Man pages for Snitkin-Lab-Umich/regentrans
A framework and R package for using genomics to study regional pathogen transmission
| aln | Klebiella pneumoniae ST258 isolate variant alignment |
| aln_mini | Subsetted alignment |
| days_between_isolates | Difference in days between isolate collection dates |
| dists | Klebiella pneumoniae ST258 isolate pairwise SNV distance |
| dists_mini | Subsetted pairwise SNV distances |
| facil_coord | Deidentified facility longitude and latitude |
| fsp | Klebiella pneumoniae ST258 gene flow |
| get_clusters | Get facility clusters on the phylogeny |
| get_frac_intra | Get fraction of intra-facility pairs for different SNV... |
| get_genetic_flow | Calculate genetic flow (Fsp) |
| get_pair_types | Get data frame of inter- and intra-facility pariwise SNV... |
| get_patient_flow | Summarize inter-facility patient transfer network |
| make_long_form | Make matrix long-form where each row represents a cell in the... |
| merge_inter_summaries | Merge summarized data about facility pairs |
| metadata | Klebiella pneumoniae ST258 isolate metadata |
| metadata_mini | Subsetted metadata |
| pt_flow | Patient flow between facilities |
| pt_trans_df | Made up patient transfer dataframe between facilities |
| reexports | dplyr pipe |
| summarize_pairs | Summarize extent of relatedness of intra- and inter-facility... |
| tr | Klebiella pneumoniae ST258 isolate phylogenetic tree |
| tr_mini | Subsetted tree |
