Man pages for ddtlcm
Latent Class Analysis with Dirichlet Diffusion Tree Process Prior
| add_leaf_branch | Add a leaf branch to an existing tree tree_old |
| add_multichotomous_tip | Add a leaf branch to an existing tree tree_old to make a... |
| add_one_sample | Functions to simulate trees and node parameters from a DDT... |
| add_root | Add a singular root node to an existing nonsingular tree |
| a_t_one | Compute divergence function |
| attach_subtree | Attach a subtree to a given DDT at a randomly selected... |
| a_t_two | Compute divergence function |
| compute_IC | Compute information criteria for the DDT-LCM model |
| create_leaf_cor_matrix | Create a tree-structured covariance matrix from a given tree |
| data_synthetic | Synthetic data example |
| ddtlcm_fit | MH-within-Gibbs sampler to sample from the full posterior... |
| ddtlcm-package | ddtlcm: Latent Class Analysis with Dirichlet Diffusion Tree... |
| div_time | Sample divergence time on an edge uv previously traversed by... |
| draw_mnorm | Efficiently sample multivariate normal using precision matrix... |
| expit | The expit function |
| exp_normalize | Compute normalized probabilities: exp(x_i) / sum_j exp(x_j) |
| H_n | Harmonic series |
| initialize | Initialize the MH-within-Gibbs algorithm for DDT-LCM |
| initialize_hclust | Estimate an initial binary tree on latent classes using... |
| initialize_poLCA | Estimate an initial response profile from latent class model... |
| initialize_randomLCM | Provide a random initial response profile based on latent... |
| J_n | Compute factor in the exponent of the divergence time... |
| log_expit | Numerically accurately compute f(x) = log(x / (1/x)). |
| logit | The logistic function |
| logllk_ddt | Calculate loglikelihood of a DDT, including the tree... |
| logllk_ddt_lcm | Calculate loglikelihood of the DDT-LCM |
| logllk_div_time_one | Compute loglikelihood of divergence times for a(t) = c/(1-t) |
| logllk_div_time_two | Compute loglikelihood of divergence times for a(t) =... |
| logllk_lcm | Calculate loglikelihood of the latent class model,... |
| logllk_location | Compute log likelihood of parameters |
| logllk_tree_topology | Compute loglikelihood of the tree topology |
| parameter_diet | Parameters for the HCHS dietary recall data example |
| plot.ddt_lcm | Create trace plots of DDT-LCM parameters |
| plot.summary.ddt_lcm | Plot the MAP tree and class profiles of summarized DDT-LCM... |
| plot_tree_with_barplot | Plot the MAP tree and class profiles (bar plot) of summarized... |
| plot_tree_with_heatmap | Plot the MAP tree and class profiles (heatmap) of summarized... |
| predict.ddt_lcm | Prediction of class memberships from posterior predictive... |
| predict.summary.ddt_lcm | Prediction of class memberships from posterior summaries |
| print.ddt_lcm | Print out setup of a ddt_lcm model |
| print.summary.ddt_lcm | Print out summary of a ddt_lcm model |
| proposal_log_prob | Calculate proposal likelihood |
| quiet | Suppress print from cat() |
| random_detach_subtree | Metropolis-Hasting algorithm for sampling tree topology and... |
| reattach_point | Attach a subtree to a given DDT at a randomly selected... |
| result_diet_1000iters | Result of fitting DDT-LCM to a semi-synthetic data example |
| sample_class_assignment | Sample individual class assignments Z_i, i = 1, ..., N |
| sample_c_one | Sample divergence function parameter c for a(t) = c / (1-t)... |
| sample_c_two | Sample divergence function parameter c for a(t) = c / (1-t)^2... |
| sample_leaf_locations_pg | Sample the leaf locations and Polya-Gamma auxilliary... |
| sample_sigmasq | Sample item group-specific variances through Gibbs sampler |
| sample_tree_topology | Sample a new tree topology using Metropolis-Hastings through... |
| simulate_DDT_tree | Simulate a tree from a DDT process. Only the tree topology... |
| simulate_lcm_given_tree | Simulate multivariate binary responses from a latent class... |
| simulate_lcm_response | Simulate multivariate binary responses from a latent class... |
| simulate_parameter_on_tree | Simulate node parameters along a given tree. |
| summary.ddt_lcm | Summarize the output of a ddt_lcm model |
| WAIC | Compute WAIC |
