Test objects for the PCMBase package

A list containing simulated trees, trait-values and model objects for tests and examples of the PCMBase package

PCMBaseTestObjects

Format

This is a list containing the following named elements representing parameters of BM, OU and MixedGaussian models with up to three traits and up to two regimes, model objects, simulated trees with partition of their nodes in up to two parts (corresponding to the two regimes), and trait data simulated on these trees.

a.H, b.H

H matrices for OU models for regimes 'a' and 'b'.

a.Theta, b.Theta

Theta vectors for OU models for regimes 'a' and 'b'.

a.Sigma_x, b.Sigma_x

Sigma_x matrices for BM and OU models for regimes 'a' and 'b'.

a.Sigmae_x, b.Sigmae_x

Sigmae_x matrices regimes 'a' and 'b'.

a.X0, b.X0

X0 vectors for regimes 'a' and 'b'.

H

an array resulting from abind(a.H, b.H).

Theta

a matrix resulting from cbind(Theta.a, Theta.b).

Sigma_x

an array resulting from abind(a.Sigma_x, b.Sigma_x).

Sigmae_x

an array resulting from abind(a.Sigmae_x, b.Sigmae_x).

model.a.1, model.a.2, model.a.3

univariate models with a single regime for each of 3 traits.

model.a.1.Omitted_X0

same as model.a.1 but omitting X0; suitable for nesting in an MGPM model.

model.a.123, model.b.123

single-regime 3-variate models.

model.a.123.Omitted_X0

single-regime 3-variate model with omitted X0 (suitable for nesting in an MGPM.

model.a.123.Omitted_X0__bSigmae_x

same as model.a.123.Omitted_X0 but with the value of Sigmae_x copied from model.b.123.

model.a.123.Omitted_X0__Omitted_Sigmae_x

same as model.a.123 but omitting X0 and Sigmae_x.

model.b.123.Omitted_X0, model.b.123.Omitted_X0__Omitted_Sigmae_x

analogical to corresponding model.a.123...

model.ab.123

a two-regime 3-variate model.

model.ab.123.bSigmae_x

a two-regime 3-variate model having Sigmae_x from b.Sigmae_x.

model_MixedGaussian_ab

a two-regime MGPM model with a local Sigmae_x for each regime.

model_MixedGaussian_ab_globalSigmae_x

a two-regime MGPM model with a global Sigmae_x.

N

number of tips in simulated trees

tree_15_tips

a tree of 15 tips used for testing clade extraction.

tree.a

a tree with one part only (one regime)

tree.ab

a tree partitioned in two parts (two regimes)

traits.a.1

trait values simulated with model.a.1.

traits.a.123

trait values simulated with model.a.123.

traits.a.2

trait values simulated with model.a.2.

traits.a.3

trait values simulated with model.a.3.

traits.ab.123

trait values simulated with model.ab.123 on tree.ab.

tree

a tree of 5 tips used for examples.

X

3-trait data for 5 tips used together with tree for examples.

model.OU.BM

a mixed Gaussian phylogenetic model for 3 traits and an OU and BM regime used in examples.