Skip to contents

Create a lookup table for isolates along with their cluster assignments.

Source: R/cluster_utils.R
get_isolate_lookup.Rd

This function creates a lookup table for isolates. The columns are:

  • cluster: the cluster assignment for the isolate.

  • isolate_id: the isolate ID.

  • patient_id: the patient ID.

  • date: the date of the isolate.

  • adm_pos: a logical value indicating if the isolate is admission positive.

  • prev_surv: the previous surveillance date for the patient.

Usage

get_isolate_lookup(clusters, dna_aln, seq2pt, adm_seqs, dates, surv_df)

Arguments

clusters

A numeric vector of cluster assignments.

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 which correspond to admission positive patient sequences.

dates

A named vector mapping sequence IDs to dates.

surv_df

A data frame with surveillance information for isolates.

Value

A data frame with columns: isolate_id, patient_id, date.