plot_historical_probs: Plots to compare historical and current probabilities

In pacific-hake/hake-assessment: Stock Assessment for Pacific Hake

Plots to compare historical and current probabilities

Description

Plot either: (a) base model's estimate of P(B_t+1 < B_t) and compare with the estimate of that from the year t assessment (using the known catch in year t) (b) base model's estimate of P(B_t+1 < B_40%) and compare with the estimates of that from the year t assessment (using the known catch in year t). Included in management presentation.

Usage

plot_historical_probs(
  model,
  hist_probs,
  type = "decline",
  end = assess_yr - 1,
  xLim = NULL,
  add.50 = TRUE,
  add.50.col = "darkgrey",
  one.year = 2019,
  add.projs = FALSE,
  num.projs = ct_levels_num,
  colors = c("red", "blue"),
  pch = c(16, 17),
  lwd.val = 1,
  legend.cex = 1,
  legend.loc = "bottomright",
  main.title = NULL,
  legend.text = c("From year t's assessment", "From current base model"),
  legend.inset = c(0, 0),
  add.to.plot = FALSE,
  ...
)

Arguments

model	A model object, created by create_rds_file()
hist_probs	A data frame containing the data found in assessment-history-probs.csv
type	"decline" to show probs of spawning biomass declining in year after historical assessment year, "decline_one_year" to show that for just one year (to explain in a talk), "bforty" to show prob of being below ⁠B_40\\%⁠ in the year after the historical assessment year
end	final year for calculations
xLim	range of x (years) axis
add.50	Whether to add horizontal line at 50%
add.50.col	Color for 50% line
one.year	A single year to plot (may automatically work for more years)
add.projs	Whether to add future projections from current base model
num.projs	Number of projection catch levels to show
colors	The colors to use for the lines in the plot
pch	change legend call also if change this
lwd.val	Line width
legend.cex	Legend font size
legend.loc	Legend location
main.title	Main title text
legend.text	Legent title text
legend.inset	Vector for how much to shift the legend, gets parsed to legend( , inset) value, so see ?legend. Will depend on figure size.
add.to.plot	whether to add to an existing plot
...	Arguments passed to combine_historical_probs()

Value

A base R plot

pacific-hake/hake-assessment documentation built on Jan. 14, 2025, 9:12 p.m.