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(v0.9.0.9014) Machine reading guidelines

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dr. M.S. (Matthijs) Berends
2020-01-27 11:05:39 +01:00
parent 423d1d3c41
commit 9a3891efe4
21 changed files with 14042 additions and 36 deletions
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7
data-raw/reproduction_of_rsi_translation.R
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@ -15,10 +15,10 @@ rsi_translation <- DRGLST1 %>%
ab = as.ab(WHON5_CODE),
ref_tbl = REF_TABLE,
dose_disk = POTENCY,
S_disk = as.disk(DISK_S),
S_disk = as.disk(min(DISK_S, 50, na.rm = TRUE)),
R_disk = as.disk(DISK_R),
S_mic = as.mic(MIC_S),
R_mic = as.mic(MIC_R)) %>%
R_mic = as.mic(ifelse(MIC_R %in% c(1025, 129, 513), as.double(MIC_R) - 1, MIC_R))) %>%
filter(!is.na(mo) & !is.na(ab) & !mo %in% c("UNKNOWN", "B_GRAMN", "B_GRAMP", "F_FUNGUS", "F_YEAST")) %>%
arrange(desc(guideline), mo, ab)
@ -42,6 +42,9 @@ rsi_translation <- bind_rows(tbl_mic, tbl_disk) %>%
mutate(mo = as.mo(mo),
ab = as.ab(ab))
# save to data-raw
write.table(rsi_translation, "data-raw/rsi_translation.txt", sep = "\t", na = "", row.names = FALSE)
# save to package
usethis::use_data(rsi_translation, overwrite = TRUE)
rm(rsi_translation)

13976
data-raw/rsi_translation.txt Normal file
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11
data-raw/whonet_bugfixes.R Normal file
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@ -0,0 +1,11 @@
# WHONET fixes
microorganisms.codes[which(microorganisms.codes$code == "SAP"), "mo"] <- as.mo("staphylococcus")
microorganisms.codes[which(microorganisms.codes$code == "PAE"), "mo"] <- as.mo("pseudomonas aeruginosa")
microorganisms.codes[which(microorganisms.codes$code == "ANI"), "mo"] <- as.mo("aspergillus nidulans")
microorganisms.codes[which(microorganisms.codes$code == "CAL"), "mo"] <- as.mo("candida albicans")
microorganisms.codes[which(microorganisms.codes$code == "ENT"), "mo"] <- as.mo("enterococcus")
microorganisms.codes[which(microorganisms.codes$code == "STR"), "mo"] <- as.mo("streptococcus")
microorganisms.codes[which(microorganisms.codes$code == "CDF"), "mo"] <- as.mo("clostridium difficile")
microorganisms.codes[which(microorganisms.codes$code == "HA-"), "mo"] <- as.mo("haemophilus influenzae")
usethis::use_data(microorganisms.codes, overwrite = TRUE)
rm(microorganisms.codes)