plot_boot_density: Make density plots of bootstrapped parameters and add...

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

Make density plots of bootstrapped parameters and add quantiles as vertical lines.

Description

Make density plots of bootstrapped parameters and add quantiles as vertical lines.

Usage

plot_boot_density(
  data,
  x_name,
  density_args = list(from = NULL, to = NULL),
  plot_args = list(xlab = NULL, ylab = "density", main = "", type = "l"),
  quantile_draw = FALSE,
  quantile_args = list(probs = c(0.05, 0.5, 0.95)),
  quantile_abline_args = list(lty = c(3, 2, 3), lwd = c(2, 2, 2), lend = "butt"),
  col_shade = "gray50",
  add_text_nsim = FALSE
)

Arguments

data	a numeric matrix or data frame that can be coerced to a numeric matrix where rows are runs and columns represent parameters or variables.
x_name	column name of a variable x to plot
density_args	arguments passed to stats::density density (excluding x)
plot_args	arguments passed to base::plot plot (excluding x and y)
quantile_draw	logical. Should quantiles of x be added to the plot as vertical lines? (e.g. confidence limits and median)
quantile_args	arguments passed to stats::quantile quantile for computing quantiles of x to add to plot as vertical lines
quantile_abline_args	arguments to pass to graphics::abline abline when plotting quantiles as vertical lines (excluding v)
col_shade	color for shading density region
add_text_nsim	logical. Should the number of simulation runs (nsim) in data be added as text to the plots?

Author(s)

Nikolai Klibansky

Examples

## Not run: 
nsim <- 100
data <- data.frame("M"=runif(nsim,0.19, 2.1),"lwb"=rnorm(nsim,mean=3))
par(mfrow=c(2,2))
plot_boot_density(data,"M")
plot_boot_density(data,"M",add_text_nsim = TRUE)
plot_boot_density(data,"lwb")
plot_boot_density(data,"lwb",add_text_nsim = TRUE,quantile_draw=TRUE,col_shade=rgb(0,0,1,0.5))

## End(Not run)

nikolaifish/bamExtras documentation built on July 21, 2023, 8:26 a.m.