multiSA (version 0.1.0)

Dfishery-class: Dfishery S4 object

Description

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

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_ymafs

Fishery weight at age. Set to 1 when fleet catch is in units of abundance. Set to stock weight at age by default (values at beginning of time step).

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.

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

See Also

MSAdata-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