mirror of https://github.com/msberends/AMR.git
53 lines
1.7 KiB
R
53 lines
1.7 KiB
R
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library(dplyr)
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library(readxl)
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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 <- read_excel("DRGLST1.xlsx")
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rsi_translation <- DRGLST1 %>%
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# only keep CLSI and EUCAST guidelines:
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filter(GUIDELINES %like% "^(CLSI|EUCST)") %>%
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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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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) & !is.na(ab)) %>%
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arrange(desc(guideline), mo, ab)
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# create 2 tables: MIC and disk
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tbl_mic <- rsi_translation %>%
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filter(method == "MIC") %>%
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select(-ends_with("_disk")) %>%
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mutate(joinstring = paste(guideline, mo, ab))
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tbl_disk <- rsi_translation %>%
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filter(method == "DISK") %>%
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select(-S_mic, -R_mic) %>%
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mutate(joinstring = paste(guideline, mo, ab)) %>%
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select(joinstring, ends_with("_disk"))
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# merge them so every record is a unique combination of method, mo and ab
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rsi_translation <- tbl_mic %>%
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left_join(tbl_disk,
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by = "joinstring") %>%
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select(-joinstring, -method) %>%
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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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S_mic = as.mic(S_mic),
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R_mic = as.mic(R_mic),
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S_disk = as.disk(S_disk),
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R_disk = as.disk(R_disk))
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# save to package
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usethis::use_data(rsi_translation, overwrite = TRUE)
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rm(rsi_translation)
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