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(v2.1.1.9247) CLSI/EUCAST 2025!

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dr. M.S. (Matthijs) Berends
2025-04-20 12:55:31 +02:00
parent 0bab49ff86
commit ea443f7483
65 changed files with 8297 additions and 1901 deletions
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19
data-raw/_reproduction_scripts/reproduction_of_dosage.R
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@ -31,12 +31,13 @@ library(dplyr)
library(readxl)
library(cleaner)
# URL:
# https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/Dosages_v_13.0_Breakpoint_Tables.pdf
# download the PDF file, open in Adobe Acrobat and export as Excel workbook
breakpoints_version <- 13
breakpoint_file <- "data-raw/v_15.0_Breakpoint_Tables.xlsx"
if (!file.exists(breakpoint_file)) {
stop("Breakpoint file not found")
}
breakpoints_version <- as.double(gsub("[^0-9.]", "", gsub(".xlsx", "", breakpoint_file, fixed = TRUE)))
dosage_source <- read_excel("data-raw/Dosages_v_12.0_Breakpoint_Tables.xlsx", skip = 4, na = "None") %>%
dosage_source <- read_excel(breakpoint_file, skip = 6, sheet = "Dosages", na = "None") %>%
format_names(snake_case = TRUE, penicillins = "drug") %>%
filter(!tolower(standard_dosage) %in% c("standard dosage", "standard dosage_source", "under review")) %>%
filter(!is.na(standard_dosage)) %>%
@ -173,6 +174,12 @@ dosage_new <- bind_rows(
# this makes it a tibble as well:
dataset_UTF8_to_ASCII()
dosage <- bind_rows(dosage_new, AMR::dosage)
dosage <- AMR::dosage |>
bind_rows(dosage_new) |>
arrange(desc(eucast_version), name) |>
distinct()
dosage <- dosage |> dataset_UTF8_to_ASCII()
usethis::use_data(dosage, internal = FALSE, overwrite = TRUE, version = 2, compress = "xz")
rm(dosage)
devtools::load_all(".")