AMR/reproduction_of_rsi_transla...

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2019-05-10 16:44:59 +02:00
library(dplyr)
library(readxl)
# Installed WHONET 2019 software on Windows (http://www.whonet.org/software.html),
# opened C:\WHONET\Codes\WHONETCodes.mdb in MS Access
# and exported table 'DRGLST1' to MS Excel
DRGLST1 <- read_excel("DRGLST1.xlsx")
rsi_translation <- DRGLST1 %>%
# only keep CLSI and EUCAST guidelines:
filter(GUIDELINES %like% "^(CLSI|EUCST)") %>%
# set a nice layout:
transmute(guideline = gsub("([0-9]+)$", " 20\\1", gsub("EUCST", "EUCAST", GUIDELINES)),
method = TESTMETHOD,
mo = as.mo(ORG_CODE),
ab = as.ab(WHON5_CODE),
ref_tbl = REF_TABLE,
dose_disk = POTENCY,
S_disk = as.disk(DISK_S),
R_disk = as.disk(DISK_R),
S_mic = as.mic(MIC_S),
R_mic = as.mic(MIC_R)) %>%
filter(!is.na(mo) & !is.na(ab)) %>%
arrange(desc(guideline), mo, ab)
# create 2 tables: MIC and disk
tbl_mic <- rsi_translation %>%
filter(method == "MIC") %>%
select(-ends_with("_disk")) %>%
mutate(joinstring = paste(guideline, mo, ab))
tbl_disk <- rsi_translation %>%
filter(method == "DISK") %>%
select(-S_mic, -R_mic) %>%
mutate(joinstring = paste(guideline, mo, ab)) %>%
select(joinstring, ends_with("_disk"))
# merge them so every record is a unique combination of method, mo and ab
rsi_translation <- tbl_mic %>%
left_join(tbl_disk,
by = "joinstring") %>%
select(-joinstring, -method) %>%
as.data.frame(stringsAsFactors = FALSE) %>%
# force classes again
mutate(mo = as.mo(mo),
ab = as.ab(ab),
S_mic = as.mic(S_mic),
R_mic = as.mic(R_mic),
S_disk = as.disk(S_disk),
R_disk = as.disk(R_disk))
# save to package
usethis::use_data(rsi_translation, overwrite = TRUE)
rm(rsi_translation)