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
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")
)
Functions return the matrix of plotted values invisibly. Figure plotted from base graphics
Class SMSE object returned by salmonMSE()
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.
Integer. Population index for multi-population model (e.g., s = 1 is the first population in the model)
Logical, whether to generate a figure (set to FALSE if only using the function to return the data matrix)
Character. Name of time variable for the figure
Logical, whether to plot individual simulations (FALSE) or the median with 95 percent confidence intervals (TRUE)
Character. Name of the state variable for the figure
Vector. Y-axis limits
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
Integer. Projection year for the state variable to plot the histogram. If missing, the last projection year is used.
Logical, whether to plot proportions or absolute numbers
Summarizing function across simulations, typically median() or mean()
For plot_Kobe, the fishery state variable to plot. Whether to plot the exploitation rate for the terminal (T) or pre-terminal fishery (PT).
Vector. X-axis limits
plot_decision_table() plot_LHG()