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Make a list or vector of life history parameters for yield-per-recruit analyses.

Source: R/makeSPR.R
makeSPR.Rd

Efficiently construct either a vector or list that contains the seven life history parameters required for Beverton-Holt yield-per-recruit analyses. The parameters can be given by the user through function arguments. Alternativvely, the von Bertalanffy parameters (Linf, K, and t0) may be extracted from an nls object created from fitting the von Bertalanffy equation to length-at-age data (object created outside this function). Similarly the log10-transformed weight-length model coefficients may be extracted from an lm object created from fitting the model to transformed weight-length data (object created outside this function). All parameter values are checked for sanity (e.g., Linf>0).

Usage

makeSPR(
  FLR = "log10",
  FLRint,
  FLRslope,
  MatAge,
  percF,
  percFSpawn,
  ageInterval = 0.1
)

Arguments

FLR

A character string to indicate if the fecundity-length relationship is log10 (logarithmic base 10) or linear

FLRint

A single numeric that represents intercept of the fecundity-length relationship.

FLRslope

A single numeric that represents slope of the fecundity-length relationship

MatAge

A single numeric that represent the maximum age.

percF

A vector of the percent of all fish that are females at age starting at age-1.

percFSpawn

A vector of the percent of females that spawn annually starting at age-1.

ageInterval

A single numeric that represents the age interval to calculate SPR in the yield-per-recruit simulation. An interval less than 1 permits calculating fecundity at finer time steps than annual.

Value

A named list that contains the given reproduction options that can be used directly in the yield-per-recruit and dynamic pool models (e.g., yprBH_SlotLL and dpmBH_MinLL).

Author

Jason C. Doll, jason.doll@fmarion.edu

Examples

# This example creates a list where fish mature at age-4. Leading 0's are used in
# the vectors for percF and percFSpawn because they do not contribute to eggs produced

SPRdat<- makeSPR(FLR = "linear", FLRint = -1057029, FLRslope = 2777.08, MatAge = 4,
                 percF=c(0,0,0,rep(0.50,27)),
                 percFSpawn = c(0,0,0,0.24,0.24,0.53,rep(1.00,24)))