inst/ACORN-app/www/markdown/help_deduplication.md

In ocelhay/ACORN: App for the exploration of ACORN data

• Deduplication by patient-episode: This filter restricts to the first isolation of each species by specimen type and patient infection episode (enrolment). For example, if E. coli was isolated from three blood cultures and one urine culture during a single CAI episode, the filter would select just the first blood culture isolate and the urine culture isolate.
• Deduplication by patient ID: This filter restricts to the first isolation of each species by patient, specimen type, and infection category (CAI or HAI). For example, if a patient was admitted two times during the surveillance period and had two episodes of community-acquired E. coli urosepsis (two E. coli urine cultures and one E. coli bacteraemia) and one hospital acquired E. coli bacteraemia secondary to a surgical complication, the filter would select just the earliest isolate from each specimen type and infection category (i.e. the E. coli from the first positive urine culture and the first positive blood culture (CAI) plus the E. coli from the first positive blood culture (HAI)).

ocelhay/ACORN documentation built on Dec. 6, 2020, 5:20 a.m.