get_patient_flow: Summarize inter-facility patient transfer network

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

Summarize inter-facility patient transfer network

Description

Summarize inter-facility patient transfer network from an edge list. Direct and indirect patient flow metrics are calculated.

Usage

get_patient_flow(pt_trans_df, locs = NULL, paths = FALSE)

Arguments

pt_trans_df	a dataframe representing a patient transfer network of 3 cols: 'source_facil', 'dest_facil, and 'n_transfers' (code doesn't support missing paths, any missing paths will be represented by 0s)
locs	vector of unique locations you want to find shortest paths between (e.g. ones for which you have sequencing data for); default to use all locations
paths	boolean value, TRUE if you want the shortest paths returned, FALSE if you don't

Details

For more details on how patient flow is calculated, see: https://aac.asm.org/content/63/11/e01622-19.

Value

the number of direct patient transfers and indirect flow metrics between each facility pair. If paths = TRUE, a list of summary (pt_trans_summary) and shortest paths used (paths).

Examples

get_patient_flow(pt_trans_df = pt_trans_df)

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