Categorize patients within clusters by epidemiological status

Categorizes each patient in a cluster based on their role in transmission:

• index: admission positive, earliest isolate, isolate in cluster

• multiply-colonized-index: admission positive, earliest isolate, isolate not in cluster

• weak-index: not admission positive, but first surveillance is positive and in cluster

• convert: had surveillance before first positive

• adm-pos: first positive is in cluster and is first surveillance

• adm-pos-convert: first positive is not in cluster but is first surveillance

• secondary-convert: first positive is not in cluster and had prior surveillance

Usage

cluster_patient_categorization(isolate_lookup, surv_df)

Arguments

isolate_lookup

A lookup table from get_isolate_lookup().

surv_df

A data frame with surveillance data (patient_id, genome_id, surv_date, result).

Value

A named list where each element is a named character vector mapping patient_id to their category within that cluster.