merge_inter_summaries: Merge summarized data about facility pairs

In Snitkin-Lab-Umich/regentrans: A framework and R package for using genomics to study regional pathogen transmission

Merge summarized data about facility pairs

Description

Merge summarized data about facility pairs including patient flow, isolate pairs, and gene flow (Fsp).

Usage

merge_inter_summaries(
  patient_flow = NULL,
  isolate_pair_summary = NULL,
  fsp_long = NULL
)

Arguments

patient_flow	output of get_patient_flow function
isolate_pair_summary	output of summarize_pairs function
fsp_long	long-form output of get_genetic_flow function

Value

merged dataframe

Examples

## Not run: 
locs <- metadata %>% dplyr::select(isolate_id, facility) %>% tibble::deframe()
pair_types <- get_pair_types(dists, locs)
isolate_pair_summary <- summarize_pairs(pair_types)
patient_flow <- get_patient_flow(pt_trans_df = pt_trans_df)
fsp_long <- make_long_form(fsp)
merge_inter_summaries(patient_flow, isolate_pair_summary, fsp_long)

## End(Not run)

Snitkin-Lab-Umich/regentrans documentation built on Jan. 29, 2023, 7:45 a.m.