Package index • treeshapesim

Simulate trees

Ultrametric trees with separately controlled imbalance and branching times.

sim_tree_shape(): Ultrametric trees with given imbalance and branching-time parameters
sim_tree_target(): Simulate trees near target values of gamma and Colless

Target shapes and grids

Shape statistics, calibration of the parameters and grids of tree shapes.

tree_shape(): Gamma statistic and Colless index of a tree
calibrate_shape(): Calibrate the shape parameters for a number of tips
shape_params(): Shape parameters that give target mean values of gamma and Colless
shape_grid(): Grid of tree shapes

Fit empirical trees

Estimate the shape parameters of a tree on the scale of the simulations.

fit_shape(): Estimate the shape parameters of a tree

Building blocks

Topology, internode intervals and their combination.

rtopology_beta(): Random topology under Aldous' beta-splitting model
intervals_lineage_rate(): Internode intervals of a pure-birth process with lineage-dependent rates
assign_ages(): Assign node ages to a topology from internode intervals