Summarize extent of relatedness of intra- and inter-facility pairs by facility pair

Summarize extent of relatedness of intra- and inter-facility pairs by facility pair

summarize_pairs(pair_types, summary_fns = c("min"), threshs = seq(5, 20, 5))

Arguments

pair_types	the output object of the get_pair_types function
summary_fns	vector of summary functions for pairwise distances as character strings (default: c("min"))
threshs	SNV thresholds to use for pairwise distances (default: seq(5, 20, 5))

Value

a summary of isolate pairs between each facility pair. leq = less than or equal to

Examples

if (FALSE) {
locs <- metadata %>% dplyr::select(isolate_id, facility) %>% tibble::deframe()
pair_types <- get_pair_types(dists, locs)
summarize_pairs(pair_types = pair_types)
}