Rage: plot_life_cycle – R documentation

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plot_life_cycle

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"
)

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.

Value

An object of class grViz representing the life cycle diagram

Author(s)

Owen R. Jones <jones@biology.sdu.dk>

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)

Rage

Life History Metrics from Matrix Population Models

v1.0.0

GPL-3

Authors

Patrick Barks [aut] (<https://orcid.org/0000-0002-5947-8151>), Danny Buss [ctb], Pol Capdevila [aut] (<https://orcid.org/0000-0002-2842-4302>), Hal Caswell [aut] (<https://orcid.org/0000-0003-4394-6894>), Judy P. Che-Castaldo [aut] (<https://orcid.org/0000-0002-9118-9202>), John Jackson [aut] (<https://orcid.org/0000-0002-4563-2840>), Tamora James [aut] (<https://orcid.org/0000-0003-1363-4742>), Owen Jones [aut, cre] (<https://orcid.org/0000-0001-5720-4686>), Sam Levin [aut] (<https://orcid.org/0000-0002-3289-9925>), William K. Petry [aut] (<https://orcid.org/0000-0002-5230-5987>), Roberto Salguero-Gomez [aut] (<https://orcid.org/0000-0002-6085-4433>), Caroline Schuette [ctb] (<https://orcid.org/0000-0002-2063-8736>), Iain Stott [aut] (<https://orcid.org/0000-0003-2724-7436>), Chelsea C. Thomas [aut] (<https://orcid.org/0000-0002-8155-9353>)

Initial release