P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-17 02:33:22 +02:00
Code Releases Activity

(v2.1.1.9260) fix antibiogram

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2025-04-29 16:15:18 +02:00
parent 6819473457
commit faa9ae0d85
31 changed files with 195 additions and 2283 deletions
Download Patch File Download Diff File Expand all files Collapse all files

23
data-raw/wisca_reprex.R Normal file
View File

@ -0,0 +1,23 @@
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")