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Plot beta credible intervals for transition matrix entries

Source: R/CrI_matrix.R
plot_transition_CrI.Rd

Creates a ggplot2 visualisation of the posterior mean transition probabilities and their credible intervals for each stage, including the probability of dying. Each panel shows the fate distribution from one source stage.

Usage

plot_transition_CrI(
  cri,
  include_dead = TRUE,
  title = "Posterior transition probabilities with credible intervals"
)

Arguments

cri

A data frame as returned by transition_CrI.

include_dead

Logical. Whether to include the dead fate in the plot. Defaults to TRUE.

title

Character. Plot title. Defaults to "Posterior transition probabilities with credible intervals".

Value

A ggplot object.

See also

transition_CrI for computing the credible intervals.

Examples

T_mat <- matrix(c(0.5, 0.3, 0.0,
                  0.2, 0.4, 0.1,
                  0.0, 0.1, 0.7), nrow = 3, ncol = 3)
F_mat <- matrix(c(0.0, 0.0, 1.5,
                  0.0, 0.0, 0.0,
                  0.0, 0.0, 0.0), nrow = 3, ncol = 3)
TF <- list(T = T_mat, F = F_mat)
N  <- c(10, 5, 8)

cri <- transition_CrI(TF, N, stage_names = c("plantula", "juvenile", "adult"))

# Include dead fate (default)
plot_transition_CrI(cri)


# Exclude dead fate
plot_transition_CrI(cri, include_dead = FALSE)