# two small FBD trees (each with at least one sampled ancestor),
# read as one sample ('n=1') with two replicates ('nr=2') -- see
# 'examples/trees/two_FBD_trees.tre' and the "Reading a tree from
# Newick" section of the online documentation for how this file was
# produced and what 'n'/'nr' do here
trs <- read_tree(n=1, nr=2, file_path="examples/trees/two_FBD_trees.tre")

# per-branch relaxed-clock rates, drawn independently of the clock model
# below; mean 1 in real space (meanlog = -sdlog^2 / 2), sdlog=0.5 as in
# Douglas et al. (2025)'s own empirical analyses ('clockSD')
n_rec_br := n_rec_branches(tree=trs)
br_specific_rel_rate ~ lognormal(n_nr_from=n_rec_br, meanlog=-0.125, sdlog=0.5, log_space="true")

# Gamma-spike punctuated relaxed clock (Douglas et al. 2025), with
# clock_rate/spike_mean/spike_shape as in their empirical analyses
phylo := gamma_spike_clock(tree=trs, attr_name="mutation_rate", clock_rate=0.001, spike_mean=0.01, spike_shape=2.0, br_specific_rel_rate=br_specific_rel_rate)