epiLinksPatientIsolates: Identifying epidemiological links with isolates from a...

In wanyuac/handyR: Handy functions for R programming.

Identifying epidemiological links with isolates from a specific patient

Description

Finding out epidemiologically linked isolates within the same each genetic cluster c as isolates of a specific patient.

Usage

epiLinksPatientIsolates(p, c, L, D, G, d_max = 90, e_max = 90)

Arguments

p	A patient ID that can be found in L
c	Genetic cluster of interest
L	A data frame of four columns: "Isolate", "Cluster", "Patient", "Lab"; "Cluster" stands for genetic clusters, and "Lab" may represent a hospital or healthcare trust.
D	A symmetric matrix of maximum days between possible collection dates of isolates
G	A symmetric matrix of genetic distances
d_max	maximum days to define an epidemiological link
e_max	maximum days to define an episode of infection or carriage

wanyuac/handyR documentation built on June 10, 2024, 1:24 a.m.