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