Compute the fraction of converts with the same source from isolate lookups

Compares two isolate lookups by examining patients categorized as "convert". This works directly with isolate lookups and is useful when the two cluster assignments do not share the same epidemiological information.

Usage

fraction_convert_same_source_from_lookups(
  isolate_lookup1,
  isolate_lookup2,
  surv_df_1,
  surv_df_2,
  converts_without_assigned_source = TRUE
)

Arguments

isolate_lookup1

A data frame from get_isolate_lookup() for the first cluster assignment.

isolate_lookup2

A data frame from get_isolate_lookup() for the second cluster assignment.

surv_df_1

A data frame with surveillance data containing columns: patient_id, genome_id, surv_date, result for the first cluster assignment.

surv_df_2

A data frame with surveillance data containing columns: patient_id, genome_id, surv_date, result for the second cluster assignment.

converts_without_assigned_source

A logical value indicating whether to include singleton converts – patients counted as converts that have no assigned source in the lookup – in the comparison, recording them with no source.

Value

A numeric value between 0 and 1 representing the fraction of convert patients whose source (index, weak index, or multiply-colonized index) is the same in both cluster assignments. Returns NA if there are no common converts.

See also

fraction_convert_same_source(), cluster_patient_categorization()