Data inputs for single species CEATTLE of the Bering Sea from 1979 to 2017

A dataset containing the inputs used for CEATTLE

Usage

BS2017SS

Format

Control

nspp

Number of species included in CEATTLE

styr

Start year of the hindcast

endyr

End year of the hindcast

projyr

End year of the forecast

nsex

Number of sexes to model in the population (1 = combined/1sex, 2 = models both female/male)

spawn_month

Spawning month of the population to adjust the numbers spawning

R_sexr

Percent of recruitment that is female (ignored if nsex = 1)

nages

Number of ages of each species included in the hindcast

minage

Minimum age for each population (i.e.does recruitment correspond to age 0, 1, 2?)

nlengths

Number of lengths of each species included in the hindcast

pop_wt_index

Weight-at-age (weight) index to use for calculation of each species population derived quantities (SSB, Consumption/Ration, Suitability, etc)

ssb_wt_index

Weight-at-age (weight) index to use for calculation of each species spawning biomass

pop_age_transition_index

Age transition matrix (e.g. growth trajectory) index to use for derived quantities of the population to convert age to length (also used in length-based predation estimation)

sigma_rec_prior

Standard deviation to use for recruitment

other_food

Other food in the ecosystem for each species

estDynamics

Estimate or fix numbers-at-age: 0 = estimate dynamics, 1 = use input numbers-at-age in NbyageFixed, 2 = multiply input numbers-at-age (NbyageFixed) by a single scaling coefficient, 3 = multiply input numbers-at-age (NbyageFixed) by age specific scaling coefficient.

est_M1

Estimate residual (multi-species mode) or total natural mortality (single-species mode). 0 = use fixed natural mortality from M1_base, 1 = estimate sex- and age-invariant M1, 2 = sex-specific (two-sex model), age-invariant M1, 3 = estimate sex- and age-specific M1.

fleet_control

Survey and fishery data specifications

index_data

Survey index in weight (kg) or numbers data

catch_data

Total catch in weight (kg) or numbers data

comp_data

Survey/fishery age or length composition data. Note if sex is 3, put female composition data then male composition data (similar to SS).

emp_sel

Empirical/fixed selectivity for surveys and fisheries (leave empty if not used)

age_trans_matrix

Age transition matrix (e.g. growth trajectory) used to convert age to length for length comp data. Can have multiple matrices for a species specified by Age_transition_index.

age_error

Aging error matrices. Can have only one per species.

weight

Weight-at-age (weight) to use for calculation of derived quantities (SSB, Consumption/Ration, Suitability, Total Catch, Survey Biomass, etc). Can have multiple weight-at-age data-sets for each species, but must be full for all years of the hindcast.

maturity

Maturity-at-age for each species

sex_ratio

Percent female at age for each species

M1_base

Residual natural mortality for each species

aLW

Parameters for weight-at-length power function for each species. . Used when estimating time-variant length-based gamma suitability (suitMode = 2) or time-variant length-based lognormal suitability (suitMode = 5)

Ceq

Which bioenergetics equation to use for each species for ft to scale max consumtion: 1 = Exponential (Stewart et al 1983), 2 = Temperature-dependendence for warm-water species (Kitchell et al 1977; sensu Holsman et al 2015), 3 = temperature dependence for cool and cold-water species (Thornton and Lessem 1979)

Cindex

Which environmental index in env_data to use to drive bioenergetics

Pvalue

This scales the maximum consumption used for ration for each species; Pvalue is in CmaxfTPvalue*ration_data

fday

Number of foraging days per year for each species

CA

Intercept of allometric mass function for calculating maximum consumption: CA * Weight ^ CB

CB

Slope of allometric mass function for calculating maximum consumption: CA * Weight ^ CB

Qc

Parameter for temperature scaling function of maximum consumption specified by Ceq

Tco

Parameter for temperature scaling function of maximum consumption specified by Ceq

Tcm

Parameter for temperature scaling function of maximum consumption specified by Ceq

Tcl

Parameter for temperature scaling function of maximum consumption specified by Ceq

CK1

Parameter for temperature scaling function of maximum consumption specified by Ceq

CK4

Parameter for temperature scaling function of maximum consumption specified by Ceq

env_data

Environmental indices such as bottom temperature data to incorporate into ration equation specificed by Ceq and Cindex. Also used to drive catchability if Catchability = 5. Will use the mean for missing years. Temperature should be in celcius.

ration_data

Annual relative foraging rate by age or input consumption at age. Multiplied by pvalue and fday to scale maximum consumption to the number of days in a year that foraging occurs.

UobsAge

Stomach proportion by numbers for each predator, prey, predator age, prey age combination. Can also be year specific by including the column, "Year"

UobsWtAge

Stomach proportion by weight for each predator, prey, predator age, prey age combination. Can also be year specific by including the column, "Year"

fleet_control: controls for survey and fisheries data

Fleet_name

Name of survey or fishery

Fleet_code

Index of survey/fishery ACROSS species

Fleet_type

0 or 'Off' = Do not estimate; 1 = 'Fishery'; 2 = 'Survey'

Species

Species number

Selectivity_index

index to use if selectivities of different surveys are to be the same

Selectivity

Selectivity to use for the species: 0 = "Fixed"; 1 = "Logistic"; 2 = "NonParametric" sensu Ianelli et al 2018; 3 = "DoubleLogistic"; 4 = "DescendingLogistic", 5 = "Hake" non-parametric sense Taylor et al, 6 = "2DAR1", 7 = "3DAR1" sensu Cheng et al 2024.

Selectivity_dimension

"Age" or "Length".

Nselages

Number of ages to estimate non-parametric selectivity.

Time_varying_sel

Whether a time-varying selectivity should be estimated for logistic, double logistic selectivity, or descending logistic. 0 = "Off", 1 = "IID" penalized deviates given sel_sd_prior or random effect, 2 = "AR1" (TODO), 3 = "Block" time blocks with no penalty, 4 = "RandomWalk" following Dorn, 5 = "RandomWalkAscending" on ascending portion of double logistic only.

Time_varying_sel_sd_prior

The fixed or initial sd to use for time varying selectivity.

Bin_first_selected

Age/length bin at which selectivity is non-zero

Acuumulation_age_lower

Ages below this will be grouped to this age for composition data. For example, if set to 2, comp data for age 2 will include 1 and 2 year olds.

Acuumulation_age_upper

Ages above this will be grouped to this age for composition data. For example, if set to 9 for a species with 10 ages, comp data for age 9 will include 9 and 10 year olds.

weight1_Numbers2

Is the observation in weight (kg) set as 1, if the observation is in numbers caught, set as 2

Weight_index

Weight-at-age (weight) index to use for calculation of derived quantities

Age_transition_index

Age transition matrix (e.g. growth trajectory) index to use for derived quantities to convert age to length

Q_index

index to use if catchability coefficients are to be set the same

Catchability

Estimate catchability? (0 or "Fixed" = fixed at prior; 1 or "Estimated" = Estimate single parameter; 2 or "Estimated-with-prior" = Estimate single parameter with prior; 3 or "Analytical" = Estimate analytical q from Ludwig and Walters 1994; - 4 = Estimate power equation; - 5 or "Environmental" = Linear equation log(q_y) = q_mu + beta * index_y; 6 or "AR1" = annual AR1 catchability deviates are fit to environmental index sensu Rogers et al 2025)

Q_prior

Starting value or fixed value for catchability

Q_sd_prior

Variance of q prior: dnorm (log_q, log_q_prior, q_sd_prior)

Time_varying_q

Whether a time-varying q should be estimated. 0 = "Off", 1 = "IID" penalized deviate or random effect, 2 = "AR1" (TODO), 3 = "Block" time blocks with no penalty; 4 = "RandomWalk" random walk from mean following Dorn 2018 (dnorm(q_y - q_y-1, 0, sigma). If Catchability = 5 or 6, this determines the environmental index to be used in the equation log(q_y) = q_mu + beta * index_y

Time_varying_q_sd_prior

The sd to use for the random walk of time varying q if set to 1

Estimate_survey_sd

Estimate survey variance (0 = use CV from index_data, 1 = yes, 2 = analytically estimate following (Ludwig and Walters 1994)

Survey_sd_prior

Starting value to be used if Estimate_sigma_index = 1

Estimate_catch_sd

Estimate fishery variance (0 = use CV from index_data, 1 = yes, 2 = analytically estimate following (Ludwig and Walters 1994)

Catch_sd_prior

Starting value to be used if Estimate_sigma_catch = 1

Comp_weights

Composition weights to be used for multinomial likelihood. These are multiplied. After running model, these will update to McAllister & Ianelli 1997 weights using the harmonic mean.

Catch_units

Units used for survey: 1 = kg; 2 = numbers

proj_F_prop

The proportion of future fishing mortality assigned to this fleet

Sex

sex codes: 0=combined; 1=use female only; 2=use male only; 3 = joint female and male