yprBH_SlotLL.R: Main function to simulate expected yield using the...

In rFAMS: Fisheries Analysis and Modeling Simulator

Main function to simulate expected yield using the Beverton-Holt Yield Per Recruit model for a slot limit

Description

Main wrapper function to estimate yield using the Beverton-Holt YPR model. This main function accepts a range of values for cf, cm, recruitment length, lower slot limit length, and upper slot limit length.

Usage

yprBH_SlotLL(
  recruitmentTL,
  lowerSL,
  upperSL,
  cfunder,
  cfin,
  cfabove,
  cmmin,
  cmmax,
  cminc,
  loi = NA,
  lhparms,
  matchRicker = FALSE
)

Arguments

recruitmentTL	A numeric representing the minimum length limit for recruiting to the fishery in mm.
lowerSL	A numeric representing the length of the lower slot limit in mm.
upperSL	A numeric representing the length of the upper slot limit in mm.
cfunder	Single value, conditional fishing mortality under the lower slot limit.
cfin	Single value, conditional fishing mortality within the lower and upper slot limit.
cfabove	Single value, conditional fishing mortality over the upper slot limit.
cmmin	Single value, minimum conditional natural mortality
cmmax	Single value, maximum conditional natural mortality
cminc	Single value, 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.

Details

Details will be filled out later

Value

A data.frame with the following calculated values:

• cm A numeric representing conditional natural mortality

• TotalYield is the calculated total yield

• TotalHarvest is the calculated total number of harvested fish

• TotalNdie is the calculated total number of fish that die of natural death

• yieldUnder is the calculated yield under the slot limit

• yieldIn is the calculated yied within the slot limit

• yieldAbove is the calculated yield above the slot limit

• exploitationUnder is the exploitation rate under the slot limit

• exploitationIn is the exploitation rate within the slot limit

• exploitationAbove is the exploitation rate above the slot limit

• NharvestUnder is the number of harvested fish under the slot limit

• NharvestIn is the number of harvested fish within the slot limit

• NharvestAbove is the number of harvested fish above the slot limit

• NdieUnder is the number of fish that die of natural death under the slot limit

• NdieIn is the number of fish that die of natural deaths within the slot limit

• NdieAbove is the number of fish that die of natural deaths above the slot limit

• avglenUnder is the average length of fish harvested under the slot limit

• avglenIn is the average length of fish harvested within the slot limit

• avglenAbove is the average length of fish harvested above the slot limit

• avgwtUnder is the average weight of fish harvested under the slot limit

• avgwtIn is the average weight of fish harvested within the slot limit

• avgwtAbove is the average weight of fish harvested above the slot limit

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

• trIn is the time for a fish to recruit to a lower length limit of the slot limit

• trOver is the time for a fish to recruit to a upper length limit of the slot limit

• NtUnder is the number of fish at time trUnder (time they become harvestable size under the slot limit)

• NtIn is the number of fish at time trIn (time they reach the lower slot limit size)

• NtAbove is the number of fish at time trAbove (time they reach the upper slot limit size)

• FUnder is the estimated instantaneous rate of fishing mortality under the slot limit

• FIn is the estimated instantaneous rate of fishing mortality within the slot limit

• FAbove is the estimated instantaneous rate of fishing mortality above the slot limit

• MUnder is the estimated instantaneous rate of natural mortality under the slot limit

• MIn is the estimated instantaneous rate of natural mortality within the slot limit

• MAbove is the estimated instantaneous rate of natural mortality above the slot limit

• ZUnder is the estimated instantaneous rate of total mortality under the slot limit

• ZIn is the estimated instantaneous rate of total mortality within the slot limit

• ZAbove is the estimated instantaneous rate of total mortality above the slot limit

• SUnder is the estimated total survival under the slot limit

• SIn is the estimated total survival within the slot limit

• SAbove is the estimated total survival above the slot limit

• cfUnder A numeric representing conditional fishing mortality

• cfIn A numeric representing conditional fishing mortality

• cfOver A numeric representing conditional fishing mortality

• recruitmentTL A numeric representing the minimum length limit for recruiting to the fishery in mm.

• lowerSL A numeric representing the length of the lower slot limit in mm.

• upperSL A numeric representing the length of the upper slot limit in mm.

• N0 A numeric representing the initial number of new recruits entering the fishery OR a vector or list that contains named values for each N0, Linf, K, t0, LWalpha, LWbeta, and tmax

• Linf A numeric representing the point estimate of the asymptotic mean length (L-infinity) from the von Bertalanffy growth model in mm

• K A numeric representing the point estimate of the Brody growth coefficient from the von Bertalanffy growth model

• t0 A numeric representing the point estimate of the x-intercept (i.e., theoretical age at a mean length of 0) from the von Bertalanffy growth model

• LWalpha A numeric representing the point estimate of alpha from the length-weight regression on the log10 scale.

• LWbeta A numeric representing the point estimate of beta from the length-weight regression on the log10 scale.

• tmax An integer representing maximum age in the population in years

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

Author(s)

Jason C. Doll, [e-mail]

Examples

#Load other required packages for organizing output and plotting
library(ggplot2)
library(dplyr)
library(tidyr)

# Custom theme for plots (to make look nice)
theme_FAMS <- function(...) {
  theme_bw() +
  theme(
    panel.grid.major=element_blank(),panel.grid.minor=element_blank(),
    axis.text=element_text(size=14,color="black"),
    axis.title=element_text(size=16,color="black"),
    axis.title.y=element_text(angle=90),
    axis.line=element_line(color="black"),
    panel.border=element_blank()
  )
}

# 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
 Res_1 <- yprBH_SlotLL(recruitmentTL=200,lowerSL=250,upperSL=325,
                       cfunder=0.25,cfin=0.6,cfabove=0.15,cmmin=0.3,cmmax=0.6,cminc=0.05,
                       loi=c(200,250,300,325,350),lhparms=LH)

 Res_1

# Plot results
# Total Yield vs Conditional Natural Mortality (cm)
ggplot(data=Res_1,mapping=aes(x=cm,y=TotalYield)) +
  geom_point() +
  geom_line() +
  labs(y="Total Yield (g)",x="Conditional Natural Mortality (cm)") +
  theme_FAMS()


# Yield under, in, and above the slot limit vs Conditional Natural Mortality (cm)
# Select columns for plotting
plot_data <- Res_1 %>%
  select(cm, yieldUnder, yieldIn, yieldAbove) %>%
  pivot_longer(!cm, names_to="YieldCat",values_to="Yield")

# Generate plot
ggplot(data=plot_data,mapping=aes(x=cm,y=Yield,group=YieldCat,color=YieldCat)) +
  geom_point() +
  scale_color_discrete(name="Yield",labels=c("Above SL","In SL","Under SL"))+
  geom_line() +
  labs(y="Total Yield (g)",x="Conditional Natural Mortality (cm)") +
  theme_FAMS() +
  theme(legend.position = "top")+
  guides(color=guide_legend(title="Yield"))

rFAMS documentation built on Feb. 11, 2026, 1:06 a.m.