Skip to contents

Main function to simulate expected yield using the Beverton-Holt Yield-per-Recruit model for a range of input parameters, including minimum length limits for harvest

Source: R/yprBH_MinLL_var.R
yprBH_minLL_var.Rd

Estimate yield using the Beverton-Holt Yield-per-Recruit (YPR) model using ranges of values for conditional fishing mortality (cf), conditional natural mortality (cm), and minimum length limits for harvest (minLL).

Usage

yprBH_minLL_var(
  lengthmin,
  lengthmax,
  lengthinc,
  cfmin,
  cfmax,
  cfinc,
  cmmin,
  cmmax,
  cminc,
  loi = NULL,
  lhparms,
  matchRicker = FALSE
)

Arguments

lengthmin

A single numeric for the lower limit of minimum length limit for harvest in mm.

lengthmax

A single numeric for the upper limit of minimum length limit for harvest in mm.

lengthinc

A single numeric for the increment to cycle from lower to upper minimum length limit for harvest in mm.

cfmin

A single numeric for minimum conditional fishing mortality.

cfmax

A single numeric for maximum conditional fishing mortality.

cfinc

A single numeric for increment to cycle from minimum to maximum conditional fishing mortality.

cmmin

A single numeric for minimum conditional natural mortality.

cmmax

A single numeric for maximum conditional natural mortality.

cminc

A single numeric for increment to cycle from minimum to maximum conditional natural mortality.

loi

A numeric vector for lengths of interest. Used to determine number of fish that reach desired lengths.

lhparms

A named vector or list that contains values for each N0, tmax, Linf, K, t0, LWalpha, and LWbeta. See makeLH for definitions of these life history parameters. Also see details.

matchRicker

A logical that indicates whether the yield function should match that in Ricker (). Defaults to TRUE. The only reason to changed to FALSE is to try to match output from FAMS. See the "YPR_FAMSvRICKER" article.

Value

A data.frame with the following calculated values:

  • yield is the estimated yield (in g).

  • exploitation is the exploitation rate.

  • Nharvest is the number of harvested fish.

  • Ndie is the number of fish that die of natural deaths.

  • Nt is the number of fish at time tr (time they become harvestable size).

  • avgwt is the average weight of fish harvested.

  • avglen is the average length of fish harvested.

  • tr is the time for a fish to recruit to a minimum length limit (i.e., time to enter fishery).

  • N at xxx mm is the number that reach the length of interest supplied. There will be one column for each length of interest.

  • F is the instantaneous rate of fishing mortality.

  • M is the instantaneous rate of natural mortality.

  • Z is the instantaneous rate of total mortality.

  • S is the (total) annual rate of survival.

For convenience the data.frame also contains the model input values (minLL derived from lengthmin, lengthmax, and lengthinc; cf derived from cfmin, cfmax, and cfinc; cm derived from cmmin, cmmax, and cminc; N0; Linf; K; t0; LWalpha; LWbeta; and tmax).

The data.frame also contains a notes value which may contain abbreviations for "issues" that occurred when computing the results and were adjusted for. The possible abbreviates are defined under "values" in the documentation for yprBH_func.

Details

Details will be filled out later

See also

yprBH_func for estimating yield from single values of cf, cm, and minLL, and yprBH_minLL_fixed for simulating yield with multiple values of cf and cm but a fixed value for minLL.

See this demonstration page for more plotting examples

Author

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

Examples

# Load other required packages for organizing output and plotting
library(dplyr)    ## for filter
library(ggplot2)  ## for ggplot et al.
library(metR)     ## geom_text_contour

# Life history parameters to be used below
LH <- makeLH(N0=100,tmax=15,Linf=592,K=0.20,t0=-0.3,LWalpha=-5.528,LWbeta=3.273)

# Estimate yield for multiple values of minLL, cf, and cm
# # This is a minimal example, lengthinc, cfinc, cminc would likely be smaller
# #   to produce finer-scaled results.
Res_1 <- yprBH_minLL_var(lengthmin=200,lengthinc=50,lengthmax=550,
                       cfmin=0.1,cfmax=0.9,cfinc=0.1,
                       cmmin=0.1,cmmax=0.9,cminc=0.1,
                       loi=c(400,450,500,550),lhparms=LH)

# Yield curves (yield vs exploitation) by varying minimum lengths,
# using cm=40
plot_dat <- Res_1 |> filter(cm==0.40)

ggplot(data=plot_dat,mapping=aes(y=yield,x=exploitation,
                                 group=minLL,color=minLL)) +
  geom_line(linewidth=1) +
  scale_color_gradient2(high="black") +
  labs(y="Yield (g)",x="Exploitation (u)",color="Min Length Limit") +
  theme_bw()


# Yield isopleths for varying minLL and exploitation with cm=0.40
# # Using same data as previous example
ggplot(data=plot_dat,mapping=aes(x=exploitation,y=minLL,z=yield)) +
  geom_contour2(aes(label = after_stat(level))) +
  xlab("Exploitation (u)") +
  ylab("Minimum length limit (mm)") +
  theme_bw()