Package index • coevolve

Datasets

authority: Political and religious authority in Austronesian societies
primates: Brain weight, body weight, diet, and sociality in primates
repeated: Example dataset with repeated observations

Fit

coev_fit(): Fit Bayesian dynamic coevolutionary model in Stan
coev_make_stancode(): Make Stan code for dynamic coevolutionary model
coev_make_standata(): Make Stan data for dynamic coevolutionary model

Summarise

print(<coevfit>): Print a summary of a fitted model represented by a coevfit object
summary(<coevfit>): Create a summary of a fitted model represented by a coevfit object

Plot

plot(<coevfit>): Trace and density plots for coevfit objects
pairs(<coevfit>): Create a matrix of output plots from a coevfit object
coev_plot_delta_theta(): Plot delta theta values from a fitted coevfit object
coev_plot_flowfield(): Plot flowfield of expected evolutionary change from a fitted coevfit object
coev_plot_pred_series(): Plot a predicted coevolutionary time series from a fitted coevfit object
coev_plot_predictive_check(): Plot predictive check from a fitted coevfit object
coev_plot_selection_gradient(): Plot selection gradient heatmap from a fitted coevfit object
coev_plot_trait_values(): Plot estimated trait values from a fitted coevfit object

Extract

extract_samples(): Extract samples (draws) from a fitted coevfit object
coev_ancestral_states(): Extract ancestral state estimates from a fitted coevolutionary model

Expose

stancode(): Expose the Stan code of a fitted model represented by a coevfit object
standata(): Expose the Stan data list for a fitted model represented by a coevfit object

Calculate

coev_calculate_delta_theta(): Calculate delta theta from a fitted coevfit object
coev_calculate_theta(): Calculate equilibrium trait values (theta) for a fitted coevfit object
coev_pred_series(): Predict a co-evolutionary time series from a fitted coevfit object

Save

save_coevfit(): Save a fitted coevfit object to a file

Simulate

coev_simulate_coevolution(): Simulate the coevolution of multiple variables in discrete time steps

Internal S3 methods

draws(<jax_fit>): Extract draws from jax_fit object
draws(<nutpie_fit>): Extract draws from nutpie_fit object
metadata(<jax_fit>): Extract metadata from jax_fit object
metadata(<nutpie_fit>): Extract metadata from nutpie_fit object
summary(<jax_fit>): Summary statistics for jax_fit object
summary(<nutpie_fit>): Compute summary statistics for nutpie_fit object