mirror of https://github.com/msberends/AMR.git
109 lines
3.8 KiB
R
109 lines
3.8 KiB
R
library(dplyr)
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library(readr)
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library(tidyr)
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# Installed WHONET 2019 software on Windows (http://www.whonet.org/software.html),
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# opened C:\WHONET\Codes\WHONETCodes.mdb in MS Access
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# and exported table 'DRGLST1' to MS Excel
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DRGLST1 <- readxl::read_excel("data-raw/DRGLST1.xlsx", na = c("", "NA", "-"))
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rsi_trans <- DRGLST1 %>%
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# only keep CLSI and EUCAST guidelines:
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filter(GUIDELINES %like% "^(CLSI|EUCST)")
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if (any(is.na(rsi_trans$BREAKPOINT_TYPE)) | !"Human" %in% rsi_trans$BREAKPOINT_TYPE) {
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stop("Check column BREAKPOINT_TYPE - something is WRONG!")
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}
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rsi_trans <- rsi_trans %>%
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filter(BREAKPOINT_TYPE == "Human") %>%
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mutate(DISK_S = ifelse(as.double(DISK_S) > 50, 50, DISK_S),
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MIC_R = ifelse(as.double(MIC_R) %in% c(1025, 129, 513), as.double(MIC_R) - 1, MIC_R)) %>%
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# set a nice layout:
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transmute(guideline = gsub("([0-9]+)$", " 20\\1", gsub("EUCST", "EUCAST", GUIDELINES)),
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method = TESTMETHOD,
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site = SITE_INF,
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mo = as.mo(ORG_CODE),
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ab = as.ab(WHON5_CODE),
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ref_tbl = REF_TABLE,
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dose_disk = POTENCY,
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S_disk = as.disk(DISK_S),
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R_disk = as.disk(DISK_R),
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S_mic = as.mic(MIC_S),
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R_mic = as.mic(MIC_R)) %>%
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filter(!is.na(mo),
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!is.na(ab),
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!mo %in% c("UNKNOWN", "B_GRAMN", "B_GRAMP", "F_FUNGUS", "F_YEAST")) %>%
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arrange(desc(guideline), mo, ab)
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print(mo_failures())
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# create 2 tables: MIC and disk
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tbl_mic <- rsi_trans %>%
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filter(method == "MIC") %>%
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mutate(breakpoint_S = as.double(S_mic), breakpoint_R = as.double(R_mic))
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tbl_disk <- rsi_trans %>%
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filter(method == "DISK") %>%
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mutate(breakpoint_S = as.double(S_disk), breakpoint_R = as.double(R_disk))
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# merge them so every record is a unique combination of method, mo and ab
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rsi_trans <- bind_rows(tbl_mic, tbl_disk) %>%
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rename(disk_dose = dose_disk) %>%
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mutate(disk_dose = gsub("µ", "u", disk_dose)) %>%
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select(-ends_with("_mic"), -ends_with("_disk"))
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# add extra CLSI general guidelines
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clsi_general <- read_tsv("data-raw/DRGLST.txt") %>%
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filter(CLSI == "X") %>%
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select(WHON5_CODE,
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disk_dose = POTENCY,
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starts_with("CLSI"),
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-c(CLSI, CLSI_ORDER)) %>%
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mutate_at(vars(matches("CLSI")), as.double) %>%
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pivot_longer(-c(WHON5_CODE, disk_dose)) %>%
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mutate(method = ifelse(name %like% "_D", "DISK", "MIC"),
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breakpoint = paste0("breakpoint_", gsub(".*([A-Z])$", "\\1", name)),
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guideline = paste0("CLSI 20", cleaner::clean_integer(name))) %>%
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filter(breakpoint != "breakpoint_I", !is.na(value)) %>%
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select(-name) %>%
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pivot_wider(names_from = breakpoint, values_from = value) %>%
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transmute(guideline,
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method,
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site = NA_character_,
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mo = as.mo("UNKNOWN"),
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ab = as.ab(WHON5_CODE),
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ref_tbl = "Generic CLSI rules",
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disk_dose = gsub("/", "-", disk_dose, fixed = TRUE),
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breakpoint_S,
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breakpoint_R)
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# add new EUCAST with read_EUCAST.R
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# 2020-04-14 did that now for 2019 and 2020
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rsi_trans <- rsi_trans %>%
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filter(guideline != "EUCAST 2019") %>%
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bind_rows(new_EUCAST) %>%
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bind_rows(clsi_general) %>%
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mutate(uti = site %like% "(UTI|urinary)") %>%
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as.data.frame(stringsAsFactors = FALSE) %>%
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# force classes again
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mutate(mo = as.mo(mo),
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ab = as.ab(ab)) %>%
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arrange(desc(guideline), ab, mo, method)
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# 2021-01-12 did that now for 2021
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rsi_trans <- rsi_trans %>%
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mutate(mo = as.character(mo)) %>%
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bind_rows(new_EUCAST) %>%
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mutate(uti = site %like% "(UTI|urinary)") %>%
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as.data.frame(stringsAsFactors = FALSE) %>%
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# force classes again
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mutate(mo = as.mo(mo),
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ab = as.ab(ab)) %>%
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arrange(desc(guideline), ab, mo, method)
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# save to package
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rsi_translation <- rsi_trans
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usethis::use_data(rsi_translation, overwrite = TRUE)
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rm(rsi_trans)
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rm(rsi_translation)
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devtools::load_all(".")
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