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(v1.0.1.9008) RIVM abbreviations for drugs
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@ -336,6 +336,170 @@ antibiotics[which(antibiotics$ab == "SXT"), "abbreviations"][[1]] <- list(c(anti
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antibiotics[which(antibiotics$ab == "SXT"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "SXT"), "abbreviations"][[1]], "trsx"))
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antibiotics[which(antibiotics$ab == "TZP"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "TZP"), "abbreviations"][[1]], "PIPTAZ"))
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antibiotics[which(antibiotics$ab == "TZP"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "TZP"), "abbreviations"][[1]], "pita"))
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# official RIVM codes (Dutch National Health Institute)
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# https://www.rivm.nl/sites/default/files/2019-09/Bijlage_4_Lijst_antibiotica%202020%201.0.pdf
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antibiotics[which(antibiotics$ab == "FCT"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "FCT"), "abbreviations"][[1]], "5flc"))
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antibiotics[which(antibiotics$ab == "AMC"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "AMC"), "abbreviations"][[1]], "amcl"))
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antibiotics[which(antibiotics$ab == "AMB"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "AMB"), "abbreviations"][[1]], "amfb"))
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antibiotics[which(antibiotics$ab == "AMH"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "AMH"), "abbreviations"][[1]], "amhl"))
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antibiotics[which(antibiotics$ab == "AMK"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "AMK"), "abbreviations"][[1]], "amik"))
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antibiotics[which(antibiotics$ab == "AMX"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "AMX"), "abbreviations"][[1]], "amox"))
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antibiotics[which(antibiotics$ab == "AMP"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "AMP"), "abbreviations"][[1]], "ampi"))
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antibiotics[which(antibiotics$ab == "SAM"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "SAM"), "abbreviations"][[1]], "amsu"))
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antibiotics[which(antibiotics$ab == "ANI"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "ANI"), "abbreviations"][[1]], "anid"))
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antibiotics[which(antibiotics$ab == "SAM"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "SAM"), "abbreviations"][[1]], "apsu"))
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antibiotics[which(antibiotics$ab == "AZM"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "AZM"), "abbreviations"][[1]], "azit"))
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antibiotics[which(antibiotics$ab == "AZL"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "AZL"), "abbreviations"][[1]], "azlo"))
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antibiotics[which(antibiotics$ab == "ATM"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "ATM"), "abbreviations"][[1]], "aztr"))
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antibiotics[which(antibiotics$ab == "PNV"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "PNV"), "abbreviations"][[1]], "bepe"))
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antibiotics[which(antibiotics$ab == "CAP"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CAP"), "abbreviations"][[1]], "capr"))
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antibiotics[which(antibiotics$ab == "CRB"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CRB"), "abbreviations"][[1]], "carb"))
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antibiotics[which(antibiotics$ab == "CAS"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CAS"), "abbreviations"][[1]], "casp"))
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antibiotics[which(antibiotics$ab == "CDC"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CDC"), "abbreviations"][[1]], "cecl"))
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antibiotics[which(antibiotics$ab == "CXA"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CXA"), "abbreviations"][[1]], "cfax"))
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antibiotics[which(antibiotics$ab == "CTB"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CTB"), "abbreviations"][[1]], "cfbu"))
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antibiotics[which(antibiotics$ab == "CEC"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CEC"), "abbreviations"][[1]], "cfcl"))
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antibiotics[which(antibiotics$ab == "CFR"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CFR"), "abbreviations"][[1]], "cfdx"))
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antibiotics[which(antibiotics$ab == "CEP"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CEP"), "abbreviations"][[1]], "cflt"))
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antibiotics[which(antibiotics$ab == "LEX"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "LEX"), "abbreviations"][[1]], "cflx"))
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antibiotics[which(antibiotics$ab == "MAN"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "MAN"), "abbreviations"][[1]], "cfmn"))
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antibiotics[which(antibiotics$ab == "CPD"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CPD"), "abbreviations"][[1]], "cfpd"))
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antibiotics[which(antibiotics$ab == "FEP"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "FEP"), "abbreviations"][[1]], "cfpi"))
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antibiotics[which(antibiotics$ab == "CPO"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CPO"), "abbreviations"][[1]], "cfpr"))
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antibiotics[which(antibiotics$ab == "CFP"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CFP"), "abbreviations"][[1]], "cfpz"))
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antibiotics[which(antibiotics$ab == "CED"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CED"), "abbreviations"][[1]], "cfrd"))
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antibiotics[which(antibiotics$ab == "CPT"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CPT"), "abbreviations"][[1]], "cfro"))
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antibiotics[which(antibiotics$ab == "CXM"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CXM"), "abbreviations"][[1]], "cfrx"))
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antibiotics[which(antibiotics$ab == "CFS"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CFS"), "abbreviations"][[1]], "cfsl"))
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antibiotics[which(antibiotics$ab == "CRO"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CRO"), "abbreviations"][[1]], "cftr"))
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antibiotics[which(antibiotics$ab == "CTT"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CTT"), "abbreviations"][[1]], "cftt"))
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antibiotics[which(antibiotics$ab == "CTX"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CTX"), "abbreviations"][[1]], "cftx"))
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antibiotics[which(antibiotics$ab == "CAZ"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CAZ"), "abbreviations"][[1]], "cftz"))
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antibiotics[which(antibiotics$ab == "CFM"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CFM"), "abbreviations"][[1]], "cfxm"))
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antibiotics[which(antibiotics$ab == "FOX"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "FOX"), "abbreviations"][[1]], "cfxt"))
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antibiotics[which(antibiotics$ab == "CZO"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CZO"), "abbreviations"][[1]], "cfzl"))
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antibiotics[which(antibiotics$ab == "CZX"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CZX"), "abbreviations"][[1]], "cfzx"))
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antibiotics[which(antibiotics$ab == "CHL"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CHL"), "abbreviations"][[1]], "chlo"))
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antibiotics[which(antibiotics$ab == "CPC"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CPC"), "abbreviations"][[1]], "cicl"))
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antibiotics[which(antibiotics$ab == "CIN"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CIN"), "abbreviations"][[1]], "cino"))
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antibiotics[which(antibiotics$ab == "CIP"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CIP"), "abbreviations"][[1]], "cipr"))
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antibiotics[which(antibiotics$ab == "CIX"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CIX"), "abbreviations"][[1]], "cipx"))
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antibiotics[which(antibiotics$ab == "CLR"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CLR"), "abbreviations"][[1]], "clar"))
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antibiotics[which(antibiotics$ab == "CLI"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CLI"), "abbreviations"][[1]], "clin"))
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antibiotics[which(antibiotics$ab == "CTR"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CTR"), "abbreviations"][[1]], "clot"))
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antibiotics[which(antibiotics$ab == "CLO"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CLO"), "abbreviations"][[1]], "clox"))
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antibiotics[which(antibiotics$ab == "COL"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "COL"), "abbreviations"][[1]], "coli"))
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antibiotics[which(antibiotics$ab == "CTC"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CTC"), "abbreviations"][[1]], "cxcl"))
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antibiotics[which(antibiotics$ab == "CYC"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CYC"), "abbreviations"][[1]], "cycl"))
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antibiotics[which(antibiotics$ab == "CCV"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CCV"), "abbreviations"][[1]], "czcl"))
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antibiotics[which(antibiotics$ab == "DAP"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "DAP"), "abbreviations"][[1]], "dapt"))
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antibiotics[which(antibiotics$ab == "DIC"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "DIC"), "abbreviations"][[1]], "dicl"))
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antibiotics[which(antibiotics$ab == "DOR"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "DOR"), "abbreviations"][[1]], "dori"))
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antibiotics[which(antibiotics$ab == "DOX"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "DOX"), "abbreviations"][[1]], "doxy"))
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antibiotics[which(antibiotics$ab == "ENX"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "ENX"), "abbreviations"][[1]], "enox"))
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antibiotics[which(antibiotics$ab == "ETP"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "ETP"), "abbreviations"][[1]], "erta"))
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antibiotics[which(antibiotics$ab == "ERY"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "ERY"), "abbreviations"][[1]], "eryt"))
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antibiotics[which(antibiotics$ab == "PHE"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "PHE"), "abbreviations"][[1]], "fene"))
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antibiotics[which(antibiotics$ab == "PHN"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "PHN"), "abbreviations"][[1]], "fepe"))
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antibiotics[which(antibiotics$ab == "FLE"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "FLE"), "abbreviations"][[1]], "fler"))
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antibiotics[which(antibiotics$ab == "FLU"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "FLU"), "abbreviations"][[1]], "fluc"))
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antibiotics[which(antibiotics$ab == "FLC"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "FLC"), "abbreviations"][[1]], "flux"))
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antibiotics[which(antibiotics$ab == "FOS"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "FOS"), "abbreviations"][[1]], "fosf"))
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antibiotics[which(antibiotics$ab == "FRM"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "FRM"), "abbreviations"][[1]], "fram"))
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antibiotics[which(antibiotics$ab == "FUS"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "FUS"), "abbreviations"][[1]], "fusi"))
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antibiotics[which(antibiotics$ab == "GAT"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "GAT"), "abbreviations"][[1]], "gati"))
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antibiotics[which(antibiotics$ab == "GEH"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "GEH"), "abbreviations"][[1]], "gehl"))
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antibiotics[which(antibiotics$ab == "GEN"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "GEN"), "abbreviations"][[1]], "gent"))
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antibiotics[which(antibiotics$ab == "GRX"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "GRX"), "abbreviations"][[1]], "grep"))
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antibiotics[which(antibiotics$ab == "IPM"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "IPM"), "abbreviations"][[1]], "imci"))
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antibiotics[which(antibiotics$ab == "IPM"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "IPM"), "abbreviations"][[1]], "imip"))
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antibiotics[which(antibiotics$ab == "ISV"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "ISV"), "abbreviations"][[1]], "isav"))
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antibiotics[which(antibiotics$ab == "ITR"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "ITR"), "abbreviations"][[1]], "itra"))
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antibiotics[which(antibiotics$ab == "KAH"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "KAH"), "abbreviations"][[1]], "kahl"))
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antibiotics[which(antibiotics$ab == "KAN"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "KAN"), "abbreviations"][[1]], "kana"))
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antibiotics[which(antibiotics$ab == "KET"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "KET"), "abbreviations"][[1]], "keto"))
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antibiotics[which(antibiotics$ab == "LVX"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "LVX"), "abbreviations"][[1]], "levo"))
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antibiotics[which(antibiotics$ab == "LIN"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "LIN"), "abbreviations"][[1]], "linc"))
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antibiotics[which(antibiotics$ab == "LNZ"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "LNZ"), "abbreviations"][[1]], "line"))
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antibiotics[which(antibiotics$ab == "LOR"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "LOR"), "abbreviations"][[1]], "lora"))
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antibiotics[which(antibiotics$ab == "MEM"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "MEM"), "abbreviations"][[1]], "mero"))
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antibiotics[which(antibiotics$ab == "MET"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "MET"), "abbreviations"][[1]], "meti"))
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antibiotics[which(antibiotics$ab == "MTR"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "MTR"), "abbreviations"][[1]], "metr"))
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antibiotics[which(antibiotics$ab == "MEZ"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "MEZ"), "abbreviations"][[1]], "mezl"))
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antibiotics[which(antibiotics$ab == "MIF"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "MIF"), "abbreviations"][[1]], "mica"))
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antibiotics[which(antibiotics$ab == "MCZ"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "MCZ"), "abbreviations"][[1]], "mico"))
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antibiotics[which(antibiotics$ab == "MNO"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "MNO"), "abbreviations"][[1]], "mino"))
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antibiotics[which(antibiotics$ab == "LTM"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "LTM"), "abbreviations"][[1]], "moxa"))
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antibiotics[which(antibiotics$ab == "MFX"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "MFX"), "abbreviations"][[1]], "moxi"))
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antibiotics[which(antibiotics$ab == "NAL"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "NAL"), "abbreviations"][[1]], "nali"))
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antibiotics[which(antibiotics$ab == "NEO"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "NEO"), "abbreviations"][[1]], "neom"))
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antibiotics[which(antibiotics$ab == "NET"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "NET"), "abbreviations"][[1]], "neti"))
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antibiotics[which(antibiotics$ab == "NIT"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "NIT"), "abbreviations"][[1]], "nitr"))
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antibiotics[which(antibiotics$ab == "NOR"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "NOR"), "abbreviations"][[1]], "norf"))
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antibiotics[which(antibiotics$ab == "NYS"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "NYS"), "abbreviations"][[1]], "nyst"))
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antibiotics[which(antibiotics$ab == "OFX"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "OFX"), "abbreviations"][[1]], "oflo"))
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antibiotics[which(antibiotics$ab == "OXA"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "OXA"), "abbreviations"][[1]], "oxal"))
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antibiotics[which(antibiotics$ab == "PEF"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "PEF"), "abbreviations"][[1]], "pefl"))
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antibiotics[which(antibiotics$ab == "PEN"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "PEN"), "abbreviations"][[1]], "peni"))
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antibiotics[which(antibiotics$ab == "PIP"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "PIP"), "abbreviations"][[1]], "pipc"))
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antibiotics[which(antibiotics$ab == "PPA"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "PPA"), "abbreviations"][[1]], "pipz"))
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antibiotics[which(antibiotics$ab == "TZP"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "TZP"), "abbreviations"][[1]], "pita"))
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antibiotics[which(antibiotics$ab == "PLB"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "PLB"), "abbreviations"][[1]], "polb"))
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antibiotics[which(antibiotics$ab == "POS"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "POS"), "abbreviations"][[1]], "posa"))
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antibiotics[which(antibiotics$ab == "PRI"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "PRI"), "abbreviations"][[1]], "pris"))
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antibiotics[which(antibiotics$ab == "QDA"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "QDA"), "abbreviations"][[1]], "quda"))
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antibiotics[which(antibiotics$ab == "RIF"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "RIF"), "abbreviations"][[1]], "rifa"))
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antibiotics[which(antibiotics$ab == "RXT"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "RXT"), "abbreviations"][[1]], "roxi"))
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antibiotics[which(antibiotics$ab == "SMX"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "SMX"), "abbreviations"][[1]], "sfmx"))
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antibiotics[which(antibiotics$ab == "SLF4"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "SLF4"), "abbreviations"][[1]], "sfmz"))
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antibiotics[which(antibiotics$ab == "SSS"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "SSS"), "abbreviations"][[1]], "sfna"))
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antibiotics[which(antibiotics$ab == "SLF"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "SLF"), "abbreviations"][[1]], "sfsz"))
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antibiotics[which(antibiotics$ab == "SPX"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "SPX"), "abbreviations"][[1]], "spar"))
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antibiotics[which(antibiotics$ab == "SPT"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "SPT"), "abbreviations"][[1]], "spec"))
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antibiotics[which(antibiotics$ab == "SPI"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "SPI"), "abbreviations"][[1]], "spir"))
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antibiotics[which(antibiotics$ab == "STH"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "STH"), "abbreviations"][[1]], "sthl"))
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antibiotics[which(antibiotics$ab == "STR1"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "STR1"), "abbreviations"][[1]], "stre"))
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antibiotics[which(antibiotics$ab == "TAZ"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "TAZ"), "abbreviations"][[1]], "tazo"))
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antibiotics[which(antibiotics$ab == "TEC"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "TEC"), "abbreviations"][[1]], "teic"))
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antibiotics[which(antibiotics$ab == "TLT"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "TLT"), "abbreviations"][[1]], "teli"))
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antibiotics[which(antibiotics$ab == "TMX"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "TMX"), "abbreviations"][[1]], "tema"))
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antibiotics[which(antibiotics$ab == "TEM"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "TEM"), "abbreviations"][[1]], "temo"))
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antibiotics[which(antibiotics$ab == "TRB"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "TRB"), "abbreviations"][[1]], "terb"))
|
||||
antibiotics[which(antibiotics$ab == "TCY"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "TCY"), "abbreviations"][[1]], "tetr"))
|
||||
antibiotics[which(antibiotics$ab == "TIC"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "TIC"), "abbreviations"][[1]], "tica"))
|
||||
antibiotics[which(antibiotics$ab == "TCC"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "TCC"), "abbreviations"][[1]], "ticl"))
|
||||
antibiotics[which(antibiotics$ab == "TGC"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "TGC"), "abbreviations"][[1]], "tige"))
|
||||
antibiotics[which(antibiotics$ab == "TIN"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "TIN"), "abbreviations"][[1]], "tini"))
|
||||
antibiotics[which(antibiotics$ab == "TOB"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "TOB"), "abbreviations"][[1]], "tobr"))
|
||||
antibiotics[which(antibiotics$ab == "TOH"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "TOH"), "abbreviations"][[1]], "tohl"))
|
||||
antibiotics[which(antibiotics$ab == "TMP"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "TMP"), "abbreviations"][[1]], "trim"))
|
||||
antibiotics[which(antibiotics$ab == "TVA"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "TVA"), "abbreviations"][[1]], "trov"))
|
||||
antibiotics[which(antibiotics$ab == "SLT4"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "SLT4"), "abbreviations"][[1]], "trsm"))
|
||||
antibiotics[which(antibiotics$ab == "SXT"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "SXT"), "abbreviations"][[1]], "trsx"))
|
||||
antibiotics[which(antibiotics$ab == "VAN"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "VAN"), "abbreviations"][[1]], "vanc"))
|
||||
antibiotics[which(antibiotics$ab == "VOR"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "VOR"), "abbreviations"][[1]], "vori"))
|
||||
antibiotics <- antibiotics %>%
|
||||
mutate(ab = as.character(ab)) %>%
|
||||
rbind(antibiotics %>%
|
||||
filter(ab == "GEH") %>%
|
||||
mutate(ab = "AMH",
|
||||
name = "Amphotericin B-high",
|
||||
abbreviations = list(c("amhl", "amfo b high", "ampho b high", "amphotericin high")))) %>%
|
||||
rbind(antibiotics %>%
|
||||
filter(ab == "GEH") %>%
|
||||
mutate(ab = "TOH",
|
||||
name = "Tobramycin-high",
|
||||
abbreviations = list(c("tohl", "tobra high", "tobramycin high")))) %>%
|
||||
rbind(antibiotics %>%
|
||||
filter(ab == "BUT") %>%
|
||||
mutate(ab = "CIX",
|
||||
atc = "D01AE14",
|
||||
name = "Ciclopirox",
|
||||
group = "Antifungals/antimycotics",
|
||||
atc_group1 = "Antifungals for topical use",
|
||||
atc_group2 = "Other antifungals for topical use",
|
||||
abbreviations = list(c("cipx"))))
|
||||
antibiotics[which(antibiotics$ab == "SSS"), "name"] <- "Sulfonamide"
|
||||
# ESBL E-test codes:
|
||||
antibiotics[which(antibiotics$ab == "CCV"), "abbreviations"][[1]] <- list(c("xtzl"))
|
||||
antibiotics[which(antibiotics$ab == "CAZ"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CAZ"), "abbreviations"][[1]], "xtz", "cefta"))
|
||||
@ -375,9 +539,6 @@ antibiotics[which(antibiotics$ab == "BPR"), "atc"] <- "J01DI01"
|
||||
antibiotics[which(antibiotics$ab == "RXT"), "name"] <- "Roxithromycin"
|
||||
antibiotics[which(antibiotics$ab == "PEN"), "atc"] <- "J01CE01"
|
||||
|
||||
|
||||
antibiotics <- antibiotics %>% arrange(name)
|
||||
|
||||
# set cephalosporins groups for the ones that could not be determined automatically:
|
||||
antibiotics <- antibiotics %>%
|
||||
mutate(group = case_when(
|
||||
@ -417,6 +578,7 @@ antibiotics <- antibiotics %>%
|
||||
# set as data.frame again
|
||||
antibiotics <- as.data.frame(antibiotics, stringsAsFactors = FALSE)
|
||||
class(antibiotics$ab) <- "ab"
|
||||
antibiotics <- antibiotics %>% arrange(name)
|
||||
|
||||
# make all abbreviations and synonyms lower case, unique and alphabetically sorted
|
||||
for (i in 1:nrow(antibiotics)) {
|
||||
|
||||
Reference in New Issue
Block a user