Dmodel S4 object

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).

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 Dmodel

ny

Integer, number of years

nm

Integer, number of seasons

na

Integer, number of ages. The first age class is zero and the last age class (plus group is age na - 1).

nl

Integer, number of length bins. Set to zero if lengths are not modeled.

nr

Integer, number of spatial regions

ns

Integer, number of stocks

lbin

Vector of lower boundary of length bins. Length nl + 1

lmid

Vector of midpoint of length bins. Length nl

Fmax

Numeric, maximum allowable instantaneous fishing mortality rate (units of per season). Defaults to 3.

y_phi

Integer, the year from which to obtain values of natural mortality and fecundity for the unfished stock-recruit replacement line (phi). Relevant if natural mortality or fecundity are time-varying. Defaults to 1.

scale_s

Vector, length ns. Multiplicative scaling factor that informs relative stock size to aid parameter estimation. Larger values implies larger stocks. Default set to 1. See make_parameters().

nyinit

Integer, number of years of spool-up to calculate equilibrium unfished and starting conditions for the population model to account for seasonal and spatial dynamics. The numerical spool-up is not needed when both nm = 1 and nr = 1, i.e., nyinit = 1. Otherwise, set to 2 * na by default.

condition

Character, either to specify the model estimates fishing mortality as a parameter ("F", default) or equal to the catch ("catch").

nitF

Integer, number of iterations to solve Baranov catch equation from observed catch if condition = "catch". Defaults to 5.

y_Fmult_f

Integer vector by fleet, the year in which to directly estimate F. Choose a year/season/region combination when the catch is average relative to the time series. Only used if condition = "F".

m_Fmult_f

Integer vector by fleet, the season in which to directly estimate F. Choose a year/season/region combination when the catch is average relative to the time series. Only used if condition = "F".

r_Fmult_f

Integer vector by fleet, the region in which to directly estimate F. Choose a year/season/region combination when the catch is average relative to the time series. Only used if condition = "F".

pbc_rdev_ys

Numeric matrix, for the fraction of lognormal bias correction (-0.5 * sd_r^2) applied to the recruitment estimates in the model. Typically between 0-1, with default of 1.

pbc_initrdev_as

Numeric matrix, for the fraction of lognormal bias correction (-0.5 * sd_r^2) applied to the initial abundance vector in the model. Typically between 0-1, with default of 1.

prior

Character vector to be evaluated in the model to return the log prior for a parameter. See example in documentation for prior.

nyret

Integer, number of recent years of data to remove from the likelihood for retrospective analysis (positive numbers). Default is zero.

See also

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