plot_statevar_ts: Plot core output from salmonMSE

In salmonMSE: Management Strategy Evaluation for Salmon Species

Plot core output from salmonMSE

Description

Various functions that plot the state variables from salmonMSE projections:

• plot_statevar_ts() produces a time series for all simulations, or with medians and 95th percentile intervals

• plot_statevar_hist() produces a histogram across all simulations for a particular year

• plot_spawners() produces a summary barplot of spawners, including NOS, HOS, and wild spawners

• plot_escapement() produces a summary figure of the proportion of spawners and broodtake to escapement

• plot_fitness() produces a summary figure of metrics (fitness, PNI, pHOS, and pWILD) related to hatchery production

• plot_fishery() produces a summary figure of metrics related to the fishery, e.g., median catch, exploitation rate or harvest rate

Usage

plot_statevar_ts(
  SMSE,
  var = "PNI",
  s = 1,
  figure = TRUE,
  xlab = "Projection Year",
  quant = FALSE,
  ylab = var,
  ylim,
  agg.fun = sum,
  ...
)

plot_statevar_hist(SMSE, var = "PNI", s = 1, y, figure = TRUE, xlab = var, ...)

plot_spawners(SMSE, s = 1, prop = TRUE, FUN = median, figure = TRUE, ylim)

plot_fitness(SMSE, s = 1, FUN = median, figure = TRUE, ylim)

plot_escapement(SMSE, s = 1, FUN = median, figure = TRUE, ylim)

plot_fishery(
  SMSE,
  s = 1,
  type = c("catch", "exploit", "harvest"),
  FUN = median,
  figure = TRUE,
  ylim,
  ylab,
  ...
)

plot_Kobe(
  SMSE,
  s = 1,
  FUN = median,
  figure = TRUE,
  xlim,
  ylim,
  xlab = expression(NOS/S[MSY]),
  ylab = expression(U/U[MSY]),
  type = c("T", "PT")
)

Arguments

SMSE	Class SMSE object returned by salmonMSE()
var	Character. Slot for the state variable in SMSE object. See slotNames(SMSE) for options. Additional supported options are: "ESS" (egg-smolt survival), "pbrood" (broodtake to escapement ratio), "pNOSesc" (NOS/natural escapement), "pHOSesc" (HOS/hatchery escapement), ⁠Total Spawners⁠ (NOS + HOS), NOS/SMSY, S/SMSY, and NOS/Sgen.
s	Integer. Population index for multi-population model (e.g., s = 1 is the first population in the model)
figure	Logical, whether to generate a figure (set to FALSE if only using the function to return the data matrix)
xlab	Character. Name of time variable for the figure
quant	Logical, whether to plot individual simulations (FALSE) or the median with 95 percent confidence intervals (TRUE)
ylab	Character. Name of the state variable for the figure
ylim	Vector. Y-axis limits
agg.fun	Function. Defines how to aggregate state variables that are reported by age. Typically, sum is used but max is also possible for reporting apical exploitation rates.
...	Additional arguments to base plot function
y	Integer. Projection year for the state variable to plot the histogram. If missing, the last projection year is used.
prop	Logical, whether to plot proportions or absolute numbers
FUN	Summarizing function across simulations, typically median() or mean()
type	For plot_Kobe, the fishery state variable to plot. Whether to plot the exploitation rate for the terminal (T) or pre-terminal fishery (PT).
xlim	Vector. X-axis limits

Value

Functions return the matrix of plotted values invisibly. Figure plotted from base graphics

See Also

plot_decision_table() plot_LHG() compare_statevar_ts()

salmonMSE documentation built on Aug. 20, 2026, 5:09 p.m.