plot_epoch_pair: Plot joint posterior of two gamma parameters

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

Plot joint posterior of two gamma parameters

Description

Plots a 2D density contour for the joint posterior of two gamma parameters from a birp object.

Usage

plot_epoch_pair(
  x,
  gamma1 = which(!x$post_gamma$is_fix)[1],
  gamma2 = which(!x$post_gamma$is_fix)[2],
  xlab = .getLabelGamma.birp(x, gamma1),
  ylab = .getLabelGamma.birp(x, gamma2),
  xlim = range(x$post_gamma$trace[, c(gamma1, gamma2)]),
  ylim = xlim,
  col = "deeppink",
  diag.col = "black",
  diag.lwd = 1,
  diag.lty = 1,
  zero.col = "black",
  zero.lwd = 1,
  zero.lty = 2,
  print.p = TRUE,
  add = FALSE,
  ...
)

Arguments

x	A birp object.
gamma1	Integer; Index of the first gamma parameter to plot on the x-axis. Default is the first inferred gamma.
gamma2	Integer; Index of the second gamma parameter to plot on the y-axis. Default is the second inferred gamma.
xlab	Character; Label for the x-axis. Default is dynamically set based on gamma1.
ylab	Character; Label for the y-axis. Default is dynamically set based on gamma2.
xlim	Numeric vector of length 2; Optional x-axis limits. Default is the range of gamma1 and gamma2 values.
ylim	Numeric vector of length 2; Optional y-axis limits. Default is the same as xlim.
col	Character or color specification; Color for contour lines. Default is "deeppink".
diag.col	Character or NA; Color of the diagonal line (y=x). Use NA to omit. Default is "black".
diag.lwd	Numeric; Line width of the diagonal line. Default is 1.
diag.lty	Numeric or character; Line type of the diagonal line. Default is 1 (solid).
zero.col	Character or NA; Color of the zero reference lines (at x=0 and y=0). Use NA to omit. Default is "black".
zero.lwd	Numeric; Line width of the zero reference lines. Default is 1.
zero.lty	Numeric or character; Line type of the zero reference lines. Default is 2 (dashed).
print.p	Logical; If TRUE, adds an annotation showing the posterior probability P(gamma1 < gamma2 | data) or P(gamma1 > gamma2 | data). Default is TRUE.
add	Logical; If TRUE, adds the contour plot to an existing plot. Default is FALSE.
...	Additional graphical parameters passed to contour.

Value

No return value; called for side effects (plotting).

See Also

birp

Examples

data <- simulate_birp(timesOfChange = 2)
est <- birp(data, timesOfChange = 2)
plot_epoch_pair(est)

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