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Plot posterior beta density curves for all transition matrix entries

Source: R/CrI_matrix.R
plot_transition_density.Rd

Creates a ggplot2 visualisation arranged as an \(n \times n\) matrix of density plots, mirroring the structure of the population projection matrix. Each panel shows the full marginal posterior beta distribution for one transition probability, with the credible interval region shaded. Columns correspond to source stages (from) and rows to destination stages (to), including the dead fate as the bottom row.

Usage

plot_transition_density(
  TF,
  N,
  P = NULL,
  priorweight = -1,
  ci = 0.95,
  stage_names = NULL,
  include_dead = TRUE,
  title = "Posterior transition probability densities"
)

Arguments

TF

A list of two matrices, T and F, as output by projection.matrix.

N

A vector of observed stage distribution at the start of the transition period.

P

A matrix of priors for each column. Defaults to uniform.

priorweight

Total weight for each column of prior as a percentage of sample size, or 1 if negative. Defaults to -1 (uninformative).

ci

Credible interval width as a probability between 0 and 1. The shaded region in each panel covers this interval. Defaults to 0.95.

stage_names

Optional character vector of stage names in the same order as the columns of the transition matrix. If NULL, names are taken from colnames(TF$T), or generic labels are used.

include_dead

Logical. Whether to include the dead fate as the bottom row of the matrix plot. Defaults to TRUE.

title

Character. Plot title.

Value

A ggplot object arranged as an \(n \times n\) grid (or \((n+1) \times n\) when include_dead = TRUE), with source stages as columns and destination stages as rows.

See also

transition_CrI, plot_transition_CrI.

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)

# Include dead fate as bottom row (default)
plot_transition_density(TF, N,
                        stage_names = c("plantula", "juvenile", "adult"))


# Transitions only, no dead row
plot_transition_density(TF, N,
                        stage_names = c("plantula", "juvenile", "adult"),
                        include_dead = FALSE)