heritable_amplitude_objective: Objective function for heritable amplitude
In jpmeagher/vbar: Variational Bayes Ancestral Reconstruction

heritable_amplitude_objective

R Documentation

Objective function for heritable amplitude

Description

Update the heritable amplitude by optimising the ELBO for taxon-specific latent traits.

Usage

heritable_amplitude_objective(
  par,
  i,
  heritable_amplitude,
  length_scale,
  taxon_specific_latent_trait_expectation,
  taxon_specific_latent_trait_outer_product_expectation,
  taxon_specific_latent_trait_covariance,
  phy,
  phylogenetic_gp,
  perform_checks = TRUE
)

Arguments

`par`	A real value on the unit interval. The heritable amplitude.
`i`	An integer value between 1 and L. The index for the heritable amplitude to be optimised.
`heritable_amplitude`	An L-dimensional vector of values on the unit interval. The current amplitude of the phylogenetic OU process. Note that this is the square root of the variance and so should be thought of as a standard deviation parameter.
`length_scale`	A positive real-valued scalar. The amplitude of the phylogenetic OU process. Note that this is the square root of the variance and so should be thought of as a standard deviation parameter.
`taxon_specific_latent_trait_expectation`	A (2S - 1)xL matrix of real values. The expected value of the taxon specific latent traits.
`taxon_specific_latent_trait_outer_product_expectation`	A LxLx(2S - 1) array of real values. The expected outer product of taxon specific latent traits under the approximate posterior.
`taxon_specific_latent_trait_covariance`	A LxLx(2S - 1) array of real values. The covariance of taxon specific latent traits under the approximate posterior.
`phy`	An object of class "phylo".
`phylogenetic_gp`	A (2S - 1)x2xL array of real values. Hyperparameters for the Gaussian process over phy.
`perform_checks`	Logical. Check if function inputs are specified correctly.