Reconstructing Etiology with Binary Decomposition

bin2dec_vec | convert binary codes to decimal integers |

compute_product_Bern_table | Compute the product Bernoulli probability table |

cuthill_mckee | Cuthill McKee (CM) algorithm |

distAB | Frobenius norm: ||AA'-BB'||_F |

do_update_Q_one | Update the current element of Q_ml or not |

equal_unit_vec | check whether a vector is equal to a unit vector with the one... |

eval_string | create a string with parts that need to be replaced by a... |

f | flip the matrix to the right form for 'image()' |

fix_cluster | adjust cluster ids by specification |

get_freq | Get frequency count for each integer |

log_f_logden | compute the log of density of inactive states' probability... |

log_f_logprima | compute the derivative of the log of density of inactive... |

log_full | Function to compute the full cluster-specific likelihood... |

log_marginal | R Function to compute the cluster-specific marginal... |

log_marginal_Q_identity | R Function to compute the cluster-specific marginal... |

log_pr_Qml_cond | Compute the full conditional probability of Q_ml given the... |

log_pr_Qml_cond_enum | Compute the full conditional probability of column Q_l given... |

mblock | obtain the indices of rows of Q that form orthogonal blocks |

merge_H_col | Merge redundant H_star by column |

merge_H_Q | Merge latent state profile matrix (H_star) and Q matrix |

merge_map | Merge mapping |

merge_Q | merge Q matrix by rows |

metrop_flip | Metroplis flipping to improve mixing |

mfm_coefficients | computing coefficients for mixture of finite mixture model |

ordered_insert | insert a cluster ID prior to "index"; mylist keeps a list of... |

ordered_next | Find the next available cluster ID to use: |

ordered_remove | remove an index from a vector of cluster ID |

order_mat_byrow | Order a binary matrix by row |

plot_individual_pred | Plot individual probabilities |

plot_population_fractions | Plot population "etiology" fractions (for known Q only) |

plot_rewind | Plot data, design matrix or co-clustering probabilities |

plot_truth | Plot truth for simulation studies |

postprocess_H_Q | Merge H and Q |

restricted_gibbs | Restricted Gibbs scan to update assignment indicators in S. |

rewind | rewind: *R*constructing *E*tiology *w*ith B*in*ary... |

sampler | Main function for model estimation |

scatterhist | Plot posterior sampling chain and the histogram on the right... |

simulate_data | simulate data from restricted latent class models |

simulate_Q | Randomly generate a Q matrix within the identifying... |

simulate_Q_dat | Randomly generate a Q matrix within the identifying condition... |

split_merge | Split-merge type update of clusterings |

summarize_latent_state_given_Q | Summarize individual latent state patterns given Q |

trunc_rbeta | Sample truncated Beta random variables |

update_alpha | sample alpha - hyperparameter for latent state prevalences... |

update_mu_PR | sample a_theta_one - hyperparameter (mean) for positive rates... |

update_positive_rate | update true and false positive rates |

update_prevalence | update latent state prevalences |

update_pseudo_n_PR | sample alpha_s - hyperparameter for positive rates theta_l,... |

update_Q | update the Q matrix element-wise |

update_Q_col_block | Block update the Q matrix by column |

z2comat | Compute the posterior co-clustering probability matrix... |

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