Files in jpmeagher/vbar

Variational Bayes Ancestral Reconstruction

LICENSE.md R/ancestral_reconstruction.R R/cavi_auxiliary_traits.R R/cavi_generic_functions.R R/cavi_latent_traits.R R/cavi_loading.R R/cavi_plvm.R R/cavi_updates.R R/data.R R/elbo.R R/initialise_plvm.R R/kernels.R R/manifest_trait_metadata.R R/manipulate_phylo.R R/namespace.R R/reparameterise_phylogenetic_ou.R R/simulate_phylogenetic_gaussian_process.R README.Rmd README.md data-raw/bat_echolocation_calls.R data-raw/bat_phylogeny.R data-raw/synthetic_data.R man/bat_echolocation_calls.Rd man/bat_phylogeny.Rd man/cavi_plvm.Rd man/check_trait_type.Rd man/compare_metadata_to_df.Rd man/compute_auxiliary_trait_elbo.Rd man/compute_continuous_auxiliary_trait_elbo.Rd man/compute_individual_specific_latent_trait_elbo.Rd man/compute_individual_specific_latent_trait_expectation.Rd man/compute_individual_specific_latent_trait_precision.Rd man/compute_internal_taxon_specific_latent_trait_expectation.Rd man/compute_internal_taxon_specific_latent_trait_precision.Rd man/compute_loading_elbo.Rd man/compute_loading_expectation.Rd man/compute_loading_row_conditional_mean_weight_matrix.Rd man/compute_loading_row_precision.Rd man/compute_loading_row_precision_list.Rd man/compute_nominal_auxiliary_trait_elbo.Rd man/compute_ordinal_auxiliary_trait_elbo.Rd man/compute_plvm_elbo.Rd man/compute_scaled_conditional_row_variance_vector.Rd man/compute_taxon_specific_latent_trait_elbo.Rd man/compute_terminal_taxon_specific_latent_trait_expectation.Rd man/compute_terminal_taxon_specific_latent_trait_precision.Rd man/exp_quad_kernel.Rd man/gaussian_outer_product_expectation.Rd man/heritable_amplitude_objective.Rd man/initialise_auxiliary_traits.Rd man/initialise_individual_specific_latent_traits.Rd man/initialise_loading.Rd man/initialise_loading_ard_precision.Rd man/initialise_plvm.Rd man/initialise_precision.Rd man/map_precision_to_auxiliary_traits.Rd man/nominal_inverse_link.Rd man/nominal_link.Rd man/nominal_probit_auxiliary_expectation.Rd man/nominal_probit_normalising_constant.Rd man/ordinal_inverse_link.Rd man/ordinal_link.Rd man/ordinal_probit_normalising_constant.Rd man/ordinal_trait_cut_off_objective.Rd man/ou_kernel.Rd man/reparameterise_phylogenetic_ou.Rd man/scale_phylo.Rd man/simulate_phylogenetic_ou.Rd man/specify_manifest_trait_metadata.Rd man/synthetic_trait_model_specification.Rd man/synthetic_traits.Rd man/update_discrete_auxiliary_traits.Rd man/update_loading_ard_precision.Rd man/update_precision.Rd man/variational_ancestral_reconstruction.Rd man/within_taxon_amplitude_objective.Rd tests/testthat.R tests/testthat/test-ancestral_reconstruction.R tests/testthat/test-cavi_auxiliary_traits.R tests/testthat/test-cavi_generic_functions.R tests/testthat/test-cavi_latent_traits.R tests/testthat/test-cavi_loading.R tests/testthat/test-cavi_plvm.R tests/testthat/test-cavi_updates.R tests/testthat/test-elbo.R tests/testthat/test-initialise_plvm.R tests/testthat/test-kernels.R tests/testthat/test-manifest_trait_metadata.R tests/testthat/test-manipulate_phylo.R tests/testthat/test-reparameterise_phylogenetic_ou.R tests/testthat/test-simulate_phylogenetic_gaussian_process.R