synthetic_trait_model_specification: Model Specification for Synthetic Traits

In jpmeagher/vbar: Variational Bayes Ancestral Reconstruction

Model Specification for Synthetic Traits

Description

The Phylogenetic Latent Variable Model (PLVM) specified in the package README. Used to illustrate the approach to ancestral reconstruction offered by Variational Inference for the PLVM.

Usage

synthetic_trait_model_specification

Format

A list of length 9:

phylogeny

An object of type phylo with S = 128 terminal taxa and S-1 internal taxa

auxiliary_traits

A named 384x37 matrix of real numbers. Auxiliary traits mapping to synthetic manifest traits.

loading

A named 37x4 matrix of real numbers

auxiliary_trait_precision

A 4-dimensional vector of positive real numbers. Precision with which auxiliary traits are observed.

auxiliary_trait_precision_vec

A D'-dimensional vector of positive real numbers. Precision for each auxiliary trait.

individual_specific_latent_traits

A 384x3 matrix of real numbers. The latent trait associated with each observed manifest trait.

taxon_specific_latent_traits

A 255x3 matrix of real numbers. The latent trait associated with each taxa.

within_taxon_sd

A 3 dimensional vector of real values on the interval (0, 1). Standard deviation of the within-taxon variation.

heritability

A 3 dimensional vector of real values on the interval (0, 1). The heritability of latent traits over the phylogeny.

ordinal_trait_cut_off

A 5-dimensional vector of increasing values. Cut-off points for the ordinal trait mapping

jpmeagher/vbar documentation built on Nov. 22, 2022, 5:48 a.m.