Prepare phylogenetic data for evolutionary models — prepare_phylo

Converts a phylogeny, species niche estimates, and environmental data into the list format required by the Stan evolutionary models.

Usage

prepare_phylo_data(
  phy,
  species,
  niche_params,
  occ_data,
  env_m_data,
  mu_anc_prior = c(0, 0),
  mu_anc_sigma = c(5, 5),
  rate_mu_scale = 1,
  rate_log_sigma_scale = 0.5,
  z_rho_anc_prior = 0,
  z_rho_anc_sigma = 1,
  rate_rho_scale = 0.5,
  alpha_mu_scale = c(1, 1),
  sigma_sq_mu_scale = c(1, 1),
  alpha_log_sigma_scale = c(1, 1),
  sigma_sq_log_sigma_scale = c(1, 1),
  alpha_rho_scale = 1,
  sigma_sq_rho_scale = 1,
  grain_size = 1
)

Arguments

phy: An object of class phylo from the ape package, representing the phylogenetic tree of the species.
species: Character vector of species names, in the same order as the rows of niche_params.
niche_params: A matrix or data.frame with columns: mu_1, mu_2 (centroid dimensions), sigma_1, sigma_2 (tolerances), rho (correlation), one row per species.
occ_data: A list of matrices, one per species, with environmental values at occurrence points.
env_m_data: A list of matrices, one per species, with environmental values at background points.
mu_anc_prior: Numeric vector of length 2, prior mean for ancestral centroid.
mu_anc_sigma: Numeric vector of length 2, prior SD for ancestral centroid.
rate_mu_scale: Numeric, scale for half-normal prior on BM rate of centroid.
rate_log_sigma_scale: Numeric, scale for half-normal prior on BM rate of log tolerances.
z_rho_anc_prior: Numeric, prior mean for ancestral z_rho (atanh(rho)).
z_rho_anc_sigma: Numeric, prior SD for ancestral z_rho.
rate_rho_scale: Numeric, scale for half-normal prior on BM rate of z_rho.
alpha_mu_scale: Numeric vector of length 2, scale for prior on OU alpha (centroid).
sigma_sq_mu_scale: Numeric vector of length 2, scale for prior on OU sigma^2 (centroid).
alpha_log_sigma_scale: Numeric vector of length 2, scale for prior on OU alpha (log tolerances).
sigma_sq_log_sigma_scale: Numeric vector of length 2, scale for prior on OU sigma^2 (log tolerances).
alpha_rho_scale: Numeric, scale for prior on OU alpha (rho).
sigma_sq_rho_scale: Numeric, scale for prior on OU sigma^2 (rho).
grain_size: Integer, grainsize for reduce_sum parallelisation.

Value

A named list suitable for passing to fit_evolution() as the stan_data argument.