Dfishery 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 Dfishery

nf

Integer, number of fleets

Cobs_ymfr

Total fishery catch

Csd_ymfr

Lognormal standard deviation of the fishery catch. Only used if Dmodel@condition = "F". Default of 0.01.

fwt_yamfs

Fishery weight at age. Set to 1 when fleet catch is in units of abundance. Set to stock weight at age by default.

CAAobs_ymafr

Fishery catch at age composition

CALobs_ymlfr

Fishery catch at length composition

fcomp_like

Character, likelihood for the fishery composition data. See type argument of like_comp() for options

CAAN_ymfr

Sample size of the catch at age vector by season if using the multinomial or Dirichlet-multinomial likelihoods

CALN_ymfr

Sample size of the catch at length vector by season if using the multinomial or Dirichlet-multinomial likelihoods

CAAtheta_f

Catch at age dispersion parameter if using the Dirichlet-multinomial likelihood. Default set to 1.

CALtheta_f

Catch at length dispersion parameter if using the Dirichlet-multinomial likelihood. Default set to 1.

sel_block_yf

Index of dummy fleets to model time blocks of selectivity

sel_f

Character vector of the functional form for selectivity. Choose between: "logistic_length", "dome_length", "logistic_age", "dome_age", "SB", "B"

Cinit_mfr

Equilibrium seasonal catch prior to the first year. One way to initialize the abundance at the start of the first year in the model. Default of zero.

SC_ymafrs

Stock composition data.

SC_aa

Boolean matrix that aggregates age classes for the stock composition data. See example.

SC_ff

Boolean matrix that aggregates fleets for the stock composition data. See example.

SC_like

Character, likelihood for the stock composition data. See type argument of like_comp() for options

SCN_ymafr

Sample size of the stock composition vector if using the multinomial or Dirichlet-multinomial likelihoods

SCtheta_f

Stock composition dispersion parameter if using the Dirichlet-multinomial likelihood. Default set to 1.

SCstdev_ymafrs

Stock composition standard deviation 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

Examples

# Aggregate stock composition for ages 1-4 and 5-10 across all fleets
na <- 10
na_SC <- 2
SC_aa <- matrix(0, na_SC, na) # Assumes dim(SC_ymafrs)[3] = na_SC
SC_aa[1, 1:4] <- SC_aa[2, 5:10] <- 1

nf <- 3
nf_SC <- 1
SC_ff <- matrix(1, nf_SC, nf) # Assumes dim(SC_ymafrs)[4] <- nf_SC