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Construct SPR input objec t

spr_input.Rd

Validates and expand inputs needed for per-recruit SPR/YPR calculations for one or multiple species. If selectivity$type = "fleets", fleet-specific selectivity curves are combined into an effective selectivity-at-age vector using a propF-weighted mean. The per-recruit calculations use this effective selectivity. Fleet details may be retained in the output for transparency and plotting, but are not required for SPR/YPR calculations.

Usage

spr_input(
  ages,
  species,
  rec_prop = NULL,
  R0 = 1,
  use_plus_group = TRUE,
  scale_selex = TRUE
)

Arguments

ages

Numeric vector of ages (e.g., a_min:a_max).

species

A named or unnamed list for single species specification, or a named list of species for multispecies specifications. See details.

rec_prop

Optional numeric vector of recruitment proportions for multispecies analyses. Must be the same length as the number of species and sum to 1. Defaults to equal proportions.

R0

Numeric scalar recruitment scaling used for per-recruit calculations (default=1, or equal proportions if inputting multiple species). If defining R0 for multiple species, R0 proportions must be a vector equal to the number of species and sum to 1.

use_plus_group

Logical. If TRUE (default), the terminal age will be treated as a plus group in pop dy equations.

scale_selex

Logical. If TRUE (default), scales selectivity so max equals 1 when possible.

Value

A named list with expanded, validated inputs for running SPR functions:

  • ages, R0, use_plus_group

  • species: named list of per-species expanded vectors and original specifications

  • rec_prop: recruitment proportions used for multispecies calculations

Details

For a single-species analysis, provide a single species specification via species (can be named or unnamed). For multispecies analyses, provide a named list of species specifications, where each element defines life history and fishery inputs for one species.

Each species specification must include:

  • len_at_age: list with type="vb" (Linf, k, t0) or type="vector" (L).

  • wt_at_age: list with type="wl" (alpha, beta) or type="vector" (W).

  • maturity: list with type="logistic" (a50, delta) or type="vector" (m).

  • selectivity: list with type="logistic" (a50, delta), type="knife_edge" (a_c), type="vector" (s), or type="fleets" (multiple fleet selectivities). For type="fleets", provide fleets = list(<fleetname> = list(propF = <weight>, selex = <selectivity_spec>), ...).

  • M: numeric scalar or vector of length length(ages).

Rules for size-at-age:

  • If wt_at_age$type = "vector", the provided weight-at-age vector is used directly in the SPR model. In this case, len_at_age is not used to determine size-at-age for the SPR calculations, and a message is emitted to make this explicit.

  • If len_at_age$type = "vb", then wt_at_age$type must be "wl" to ensure consistency between growth and weight conversion.

Examples