plot_phase: Create plot of the relative fishing intensity in year t-1...
In pacific-hake/hake-assessment: Stock Assessment for Pacific Hake

plot_phase

R Documentation

Create plot of the relative fishing intensity in year t-1 against relative spawning biomass in year t, as a historical look at the fishery for the MCMC given by model

Description

Create plot of the relative fishing intensity in year t-1 against relative spawning biomass in year t, as a historical look at the fishery for the MCMC given by model

Usage

plot_phase(
  model,
  start_yr,
  end_yr,
  x_lim = c(0, 1.5),
  y_lim = c(0, 1.2),
  biomass_scale = 1e+06,
  init_lbl_x_off = 0,
  init_lbl_y_off = 0,
  final_lbl_x_off = 0,
  final_lbl_y_off = 0,
  cross_line_width = 1,
  cross_line_color = "grey",
  title_y_font_size = axis_title_font_size,
  detail_b40_outliers = FALSE,
  detail_fspr_outliers = FALSE,
  show_joint_prob_points = FALSE,
  joint_point_color = "purple"
)

Arguments

`model`	A model, created by `create_rds_file()`
`start_yr`	The minimum year in the plot
`end_yr`	The maximum year in the plot
`x_lim`	Vector of two values for minimum and maximum x-axis values
`y_lim`	Vector of two values for minimum and maximum y-axis values
`biomass_scale`	Amount to divide biomass by so the axis has small nums
`init_lbl_x_off`	Initial year label x offset in units of axis
`init_lbl_y_off`	Initial year label y offset in units of axis
`final_lbl_x_off`	Final year label x offset in units of axis
`final_lbl_y_off`	Final year label y offset in units of axis
`detail_b40_outliers`	Shade the part of the plot less that B40, plot the missing points at the lower 2.5% of the depletion distribution, draw a box around those points and show a label with the description
`detail_fspr_outliers`	Shade the part of the plot greater than FSPR = 1, plot the missing points at the upper 2.5% of the FSPR distribution, draw a box around those points and show a label with the description
`show_joint_prob_points`	Logical. If `TRUE`, show jittered points near the X and Y points and a scatterplot in the upper left corner showing where the joint probabilities are `TRUE`
`joint_point_color`	If `show_joint_prob_points` is `TRUE`, this is the color of those points