PCMDefaultModelTypes: Class names for the the default PCM and MGPM model types

In venelin/PCMBase: Simulation and Likelihood Calculation of Phylogenetic Comparative Models

Class names for the the default PCM and MGPM model types

Description

Utility functions returning named character vector of the model class-names for the default model types used for PCM and MixedGaussian model construction.

Usage

PCMDefaultModelTypes()

MGPMDefaultModelTypes()

Value

Both, PCMFDefaultModelTypes and MGPMDefaultModelTypes return a character string vector with named elements (A,B,C,D,E,F) defined as follows (Mitov et al. 2019a):

A.

BM (H = 0, diagonal \Sigma): BM, uncorrelated traits.

B.

BM (H = 0, symmetric \Sigma): BM, correlated traits.

C.

OU (diagonal H, diagonal \Sigma): OU, uncorrelated traits.

D.

OU (diagonal H, symmetric \Sigma): OU, correlated traits, but simple (diagonal) selection strength matrix.

E.

OU (symmetric H, symmetric \Sigma): An OU with nondiagonal symmetric H and nondiagonal symmetric \Sigma.

F.

OU (asymmetric H, symmetric \Sigma): An OU with nondiagonal asymmetric H and nondiagonal symmetric \Sigma.

The only difference between the two functions is that the model types returned by PCMFDefaultModelTypes have a global parameter X0, while the model types returned by MGPMFDefaultModelTypes have an omitted parameter X0.

References

[Mitov et al. 2019a] Mitov, V., Bartoszek, K., & Stadler, T. (2019). Automatic generation of evolutionary hypotheses using mixed Gaussian phylogenetic models. Proceedings of the National Academy of Sciences of the United States of America, 35, 201813823. http://doi.org/10.1073/pnas.1813823116

See Also

Args_MixedGaussian_MGPMDefaultModelTypes

venelin/PCMBase documentation built on March 14, 2024, 8:24 p.m.