plot_trend: Plot Posterior Trend Estimates

In birp: Testing for Population Trends Using Low-Cost Ecological Count Data

Plot Posterior Trend Estimates

Description

Visualizes posterior trends from a birp object by plotting the median and quantile intervals of the estimated relative densities over time. Optionally, vertical lines can be added to mark epoch boundaries and survey timepoints.

Usage

plot_trend(
  x,
  CI_group = 1,
  n_points = 1000,
  quantiles = c(0.99, 0.9, 0.5, 0.25),
  quantile.col = gray(seq(1, 0, length.out = length(quantiles) + 2)[2:(length(quantiles)
    + 1)]),
  quantile.border = NA,
  median.col = "deeppink",
  median.lwd = 2,
  median.lty = 1,
  epoch.col = "black",
  epoch.lwd = 1,
  epoch.lty = 1,
  times.col = "black",
  times.lwd = 1,
  times.lty = 2,
  log = FALSE,
  xlab = "Time",
  ylab = paste(c("log", "Relative Density")[c(log, TRUE)], collapse = " "),
  main = x$CI_groups[CI_group],
  ...
)

Arguments

x	A birp object containing MCMC trace and model outputs.
CI_group	Integer; Index of the control-intervention group to plot. Default is 1.
n_points	Integer; Number of points to evaluate the trend over time. Default is 1000.
quantiles	Numeric vector; Quantiles to plot as shaded intervals. Must be in (0, 1). Default is c(0.99, 0.9, 0.5, 0.25).
quantile.col	Character vector or color values; Fill colors for quantile polygons. Default is shades of gray.
quantile.border	Character or NA; Border color for quantile polygons. Use NA to omit borders. Default is NA.
median.col	Character; Color of the median trend line. Default is "deeppink".
median.lwd	Numeric; Line width for the median trend. Default is 1.
median.lty	Numeric or character; Line type for the median trend line. Default is 1 (solid).
epoch.col	Character or color specification; Color for lines representing epoch boundaries. Default is "black".
epoch.lwd	Numeric; Line width for epoch boundary lines. Default is 1.
epoch.lty	Numeric or character; Line type for epoch boundary lines. Default is 1 (solid).
times.col	Character or color specification; Color for vertical lines representing measurement times. Default is "black".
times.lwd	Numeric; Line width for measurement time lines. Default is 1.
times.lty	Numeric or character scalar; Line type for measurement time lines. Default is 2 (dashed).
log	Logical; If TRUE, plot relative densities on a logarithmic scale; otherwise plot on the original scale. Default is FALSE.
xlab	Character; Label for the x-axis. Default is "Time".
ylab	Character; Label for the y-axis. Default dynamically set to either "log Relative Density" or "Relative Density".
main	Character; Main title of the plot. Defaults to the name of the selected CI group.
...	Additional graphical parameters passed to the base plot function.

Value

No return value, called for side effects.

See Also

birp

Examples

data <- simulate_birp()
est <- birp(data)
plot_trend(est)

birp documentation built on Nov. 3, 2026, 1:09 a.m.