Fraction of Converts with Same Source Across Cluster Assignments

Compares two cluster assignments by examining patients categorized as "convert". For each patient who is a convert in both assignments, checks whether the source patient (categorized as "index" or "weak-index") in their respective clusters is the same across both assignments.

Usage

fraction_convert_same_source(
  clusters1,
  clusters2,
  dna_aln,
  seq2pt,
  adm_seqs,
  dates,
  surv_df
)

Arguments

clusters1

A named vector of cluster assignments where names are isolate IDs and values are cluster numbers.

clusters2

A named vector of cluster assignments where names are isolate IDs and values are cluster numbers.

dna_aln

A DNA alignment object of class DNAbin.

seq2pt

A named vector mapping sequence IDs to patient IDs.

adm_seqs

A vector of sequence IDs corresponding to admission positive patients.

dates

A named vector mapping sequence IDs to dates.

surv_df

A data frame with surveillance data containing columns: patient_id, genome_id, surv_date, result.

Value

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

Details

The function:

1. Creates isolate lookups for both cluster assignments

2. Categorizes patients in both using cluster_patient_categorization()

3. Identifies patients categorized as "convert" in both assignments

4. For each such convert, finds the "index" or "weak-index" patient in their cluster for each assignment

5. Returns the fraction where the source patient matches

See also

fraction_convert_same_source_from_lookups(), cluster_patient_categorization(), get_isolate_lookup()