Dstock 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 Dstock

m_spawn

Integer, season of spawning. Defaults to 1. The progeny will enter the age structure in the same season.

m_advanceage

Integer, season in which to advance age classes (corresponding to calendar year) to the next age class. Defaults to 1.

len_ymas

Length-at-age. Only needed if Dmodel@nl > 0 to fit length composition (you may want to calculate the growth at the middle of the time step). calc_growth() may be a helpful function.

sdlen_ymas

Standard deviation in length-at-age

LAK_ymals

Length-at-age probability array. If empty, values will be calculated by check_data() with calc_LAK().

mat_yas

Proportion mature by age class. Ignored if maturity ogive is estimated, e.g., when fitting to close-kin genetic data.

swt_ymas

Stock weight-at-age (at beginning of time step). See calc_growth() example.

fec_yas

Fecundity, i.e., spawning output, of mature animals. Default uses stock weight at age.

M_yas

Natural mortality. Instantaneous units per year. Ignored if M is estimated.

SRR_s

Character vector of stock-recruit relationship by stock. See SRR argument in calc_recruitment() for options.

delta_s

Fraction of season that elapses when spawning occurs, e.g., midseason spawning occurs when delta_s = 0.5. Default is zero.

presence_rs

Logical matrix indicating presence/absence of stock s in region r. Used to constrain movement matrix. Default is TRUE for all stocks and regions.

natal_rs

The fraction of the mature stock s in region r that spawns at time of spawning. See example. Default is 1 for all stocks and regions.

See also

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

Examples

# Set natal_rs matrix so that the spawning output of stock 1 is
# calculated from mature animals present in regions 1, 2.
# Similarly for stock 2, spawning output from areas 2 and 3.
nr <- 4
ns <- 2
natal_rs <- matrix(0, nr, ns)
natal_rs[1:2, 1] <- natal_rs[2:3, 2] <- 1