plot_boot_phase: Phase plots for bootstrapped data

In nikolaifish/bamExtras: Functions and Data in Support of Stock Assessments with the Beaufort Assessment Model (BAM)

Phase plots for bootstrapped data

Description

Bivariate scatter plots, specially formatted for making phase plots for stock and fishery status results.

Usage

plot_boot_phase(
  x,
  y,
  xref = NULL,
  yref = NULL,
  col_point = rgb(0, 0, 0, 0.2),
  col_quant = "green4",
  col_ref = "black",
  col_text = "blue",
  probs = c(0.05, 0.95),
  text_x_adj = c(0, 0, 0, 0),
  text_y_adj = c(0, 0, 0, 0),
  ...
)

Arguments

x	x values from bootstrapping. numeric vector
y	y values from bootstrapping. numeric vector
xref	x reference value (e.g. base run value).
yref	y reference value (e.g. base run value).
col_point	color for (x,y) points
col_quant	color for quantile lines
col_ref	color for (xref,yref) points
col_text	color for percentages plotted in each quadrant
probs	quantile probabilities to compute length of error bars.
text_x_adj	text (percentages in each quadrant) adjustment to x
text_y_adj	text (percentages in each quadrant) adjustment to y
...	other parameters to pass to plot

Author(s)

Nikolai Klibansky

Examples

nsim <- 1000
x <- rnorm(n=nsim,mean=1.1,sd=.2)
y <- 1*(1/x)+rnorm(n=nsim,mean=0.1,sd=.1)
par(mfrow=c(2,2))
plot_boot_phase(x,y)
plot_boot_phase(x,y,xref=1.2,yref=1.1)
plot_boot_phase(x,y,xref=1.2,yref=1.1,xlab="F/Fmsy",ylab="SSB/SSBmsy")
plot_boot_phase(x,y,xref=1.2,yref=1.1,xlab="F/Fmsy",ylab="SSB/SSBmsy",col_point=rainbow(nsim,alpha=0.3))

nikolaifish/bamExtras documentation built on April 17, 2025, 9:44 p.m.