plot_life_cycle: Plot a life cycle diagram from a matrix population model

In Rage: Life History Metrics from Matrix Population Models

Plot a life cycle diagram from a matrix population model

Description

Plots the life cycle diagram illustrated by a matrix population model. This function processes the matrix model and passes the information to the graphViz function in DiagrammeR. See http://rich-iannone.github.io/DiagrammeR/.

Usage

plot_life_cycle(
  matA,
  stages,
  title = NULL,
  shape = "egg",
  fontsize = 10,
  nodefontsize = 12,
  edgecol = "grey",
  node_order = NULL
)

Arguments

matA	A matrix population model (i.e., a square projection matrix)
stages	Optional vector of stage class labels. If missing, it first attempts to infer them from dimnames(matA). If these are also NULL, then reverts to integers 1:ncol(A).
title	Optional title for the plot. Defaults to NULL.
shape	The shape to be used for the stages of the diagram. Any node shape accepted by graphViz is acceptable.
fontsize	Size of the font used in the diagram.
nodefontsize	Size of the font used in the node part of the diagram.
edgecol	Colour of the arrows in the diagram.
node_order	An optional numeric vector giving the order that the nodes should be presented in the plot. Default is 'NULL' whereby the order is the same as 'stages', or row/column names, of the matrix.

Value

An object of class grViz representing the life cycle diagram

Author(s)

Owen R. Jones <[e-mail]>

Examples

matA <- rbind(
  c(0.1, 0, 0, 0, 1.4),
  c(0.5, 0.2, 0, 0, 0),
  c(0, 0.3, 0.3, 0, 0),
  c(0, 0, 0.4, 0.4, 0.1),
  c(0, 0, 0, 0.1, 0.4)
)

plot_life_cycle(matA)

# Change the order of the nodes and give them names
plot_life_cycle(matA,
  stages = c("A", "B", "C", "D", "E"),
  node_order = 5:1
)

Rage documentation built on Sept. 30, 2023, 1:06 a.m.