Man pages for skgallagher/TBornotTB
Analyze Tuberculosis Patients in Maryland
| assign_infector | Assign an infector ID to someone in previous generation |
| assign_smear | Assign a fixed number of smears to the group |
| cluster_like_smear | Calculate the likelihood for a cluster of this size |
| count_infections | Count the number of infections each person gives |
| draw_n_gen | Draw the number of generations for a fixed cluster size |
| draw_part | Draw the number in each generation g |
| draw_part_from_list | Draw partition from pre-computed list |
| flip_til_failure | Simulate the process of flipping until failure for a single... |
| format_to_outsider | Make the root node an outsider and adjust accordingly |
| generate_part_list | Generate list of lists of partitions |
| generate_parts | Generate all unique partitions* of size n |
| generation_infection | Infect the current generation given the previous generation |
| get_i | Count the number of smear positive transmissions |
| get_weight_list | Get the weights of g |
| get_weights_from_table | Get empirical weights from a pre-computed table |
| idistrib1e4 | Pre-computed table of empirical distributions |
| impute_root | Impute the root node for an observed cluster |
| impute_root_inner | Impute the root node for an observed cluster (inner function) |
| iter_est_ws | Iterative Step to find best parameters with weighted sampling |
| likelihood_weighted | Calculate average likelihood over isomorphic trees |
| like_sampled_cond | Calculate the likelihood for a cluster of size n and n_pos |
| loglike_all_clusts | Calculate the log likelihood for data |
| loglike_clust_cond | Calculate the log likelihood of a cluster conditioned on size... |
| loglike_cluster_summary | Calculate the log likelihood for data |
| loglike_cond_fast | Calculate the log likelihood of a cluster conditioned on size... |
| loglike_fast | Calculate the log likelihood of a cluster conditioned on size... |
| loglike_obs_data | Calculate the log likelihood of a cluster conditioned on size... |
| loglike_weighted_total | Calculate the log likelihood using weighted sampling |
| move_up_gen | Change ID by subtracting one to the generation |
| part_to_cluster | Take the partitions by generations and turn it into a full... |
| pipe | Pipe operator |
| prob_trans | Get the probability of transferring infection based on smear |
| sample_connections | Sample connections and form a tree |
| sample_i | Sample and summarize a tree for given generation sizes |
| sample_tree_perm | Sample the actual tree for given permutation |
| sample_uniform_trees | Sample uniform trees |
| sample_uniform_trees_nx | Sample uniform trees |
| sample_uniform_trees_nxo | Sample uniform trees many root nodes |
| sample_unique_perms | Sample unique permutations from a partition space |
| sample_unique_perms_o | Sample unique permutations from a partition space (now with... |
| simulate_cond_bp | Simulate a single branching process conditioned on the given... |
| simulate_flip_til_failure | Simulate the process of flipping until failure for K clusters |
| simulate_many_cond_bp | Wrapper for simulate_cond_bp |
| simulate_outbreak | Simulate the process of flipping until failure for K clusters |
| summarize_clusters | Summarize the clusters |
| summarize_cond_trees | Summarize sampled trees |
| unique_perm | Generate unique permutations |
