|
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 thresholds |
|
get_genetic_flow()
|
Calculate genetic flow (Fsp) |
|
get_pair_types()
|
Get data frame of inter- and intra-facility pariwise SNV distances |
|
get_patient_flow()
|
Summarize inter-facility patient transfer network |
|
make_long_form()
|
Make matrix long-form where each row represents a cell in the matrix |
|
merge_inter_summaries()
|
Merge summarized data about facility pairs |
|
metadata
|
Klebiella pneumoniae ST258 isolate metadata |
|
metadata_mini metadata_mini
|
Subsetted metadata |
|
pt_flow
|
Patient flow between facilities |
|
pt_trans_df
|
Made up patient transfer dataframe between facilities |
|
summarize_pairs()
|
Summarize extent of relatedness of intra- and inter-facility pairs by facility pair |
|
tr
|
Klebiella pneumoniae ST258 isolate phylogenetic tree |
|
tr_mini
|
Subsetted tree |