Phenotype-based first isolate determination selects too many isolates

[Matthijs Berends]

Phenotype-based first isolate determination selects too many isolates:

tibble(mo = as.mo("S. aureus"),
       fluclox = as.sir(rep(c("S", "R"), 5)),
       cefoxitin = fluclox,
       date = Sys.Date() - c(-10:-1),
       id = "A") %>% 
    mutate(phenotype = first_isolate(method = "phenotype", col_patient_id = "id"),
           episode = first_isolate(method = "episode", col_patient_id = "id"),
           patient = first_isolate(method = "patient", col_patient_id = "id"),
           isolate = first_isolate(method = "isolate", col_patient_id = "id"))

Should only return TRUE for each phenotype.

[Matthijs Berends]

So, the problem here was that the phenotype-based algorithm checked the antimicrobial results in the previous row only.

In the new version of AMR, antimicrobial results of all isolates found in a patient will be checked. This leads to this result (notice how the phenotype column are now not all TRUE anymore):

tibble(mo = as.mo("S. aureus"),
       fluclox = as.sir(rep(c("S", "R"), 5)),
       cefoxitin = fluclox,
       date = Sys.Date() - c(-10:-1),
       id = "A") %>% 
    mutate(phenotype = first_isolate(method = "phenotype", col_patient_id = "id"),
           episode = first_isolate(method = "episode", col_patient_id = "id"),
           patient = first_isolate(method = "patient", col_patient_id = "id"),
           isolate = first_isolate(method = "isolate", col_patient_id = "id"))

When adding another antibiotic, it can clearly be seen that the algorithm now works as expected:

tibble(mo = as.mo("S. aureus"),
       fluclox = as.sir(rep(c("S", "R"), 5)),
       cefoxitin = fluclox,
       genta = as.sir(c(rep("S", 5), rep("R", 5))),
       date = Sys.Date() - c(-10:-1),
       id = "A") %>% 
    mutate(phenotype = first_isolate(method = "phenotype", col_patient_id = "id"),
           episode = first_isolate(method = "episode", col_patient_id = "id"),
           patient = first_isolate(method = "patient", col_patient_id = "id"),
           isolate = first_isolate(method = "isolate", col_patient_id = "id"))

As intended, it now only returns TRUE for each phenotype.