mirror of
https://github.com/msberends/AMR.git
synced 2025-05-02 07:03:58 +02:00
24 lines
977 B
R
24 lines
977 B
R
df <- example_isolates |>
|
|
filter_first_isolate(method = "e", episode_days = 14) |>
|
|
mutate(mo = ifelse(mo_genus(mo) == "Klebsiella", as.mo("Klebsiella"), mo)) |>
|
|
top_n_microorganisms(10)
|
|
|
|
out_new <- df |> antibiogram(c("TZP","TZP+GEN","TZP+TOB"), wisca = TRUE, syndromic_group = "ward")
|
|
out_nonwisca <- df |> antibiogram(c("TZP","TZP+GEN","TZP+TOB"),
|
|
syndromic_group = "ward",
|
|
mo_transform = function(x) "",
|
|
digits = 1,
|
|
minimum = 10,
|
|
formatting_type = 14) |>
|
|
as_tibble() |>
|
|
select(-Pathogen)
|
|
|
|
# parameters_amr.R#L110: no filter on ward, so pts are only in 1 ward, depending on order of data
|
|
# parameters_amr.R: number of first isolates are determined on the whole data set, while Klebsiella is aggregated afterwards (=duplicates on genus level)
|
|
|
|
source("~/Downloads/estimate_definition_amr.R")
|
|
|
|
|
|
|
|
|