Man pages for mrajeev08/treerabid
Reconstruct Rabies Transmission Trees
| add_uncertainty | Add uncertainty |
| assign_progen | Assign progenitor |
| boot_trees | Wrapper function for bootstrapped trees: reproducibly & in... |
| build_all_links | Summarize links between cases across bootstrapped... |
| build_consensus_links | Build consensus links between cases (i.e. most often selected... |
| build_consensus_tree | Build the consensus tree (i.e. the tree with the highest... |
| build_known_tree | Reconstruct known tree (i.e. from tracing data) |
| build_tree | Reconstruct transmission trees from a case line list. |
| check_lineages | Get the number of lineages in each chain |
| check_loops | Helper function to check for loops |
| dist_gamma1 | Gamma dispersal kernel |
| dist_gamma2 | Convolved Gamma dispersal kernel |
| dist_gamma_mixed | Mixture gamma dispersal kernel |
| dist_lnorm1 | Lognormal dispersal kernel |
| dist_lnorm2 | Convolved lognormal dispersal kernel |
| dist_lnorm_mixed | Mixture lognormal dispersal kernel |
| dist_weibull1 | Weibull dispersal kernel |
| dist_weibull2 | Convolved Weibull dispersal kernel |
| dist_weibull_mixed | Mixture weibull dispersal kernel |
| find_lineages | Find the links to fix too resolve lineage discrepancies |
| find_lins_to_fix | Internal function for finding mismatched lineages to fix |
| find_loops_to_fix | Internal function for finding loops to fix |
| fit_sims_pi | Fit detection probability given observed time differences... |
| get_chain_membership | Get membership (i.e. chain id) for each case |
| get_chain_persistence | Get duration of chain persistence in days |
| get_chain_stats | Get chain size & lengths |
| get_edge_dt | Internal function for getting edges between mismatched... |
| get_gr | Helper function to get graph from links |
| get_graph | Turn a transmssion tree into a graph object |
| get_membership | Internal function for checking membership of chains AFTER... |
| list_funs | Helper for functions to export to foreach loop in boot_trees |
| select_progenitor | Wrapper to select single progenitor in each case |
| si_fun_lnorm | Example serial interval function for input |
| si_gamma1 | Gamma distribution for probabilities and cutoff for serial... |
| si_gamma2 | Convolved gamma serial interval |
| si_lnorm1 | Lognormal serial interval |
| si_lnorm2 | Convolved serial interval |
| sim_generations | Simulate the number of generations between two linked cases... |
| sim_times_pi | Simulate times given generation function & pi, for validating... |
| si_weibull1 | Baseline weibull serial interval |
| si_weibull2 | Baseline weibull serial interval |
