plot_LRP: Plot historical dynamics relative to candidate limit...

In Blue-Matter/RPC: Reference Point Calculator

Plot historical dynamics relative to candidate limit reference points

Description

Generate LRP figures. See details below on various functions.

Usage

LRP_SSBhist(
  x,
  figure = c("ts", "prob", "none"),
  SSB_y,
  prob_ratio = 1,
  prob_ylim = c(0, 1)
)

LRP_SSBMSY(
  x,
  figure = c("ts", "prob", "none"),
  prob_ratio = 1,
  prob_ylim = c(0, 1)
)

LRP_SSB0(
  x,
  figure = c("ts", "prob", "none"),
  type = c("equilibrium", "initial", "dynamic"),
  prob_ratio = 0.4,
  prob_ylim = c(0, 1)
)

LRP_SP(x, figure = c("ts", "phase", "none"), Bunit = c("B", "VB", "SSB"))

LRP_R(
  x,
  figure = c("ts", "SR", "none"),
  SR_xlim,
  SR_ylim,
  SR_y_RPS0,
  SR_include = 1:3
)

LRP_RPS(x, figure = c("ts", "none"))

LRP_SPR(
  x,
  figure = c("ts", "prob", "none"),
  prob_ratio = 0.4,
  prob_ylim = c(0, 1)
)

LRP_FMSY(
  x,
  figure = c("ts", "prob", "none"),
  prob_ratio = 1,
  prob_ylim = c(0, 1)
)

LRP_Fmed(
  x,
  figure = c("ts", "prob", "none"),
  prob_ratio = 1,
  prob_ylim = c(0, 1)
)

LRP_50Rmax(
  x,
  figure = c("ts", "prob", "none"),
  prob_ratio = 1,
  prob_ylim = c(0, 1),
  sims = 1:25
)

LRP_RPS90(
  x,
  figure = c("ts", "prob", "none"),
  prob_ratio = 1,
  prob_ylim = c(0, 1),
  sims = 1:25
)

Arguments

x	An object of class Hist, or a shiny reactivevalues object containing a slot named MSEhist containing the Hist object.
figure	Character, whether to return a time series plot ("ts"), probability plot ("prob"), or no figure ("none").
SSB_y	The year (relative to OM@CurentYr) to compare annual SSB values (only if prob_ratio is a numeric).
prob_ratio	Numeric. If figure = "prob", numeric that indicates a threshold. Functions return annual probabilities of exceeding this threshold.
prob_ylim	The y-axis range of the figure if figure = "prob".
type	For LRP_SSB0, whether the SSB0 is the equilibrium, initial, or dynamic value (see App for description).
Bunit	The metric for stock biomass, either total biomass, vulnerable biomass, or spawning biomass.
SR_xlim	Optional x-axis range for the stock recruit plot. Only used if figure = "SR".
SR_ylim	Optional y-axis range for the stock recruit plot. Only used if figure = "SR".
SR_y_RPS0	The year (relative to OM@CurrentYr) for which to plot unfished recruits per spawner, Only used if figure = "SR", and any(SR_include == 3).
SR_include	A vector including any of c(1, 2, 3) that indicates what to plot in the stock-recruit figure. 1 = individual S-R pairs, 2 = stock-recruit relationship, 3 = reference recruits-per-spawner (R/S) lines (maximum R/S corresponding to stock-recruit alpha, median historical R/S, and year-specific unfished R/S).
sims	A subset of simulations to plot (to reduce time to produce figure)

Details

LRP_SSBhist returns annual spawning biomass (SSB) relative to the annual probability that SSB exceeds some historical value (corresponding to the year in SSB_y).

LRP_SSBMSY returns annual SSB/SSBMSY or the annual probability that SSB/SSBMSY exceeds prob_ratio.

LRP_SSB0 returns annual SSB/SSB0 or the annual probability that SSB/SSB0 exceeds prob_ratio.

LRP_SP returns annual surplus production (annual change in biomass - catch) and per capita surplus production.

LRP_R returns either annual recruitment (as a figure or table) or a stock recruit figure.

LRP_RPS returns annual recruits-per-spawner.

LRP_SPR returns annual spawning potential ratio.

LRP_FMSY returns annual F and F/FMSY.

LRP_Fmed returns F and Fmed (the fishing mortality corresponding to the historical median recruits per spawner, frequently also referred to as the F-replacement F).

LRP_50Rmax returns SSB50%Rmax, the SSB corresponding to 50

LRP_RPS90 returns SSB 90%ile R/S, the SSB corresponding to the intersection of the 90the percentile of both historical recruitment and recruits-per-spawner.

Value

Returns invisibly a list with matrices and arrays used to generate various plots associated with time series and probabilities.

Author(s)

Q. Huynh

References

Mace, P.M. 1994. Relationships between Common Biological Reference Points Used as Thresholds and Targets of Fisheries Management Strategies. CJFAS. 51:110-122. https://doi.org/10.1139/f94-013

Myers, et al. 1994. In search of thresholds for recruitment overfishing. ICES JMS. 51:191–205. https://doi.org/10.1006/jmsc.1994.1020

Examples

library(MSEtool)
Hist <- MSEtool::runMSE(MSEtool::testOM, Hist = TRUE, silent = TRUE)

LRP <- LRP_SSBhist(Hist, SSB_y = 50, prob_ratio = 0.5)
str(LRP)

LRP_50Rmax(Hist)

Blue-Matter/RPC documentation built on Feb. 3, 2025, 11:20 a.m.