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Update clinical breakpoints and fix some as.mo() bugs (#117)

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* Updates clinical breakpoints EUCAST/CLSI 2023, fixes #102, fixes #112, fixes #113, fixes #114, fixes #115
* docs
* implement ecoffs
* unit tests
This commit is contained in:
Dr. Matthijs Berends
2023-06-22 15:10:59 +02:00
committed by GitHub
parent 9591688811
commit f065945d7b
55 changed files with 43056 additions and 18400 deletions
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13
data-raw/reproduction_of_dosage.R
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@@ -32,9 +32,9 @@ library(readxl)
library(cleaner)
# URL:
# https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/Dosages_v_11.0_Breakpoint_Tables.pdf
# 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 <- 12
breakpoints_version <- 13
dosage_source <- read_excel("data-raw/Dosages_v_12.0_Breakpoint_Tables.xlsx", skip = 4, na = "None") %>%
format_names(snake_case = TRUE, penicillins = "drug") %>%
@@ -170,10 +170,9 @@ dosage_new <- bind_rows(
) %>%
arrange(name, administration, type) %>%
filter(!is.na(dose), dose != ".") %>%
as.data.frame(stringsAsFactors = FALSE)
rownames(dosage_new) <- NULL
dosage <- bind_rows(dosage_new, AMR::dosage) %>%
# this makes it a tibble as well:
dataset_UTF8_to_ASCII()
usethis::use_data(dosage, internal = FALSE, overwrite = TRUE, version = 2)
dosage <- bind_rows(dosage_new, AMR::dosage)
usethis::use_data(dosage, internal = FALSE, overwrite = TRUE, version = 2, compress = "xz")