Dsurvey 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 Dsurvey

ni

Integer, number of indices of abundance. Zero is possible.

Iobs_ymi

Observed indices

Isd_ymi

Lognormal standard deviation of the observed indices

unit_i

Character vector, units of the index. Set to "B" to use stock weight at age (default) or "N" for abundance (numbers).

IAAobs_ymai

Array, survey age composition

IALobs_ymli

Array, survey length composition

icomp_like

Character, likelihood for the composition data. See like_comp() for options

IAAN_ymi

Array, sample size of the index age composition by season if using the multinomial or Dirichlet-multinomial likelihoods

IALN_ymi

Array, sample size of the index length composition by season if using the multinomial or Dirichlet-multinomial likelihoods

IAAtheta_i

Numeric vector, survey age composition dispersion parameter if using the Dirichlet-multinomial likelihood

IALtheta_i

Numeric vector, index length composition dispersion parameter if using the Dirichlet-multinomial likelihood

samp_irs

Boolean array that specifies the regions and stocks sampled by the index. samp[i, r, s] indicates whether index i operates in region r and catches stock s.

sel_i

Character vector, functional forms for selectivity. See "type" argument in conv_selpar() for options.

delta_i

Numeric vector, The elapsed fraction of time in the seasonal time step (between 0 - 1) when the index samples the population. Set to a negative number (-1) to sample over the duration of the timestep, i.e., (1 - exp(-Z))/Z.

See also

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