This function categorizes the overlap of isolates in a cluster, based on the earliest collected isolate from all patients deemed to be in the cluster (hereafter referred to as the "index isolate"), and overlap explanations for other isolates in the cluster. The categories are:
"patient-to-patient": if the index isolate is admission-positive and there is overlap explanation for all other converts in the cluster.
"weak-index": if the index isolate is not admission-positive but is the first surveillance for the patient after admission and there is overlap explanation for all other isolates in the cluster.
"missing-intermediate": if the index isolate is admission-positive but at least one other convert in the cluster has no overlap explanation.
"false-negative-index": if the index isolate is not admission-positive but there is overlap explanation for all other converts in the cluster barring one (deemed to be the false negative index).
"missing-source": if the index isolate is not admission-positive and there is no overlap explanation for more than one convert in the cluster.
"multiply-colonized-index": if the index isolate is not in the cluster but is admission-positive, this is a "multiply-colonized index" if there is overlap explanation for all other isolates in the cluster.
"multiply-colonized-index-missing-intermediate": if the index isolate is not in the cluster but is admission-positive, and at least one other convert in the cluster has no overlap explanation.
"inexplicable": catch-all category for cases that do not fit into the other categories. Currently, index and overlap explanations are not enough to explain these clusters.
Arguments
- isolate_lookup
A lookup table for isolates and their clusters assignments which has other relevant epidemiological information. For more information, see
get_isolate_lookup().- cluster_overlap_df
A data frame with overlap information for isolate pairs. For more information, see
cluster_isolate_overlap().- surv_df
A data frame with surveillance information for isolates.