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Plot flowfield of expected evolutionary change from a fitted coevfit object

Source: R/coev_plot_flowfield.R
coev_plot_flowfield.Rd

Plot a flowfield of the expected evolutionary dynamics from a fitted coevfit object, with help from the phaseR package.

Usage

coev_plot_flowfield(
  object,
  var1,
  var2,
  nullclines = FALSE,
  limits = c(-2.5, 2.5)
)

Arguments

object

An object of class coevfit

var1

A character string of length one equal to one of the coevolving variables in the model (strictly case-sensitive)

var2

A character string of length one equal to one of the coevolving variables in the model (strictly case-sensitive)

nullclines

Logical (defaults to FALSE); whether to show coloured nullclines to indicate where each variable is at equilibrium, depending on the state of the other

limits

A numeric vector of length 2 (defaults to c(-2.5, 2.5)); specifying the lower limit and the upper limit of the x and y axes.

Value

A flowfield plot drawn directly to the device

Details

The flowfield visualises the change in two coevolving traits depending on their current states, with the direction and strength of change depicting with the direction and size of arrows. If nullclines are included, they represent the parameter combinations where each trait is at equilibrium, depending on the state of the other trait.

If three or more traits were included in the model, other traits are held at their median values during the computations. Note that flowfield plots can potentially produce misleading pictures of coevolutionary dynamics when other traits are held constant in models with three or more traits.

If the plot does not look right, the user might try zooming out from the default parameter space by setting wider limits. For some variables (e.g., continuous and count variables), the default limits may not be suitable.

References

Ringen, E., Martin, J. S., & Jaeggi, A. (2021). Novel phylogenetic methods reveal that resource-use intensification drives the evolution of "complex" societies. EcoEvoRXiv. doi:10.32942/osf.io/wfp95

Sheehan, O., Watts, J., Gray, R. D., Bulbulia, J., Claessens, S., Ringen, E. J., & Atkinson, Q. D. (2023). Coevolution of religious and political authority in Austronesian societies. Nature Human Behaviour, 7(1), 38-45. 10.1038/s41562-022-01471-y

See also

coev_plot_selection_gradient

Author

Scott Claessens scott.claessens@gmail.com, Erik Ringen erikjacob.ringen@uzh.ch

Examples

if (FALSE) { # \dontrun{
# fit dynamic coevolutionary model
fit <- coev_fit(
  data = authority$data,
  variables = list(
    political_authority = "ordered_logistic",
    religious_authority = "ordered_logistic"
  ),
  id = "language",
  tree = authority$phylogeny,
  # additional arguments for cmdstanr::sample()
  chains = 4,
  parallel_chains = 4,
  seed = 1
  )

# plot flow field
coev_plot_flowfield(
  object = fit,
  var1 = "political_authority",
  var2 = "religious_authority"
  )
} # }