Man pages for thednainus/HIVepisimAnalysis
Functions to analyse results from network analysis
| add_observed_values | Add observed values for phyloscanner results |
| add_observed_values_direction | Add observed values for phyloscanner results for direction |
| add_observed_values_directness | Add observed values for phyloscanner results for directness |
| add_root_edge | Add root edge to phylogenetic tree |
| add_root_edge2 | Add root edge to phylogenetic tree |
| add_sampled_times | Function to add the sampled times for transmission pairs |
| check_linked_transmissions | Check whether a pair of individuals are linked by two or more... |
| check_true_pair | Check whether a pair of individuals represent a transmission... |
| check_true_pair_directness | Check whether a pair of individuals represent a transmission... |
| check_true_transmissions | Check whether a pair of individuals represent a true... |
| compute_log_importance_weight_incidence | Calculate the log importance weight based on observed and... |
| compute_log_importance_weight_newDx | Calculate the log importance weight based on observed and... |
| convert_branches | Scale branch length from a phylogenetic tree |
| create_inf_csv | Create transmission matrix csv |
| create_inf_csv2 | Create transmission matrix csv |
| create_sample_csv | Get sample csv file |
| create_sample_csv2 | Get sample csv file |
| create_times_tsv | Get tsv for times |
| create_transmissions_tsv | Create transmission matrix tsv |
| days2years | Convert days to years |
| est_sampleSize | Estimation sample size based on percentage provided by user. |
| get_cd4s | Get CD4s by node IDs |
| get_cd4s_sampling | Get CD4s by node IDs at time of sampling |
| get_chain | Get transmission chains |
| get_difference | Estimate difference between sampling time and time of... |
| get_epi_data | Get epi data for simulation runs |
| get_id_by_location | Get ID of individuals by location |
| get_n_by_origin | Get total number of individuals in network by region |
| get_newids | Get a sampled ID (sid) and vector of IDs to sample from |
| get_newTip_names | Get tip names based on duplicated rows. |
| get_origin_at_samplingTime | Get origin at time of sampling |
| get_precision_recall | Get rates to construct ROC curve |
| get_rates | Get rates to construct ROC curve |
| get_rates2 | Get rates to construct ROC curve |
| get_subset_tips | Get subset of susceptibles and infected individuals |
| get_tip_cherry | Get tip names for cherries in a phylogenetic tree |
| get_tipNames | Get tip names of phylogenetic tree based on transmission... |
| get.transmat.phylo | Get transmat infection tree for each seed or for specified... |
| keep_row | Get index of rows to keep in transmission matrix |
| merge_trees | Merge phylogenetic trees into a single tree |
| name_of_tips | Get tip names. |
| order_IDs_byDate | Remove duplicated rows and order by date of transmission |
| recency_test | Get which IDs are at early stage of HIV infection in the past... |
| reorder_tip_names | Reorder tip names |
| replace_dups | Replace duplicates. |
| sampleIDs | Sample IDs of individuals diagnosed, active and not on ART |
| sampleIDs2 | Sample IDs of individuals who have been diagnosed, are active... |
| selectIDs | Get IDs before sampled time. |
| set_sampledIDs | Set a dataframe of sampled IDs (sid) and their sampled times. |
| split_dirs | Function to split vector of with names of directories into... |
| summarize_all_data | Summarize all results obtained with phyloscanner |
| summarize_data | Summarize data for statistics calculated for infector... |
| summarize_trans | Summarize results obtained with phyloscanner. |
| summarize_trans_compl | Summarize results obtained with phyloscanner. |
| summaryW | Summarize infector probability (W) for phylogenetic trees |
| summaryW2 | Summarize infector probability (W) for phylogenetic trees |
| time_atSeroconversion | Get the time of duplicates at seroconversion. |
| validadeW | Title Validate infector probability calculation |
| wiw | Who infected whom |
