Plot output from salmonMSE

Various functions that plot the state variables from salmonMSE projections:

plot_statevar_ts() produces a time series for all simulations, or with confidence 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,
  ...
)

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: "pHOScensus", "pNOB", "pbrood" (broodtake to escapement ratio), "pNOSesc" (NOS/natural escapement), "pHOSesc" (HOS/hatchery escapement), 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
...: 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

Usage

Arguments

Value

See also