Array. Tag dispersion parameter (by stock) if using the Dirichlet-multinomial likelihoods. Default set to 1.

tagstdev_s

Array. Tag standard deviation (by stock) if using the lognormal likelihood. Default set to 0.1.

See also

MARSdata-class check_data() Dmodel-class Dstock-class Dfishery-class Dsurvey-class DCKMR-class Dtag-class