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("data-raw/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) print(mo_failures()) # 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) devtools::load_all(".")