multiSA (version 0.1.0)

MSAdata-class: MSAdata 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

Dmodel

Class Dmodel containing parameters for model structure (number of years, ages, etc.)

Dstock

Class Dstock containing stock parameters (growth, natural mortality, etc.)

Dfishery

Class Dfishery containing fishery data (catch, size and stock composition, etc.)

Dsurvey

Class Dsurvey containing survey data (indices of abundance)

DCKMR

Class DCKMR containing genetic close-kin data

Dtag

Class Dtag containing tagging data

Dlabel

Class Dlabel containing names for various dimensions. Used for plotting.

Misc

List for miscellaneous inputs as needed

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.

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.

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.

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.

Slots inherited from DCKMR

POP_s

A list by stock of data frames for parent-offspring pairs. Each row in the data frame corresponds to a "sampling unit" defined by the columns:

a	Capture year of parent
t	Age at capture of parent
y	Birth year of offspring
n	Number of pairwise comparisons
m	Number of POPs

HSP_s

A list by stock of data frames for half-sibling pairs. Each row in the data frame corresponds to a "sampling unit" defined by the columns:

yi	Birth year of older sibling
yj	Birth year of younger sibling
n	Number of pairwise comparisons
m	Number of HSPs

CKMR_like

Character, likelihood for the POP and HSP sampling units. See type argument in like_CKMR() for options.

Slots inherited from Dtag

tag_ymarrs

Array. Number of tags that move between regions. Informs movement matrices of stocks between time steps.

tag_ymars

Array. Number of tags distributed among regions. Informs stock distribution (within time step).

tag_yy

Boolean matrix that aggregates years for the tag data. Only used for the tag movement array tag_ymarrs.

tag_aa

Boolean matrix that aggregates ages for the tag data.

tag_like

Character. Likelihood for the tagging data, either the vector of proportions by region of origin for tag_ymarrs, or by region of stock distribution for tag_ymars. See type argument of like_comp() for options

tagN_ymars

Array. Sample size of the tag movement vectors if using the multinomial or Dirichlet-multinomial likelihoods.

tagN_ymas

Array. Sample size of the tag distribution vectors if using the multinomial or Dirichlet-multinomial likelihoods.

tagtheta_s

Array. Tag dispersion parameter (by stock) if using the Dirichlet-multinomial likelihoods. Default set to 1.

tagstdev_s

Array. Tag standard deviation (by stock) if using the lognormal likelihood. Default set to 0.1.

Slots inherited from Dlabel

year

Vector of years. Length Dmodel@ny

season

Vector of season names. Length Dmodel@nm

age

Vector of ages. Length Dmodel@na

region

Vector of region names. Length Dmodel@nr

stock

Vector of stock names. Length Dmodel@ns

fleet

Vector of fleet names. Length Dfishery@nf

index

Vector of index of abundance names. Length Dsurvey@ni

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

# 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

# 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