create_tree: Generate a simulated tree

In cfhammill/hierarchyTrees: Code for testing taxonomy tree models

Description

Create a simulated tree from a noise sd, named vectors of leaf effects, volumes, individual effects, metadata, and an initial tree

Usage

create_tree(noise_sd, leaf_effects, leaf_volumes, indiv_effects, metadata,
  base_tree, intercept_sd = 0, extra_effects = NA)

Arguments

noise_sd	What should the sd of the gaussian noise added to observations be
leaf_effects	A named vector of effects to apply to the leaves
indiv_effects	A vector of individual level effects
metadata	A vector containing a covariate with elements matching the elements of the indiv effects / tree volumes.
base_tree	A tree indicating the ontology, should contain volumes already to be overwritten.
extra_effects	A named vector of extra effects to be applied at nodes. Default NA for no extra effects
leaf_volume	A named vector of scaling constants to be applied to the leaf nodes, converting them to volume scale.

Value

A two element list containing

1. The simulated tree

2. A vector with the composite leaf_effects generated by adding extra_effects to leaf_effects where applicable.

cfhammill/hierarchyTrees documentation built on Feb. 8, 2020, 2:54 a.m.