Plot a Markov chain with ggplot2 — autoplot.markovchain • markovchain

Creates a ggplot2 representation of a discrete-time Markov chain. Nodes are states and directed edges represent transitions with positive probability. Communicating classes are shown with different node fills.

Usage

autoplot.markovchain(
  object,
  threshold = 0,
  show_probabilities = TRUE,
  digits = 2,
  node_size = 6,
  edge_width = 1,
  type = c("graph", "eigenvalues", "flow", "comparison"),
  steps = 20,
  initial = NULL,
  other = NULL,
  what = c("transition", "stationary"),
  ...
)

Arguments

object: An object of class `markovchain`.
threshold: Minimum transition probability to display. Defaults to 0.
show_probabilities: Logical; whether to label edges with transition probabilities. Defaults to `TRUE`.
digits: Number of digits used to format transition probabilities.
node_size: Size of state nodes in the ggplot2 plot.
edge_width: Minimum width multiplier for transition edges.
type: Type of plot: "graph" (default) draws the transition graph; "eigenvalues" draws the eigenvalues of the transition matrix in the complex plane together with the unit circle; "flow" draws the evolution of the distribution over the states, as computed by redistribute; "comparison" compares object with the chains in other.
steps: Number of steps of the "flow" plot. Defaults to 20. Ignored for the other types.
initial: Initial distribution of the "flow" plot, see redistribute. Defaults to the uniform distribution. Ignored for the other types.
other: For type = "comparison": a markovchain object or a (possibly named) list of them, to be compared with object. All chains must be defined on the same set of states, which are matched by name, so their order may differ. Ignored for the other types.
what: For type = "comparison": "transition" (default) draws the transition matrices side by side as heatmaps on a common probability scale; "stationary" compares the stationary distributions as grouped bars (every chain must then be irreducible). Ignored for the other types.
...: Currently unused, reserved for future extensions.

Value

A ggplot object.

Examples

if (requireNamespace("ggplot2", quietly = TRUE)) {
  weather <- matrix(c(0.7, 0.2, 0.1,
                      0.3, 0.4, 0.3,
                      0.2, 0.45, 0.35),
                    nrow = 3, byrow = TRUE,
                    dimnames = list(c("sunny", "cloudy", "rain"),
                                    c("sunny", "cloudy", "rain")))
  mc <- new("markovchain", states = rownames(weather),
            transitionMatrix = weather, name = "Weather")
  ggplot2::autoplot(mc)
  ggplot2::autoplot(mc, type = "eigenvalues")
  ggplot2::autoplot(mc, type = "flow", steps = 10, initial = "rain")

  # compare with a "stickier" version of the same chain
  sticky <- lazyChain(mc, alpha = 0.5)
  sticky@name <- "Lazy weather"
  ggplot2::autoplot(mc, type = "comparison", other = sticky)
  ggplot2::autoplot(mc, type = "comparison", other = sticky,
                    what = "stationary")
}