Man pages for jpmeagher/vbar
Variational Bayes Ancestral Reconstruction
| bat_echolocation_calls | Bat scholocation call recordings |
| bat_phylogeny | Bat Phylogeny |
| cavi_plvm | CAVI for the PLVM |
| check_trait_type | Check trait type specification |
| compare_metadata_to_df | Compare Metadata to Manifest Traits |
| compute_auxiliary_trait_elbo | Auxiliary Trait ELBO |
| compute_continuous_auxiliary_trait_elbo | Continuous Trait ELBO |
| compute_individual_specific_latent_trait_elbo | Individual Specific Latent Trait Trait ELBO |
| compute_individual_specific_latent_trait_expectation | Compute Individual-specific Latent Trait Expectation |
| compute_individual_specific_latent_trait_precision | Compute Individual-specific Latent Trait Precision |
| compute_internal_taxon_specific_latent_trait_expectation | Compute Internal Taxon-specific Latent Trait Expectation |
| compute_internal_taxon_specific_latent_trait_precision | Compute Internal Taxon-specific Latent Trait Precision |
| compute_loading_elbo | Loading ELBO |
| compute_loading_expectation | Compute Loading Expectation |
| compute_loading_row_conditional_mean_weight_matrix | Loading Row Conditional Mean Weight |
| compute_loading_row_precision | Compute precision for a row of the Loading Matrix |
| compute_loading_row_precision_list | Compute precision for each row of the Loading Matrix |
| compute_nominal_auxiliary_trait_elbo | Nominal Trait ELBO |
| compute_ordinal_auxiliary_trait_elbo | Ordinal Trait ELBO |
| compute_plvm_elbo | PLVM ELBO |
| compute_scaled_conditional_row_variance_vector | Compute the Scaled Conditional Row Variance of the Loading |
| compute_taxon_specific_latent_trait_elbo | Taxon Specific Latent Trait Trait ELBO |
| compute_terminal_taxon_specific_latent_trait_expectation | Compute Terminal Taxon-specific Latent Trait Expectation |
| compute_terminal_taxon_specific_latent_trait_precision | Compute Terminal Taxon-specific Latent Trait Precision |
| exp_quad_kernel | The Exponentiated Quadratic kernel |
| gaussian_outer_product_expectation | Compute outer product expectation |
| heritable_amplitude_objective | Objective function for heritable amplitude |
| initialise_auxiliary_traits | Initialise Auxiliary Traits |
| initialise_individual_specific_latent_traits | Initialise the Individual-specific latent traits |
| initialise_loading | Initialis Loading |
| initialise_loading_ard_precision | Initialise ARD Precision |
| initialise_plvm | Initialise CAVI for a PLVM |
| initialise_precision | Initialise Precision |
| map_precision_to_auxiliary_traits | Map Precision Parameters to Auxiliary Traits |
| nominal_inverse_link | Nominal Inverse Link Function |
| nominal_link | Nominal Link Function |
| nominal_probit_auxiliary_expectation | Expectation of multinomial probit auxiliary variables |
| nominal_probit_normalising_constant | Nominal Probit Normalising Constant |
| ordinal_inverse_link | Ordinal Trait Inverse Link Function |
| ordinal_link | Ordinal Trait Link function |
| ordinal_probit_normalising_constant | Ordinal Probit Normalising Constant |
| ordinal_trait_cut_off_objective | Objective function for the ordinal trait cut off point |
| ou_kernel | The Ornstein-Uhlenbeck kernel |
| reparameterise_phylogenetic_ou | Reparameterise phylogenetic Ornstein-Uhlenbeck |
| scale_phylo | Rescale a Phylogenetic tree |
| simulate_phylogenetic_ou | Simulate a Phylogenetic Ornstein-Uhlenbeck process |
| specify_manifest_trait_metadata | Specify Manifest Trait Metadata |
| synthetic_trait_model_specification | Model Specification for Synthetic Traits |
| synthetic_traits | Synthetic Phenotypic Traits |
| update_discrete_auxiliary_traits | Update Discrete Auxiliary Traits |
| update_loading_ard_precision | Update ARD loading precision |
| update_precision | Update auxiliary trait precision |
| variational_ancestral_reconstruction | Ancestral Trait Reconstruction |
| within_taxon_amplitude_objective | Objective function for within-taxon amplitude |
