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eastern Gulf of Alaska data

Source: R/data.R
gulf_of_alaska.Rd

Data used to demonstrate size-structured modelling including bottom-up linkages. data(gulf_of_alaska) loads a list that includes four components:

  • years the set of years modeled

  • taxa the set of taxa (including each stanza for age-structured populations)

  • type is a character vector indicating for each taxon (as vector names) whether it is a heterotroph, autotroph, or detritus pool

  • biomass_data is a long-form data-frame with three columns, providing the Year, Mass (in relative units for copepods and euphausiids, and million metric tons for Pollock and sablefish), and Taxon for each year with available data

  • catch_data is a long-form data-frame with three columns, providing the Year, Mass (in million metric tons), and Taxon for each year with available data

  • P_over_B is a numeric vector with the unitless ratio of biomass production to population biomass for each taxon (as vector names)

  • Q_over_B is a numeric vector with the unitless ratio of biomass consumption to population biomass for each taxon (as vector names)

  • EE is a numeric vector with the ecotrophic efficiency for each taxa, in this case provided only for the detritus pool and determining its turn-over rate

  • Diet_proportions is a numeric matrix where each column lists the proportion of biomass consumed for each predator (column) that is provided by each prey (row)

  • agecomp_data is a named list with age-composition samples for any age-structured population (named list element), where each list element is a matrix with named rows indicating years, and columns indicating integer ages

  • stanza_groups is a character vector with names matching taxa, and elements indicating multi-stanza groups (i.e., age-structured populations)

  • Amax is a numeric vector indicating the maximum age (in years) for each stanza as indicated in names(stanza_groups).

  • Leading is a Boolean vector indicating which stanza is used for estimating biomass (and therefore recruitment) for each names(stanza_groups).

  • K is a numeric vector with the generalized von Bertalanffy growth coefficient (in weight not length) for each unique(stanza_groups)

  • d is a numeric vector with the generalized von Bertalanffy growth coefficient (in weight not length) for each unique(stanza_groups)

  • Amat is a numeric vector with the age at 50% maturity (in years) for each unique(stanza_groups). If provided, it is used to back-calculate and replace the value for Wmat

  • Wmat is a numeric vector with the weight at 50% maturity (relative to W_inf) for each unique(stanza_groups).

  • Wmatslope is a numeric vector with the slope of the logistic maturity at weight (relative to W_inf) for each unique(stanza_groups)

Usage

data(gulf_of_alaska)

Details

The data compiled come from a variety of sources:

  • Sablefish biomass index and age-comps are from a cooperative longline survey, and the index is treated as a relative index.

  • Pollock biomass index and age-comps are from a bottom trawl survey, and the index is treated as a relative index with a prior on the catchability coefficient.

  • Copepod biomass is from an oblique tow bongo net survey, with data provided by Dave Kimmel.

  • Euphausiid biomass is from the Seward Long-Term Ecological Research program, provided by Russ Hopcroft to the Ecological Status Report.

  • Other P_over_B, Q_over_B and Diet_proportions values are derived from Rpath models, provided by Bia Dias.

  • Age-structed inputs are determined based on life-history information and biological samples. See Thorson et al. (In review) for more details regarding data standardization and sources