Plot estimated trait values from a fitted coevfit object

Produce a pairs plot of the estimated trait values for taxa from a fitted coevfit object. The plot includes scatterplot(s) of median estimated trait values, heatmap(s) of median estimated trait values, and density plots of the marginal distributions for each variable with associated posterior uncertainty.

coev_plot_trait_values(
  object,
  variables = NULL,
  ndraws = 50,
  tree_id = NULL,
  xlim = NULL,
  ylim = NULL
)

Arguments

object

An object of class coevfit

variables

If NULL (default), the function returns a pairs plot including all coevolving variables from the model. Otherwise, a character vector declaring the variables to be included.

ndraws

An integer indicating the number of draws to return in the density plots on the diagonal. The default and maximum number of draws is the size of the posterior sample.

tree_id

An integer indicating the tree ID to use when making posterior predictions. Set to NULL by default, which will use draws from every tree, integrating phylogenetic uncertainty.

xlim

Limits for the x-axis. If NULL (default), limits are set to the minimum and maximum estimated trait values.

ylim

Limits for the y-axis. If NULL (default), limits are set to the minimum and maximum estimated trait values.

Value

A patchwork of ggplot objects

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

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
  )

# pairs plot of trait values
coev_plot_trait_values(fit)
} # }