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

Arguments

SMSE

Class SMSE object returned by salmonMSE()

var

Character. Slot for the state variable in SMSE object. See slotNames(SMSE) for options.

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

Character the fishery state variable to plot

Value

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

See also

plot_decision_table()