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< h1 > Determine multidrug-resistant organisms (MDRO)< / h1 >
< div class = "hidden name" > < code > mdro.Rd< / code > < / div >
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< p > Determine which isolates are multidrug-resistant organisms (MDRO) according to (country-specific) guidelines.< / p >
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< / div >
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< pre class = "usage" > < span class = 'fu' > mdro< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > guideline< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > , < span class = 'kw' > col_mo< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > , < span class = 'kw' > info< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > ,
< span class = 'kw' > verbose< / span > < span class = 'kw' > =< / span > < span class = 'fl' > FALSE< / span > , < span class = 'no' > ...< / span > )
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< span class = 'fu' > brmo< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > guideline< / span > < span class = 'kw' > =< / span > < span class = 'st' > "BRMO"< / span > , < span class = 'no' > ...< / span > )
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< span class = 'fu' > mrgn< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > guideline< / span > < span class = 'kw' > =< / span > < span class = 'st' > "MRGN"< / span > , < span class = 'no' > ...< / span > )
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< span class = 'fu' > mdr_tb< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > guideline< / span > < span class = 'kw' > =< / span > < span class = 'st' > "TB"< / span > , < span class = 'no' > ...< / span > )
< span class = 'fu' > eucast_exceptional_phenotypes< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > guideline< / span > < span class = 'kw' > =< / span > < span class = 'st' > "EUCAST"< / span > , < span class = 'no' > ...< / span > )< / pre >
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< h2 class = "hasAnchor" id = "arguments" > < a class = "anchor" href = "#arguments" > < / a > Arguments< / h2 >
< table class = "ref-arguments" >
< colgroup > < col class = "name" / > < col class = "desc" / > < / colgroup >
< tr >
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< th > x< / th >
< td > < p > table with antibiotic columns, like e.g. < code > AMX< / code > and < code > AMC< / code > < / p > < / td >
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< / tr >
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< tr >
< th > guideline< / th >
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< td > < p > a specific guideline to mention, see Details. EUCAST guidelines will be used when left empty, see Details.< / p > < / td >
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< / tr >
< tr >
< th > col_mo< / th >
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< td > < p > column name of the IDs of the microorganisms (see < code > < a href = 'as.mo.html' > as.mo< / a > < / code > ), defaults to the first column of class < code > mo< / code > . Values will be coerced using < code > < a href = 'as.mo.html' > as.mo< / a > < / code > .< / p > < / td >
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< / tr >
< tr >
< th > info< / th >
< td > < p > print progress< / p > < / td >
< / tr >
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< tr >
< th > verbose< / th >
< td > < p > print additional info: missing antibiotic columns per parameter< / p > < / td >
< / tr >
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< tr >
< th > ...< / th >
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< td > < p > column name of an antibiotic, see section Antibiotics< / p > < / td >
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< / tr >
< / table >
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< h2 class = "hasAnchor" id = "source" > < a class = "anchor" href = "#source" > < / a > Source< / h2 >
< p > EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (< a href = 'http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf' > link< / a > )< / p >
< p > World Health Organization "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis" (< a href = 'https://www.who.int/tb/publications/pmdt_companionhandbook/en/' > link< / a > )< / p >
< p > Rijksinstituut voor Volksgezondheid en Milieu "WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) [ZKH]" (< a href = 'https://www.rivm.nl/Documenten_en_publicaties/Professioneel_Praktisch/Richtlijnen/Infectieziekten/WIP_Richtlijnen/WIP_Richtlijnen/Ziekenhuizen/WIP_richtlijn_BRMO_Bijzonder_Resistente_Micro_Organismen_ZKH' > link< / a > )< / p >
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< h2 class = "hasAnchor" id = "value" > < a class = "anchor" href = "#value" > < / a > Value< / h2 >
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< ul >
< li > < p > TB guideline - function < code > mdr_tb()< / code > or < code > mdro(..., guideline = "TB")< / code > :< br / > Ordered factor with levels < code > Negative < Mono-resistant < Poly-resistant < Multi-drug-resistant < Extensive drug-resistant< / code > < / p > < / li >
< li > < p > German guideline - function < code > mrgn()< / code > or < code > mdro(..., guideline = "MRGN")< / code > :< br / > Ordered factor with levels < code > Negative < 3MRGN < 4MRGN< / code > < / p > < / li >
< li > < p > Everything else:< br / > Ordered factor with levels < code > Negative < Positive, unconfirmed < Positive< / code > . The value < code > "Positive, unconfirmed"< / code > means that, according to the guideline, it is not entirely sure if the isolate is multi-drug resistant and this should be confirmed with additional (e.g. molecular) tests< / p > < / li >
< / ul >
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< h2 class = "hasAnchor" id = "details" > < a class = "anchor" href = "#details" > < / a > Details< / h2 >
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< p > Currently supported guidelines are (case-insensitive):< / p > < ul >
< li > < p > < code > guideline = "EUCAST"< / code > : The European international guideline - EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (< a href = 'http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf' > link< / a > )< / p > < / li >
< li > < p > < code > guideline = "TB"< / code > : The international guideline for multi-drug resistant tuberculosis - World Health Organization "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis" (< a href = 'https://www.who.int/tb/publications/pmdt_companionhandbook/en/' > link< / a > )< / p > < / li >
< li > < p > < code > guideline = "MRGN"< / code > : The German national guideline - Mueller et al. (2015) Antimicrobial Resistance and Infection Control 4:7. DOI: 10.1186/s13756-015-0047-6< / p > < / li >
< li > < p > < code > guideline = "BRMO"< / code > : The Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu "WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) [ZKH]" (< a href = 'https://www.rivm.nl/Documenten_en_publicaties/Professioneel_Praktisch/Richtlijnen/Infectieziekten/WIP_Richtlijnen/WIP_Richtlijnen/Ziekenhuizen/WIP_richtlijn_BRMO_Bijzonder_Resistente_Micro_Organismen_ZKH' > link< / a > )< / p > < / li >
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< / ul >
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< p > Please suggest your own (country-specific) guidelines by letting us know: < a href = 'https://gitlab.com/msberends/AMR/issues/new' > https://gitlab.com/msberends/AMR/issues/new< / a > .< / p >
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< h2 class = "hasAnchor" id = "antibiotics" > < a class = "anchor" href = "#antibiotics" > < / a > Antibiotics< / h2 >
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< p > To define antibiotics column names, leave as it is to determine it automatically with < code > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / code > or input a text (case-insensitive), or use < code > NULL< / code > to skip a column (e.g. < code > TIC = NULL< / code > to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.< / p >
< p > The following antibiotics are used for the functions < code > < a href = 'eucast_rules.html' > eucast_rules< / a > < / code > and < code > mdro< / code > . These are shown below in the format '< strong > antimicrobial ID< / strong > : name (< a href = 'https://www.whocc.no/atc/structure_and_principles/' > ATC code< / a > )', sorted by name:< / p >
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< p > < strong > AMK< / strong > : amikacin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01GB06' > J01GB06< / a > ),
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< strong > AMX< / strong > : amoxicillin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01CA04' > J01CA04< / a > ),
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< strong > AMC< / strong > : amoxicillin/clavulanic acid (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01CR02' > J01CR02< / a > ),
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< strong > AMP< / strong > : ampicillin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01CA01' > J01CA01< / a > ),
< strong > AZM< / strong > : azithromycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01FA10' > J01FA10< / a > ),
< strong > AZL< / strong > : azlocillin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01CA09' > J01CA09< / a > ),
< strong > ATM< / strong > : aztreonam (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DF01' > J01DF01< / a > ),
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< strong > CAP< / strong > : capreomycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J04AB30' > J04AB30< / a > ),
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< strong > RID< / strong > : cefaloridine (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DB02' > J01DB02< / a > ),
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< strong > CZO< / strong > : cefazolin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DB04' > J01DB04< / a > ),
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< strong > FEP< / strong > : cefepime (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DE01' > J01DE01< / a > ),
< strong > CTX< / strong > : cefotaxime (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DD01' > J01DD01< / a > ),
< strong > FOX< / strong > : cefoxitin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DC01' > J01DC01< / a > ),
< strong > CED< / strong > : cefradine (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DB09' > J01DB09< / a > ),
< strong > CAZ< / strong > : ceftazidime (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DD02' > J01DD02< / a > ),
< strong > CRO< / strong > : ceftriaxone (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DD04' > J01DD04< / a > ),
< strong > CXM< / strong > : cefuroxime (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DC02' > J01DC02< / a > ),
< strong > CHL< / strong > : chloramphenicol (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01BA01' > J01BA01< / a > ),
< strong > CIP< / strong > : ciprofloxacin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01MA02' > J01MA02< / a > ),
< strong > CLR< / strong > : clarithromycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01FA09' > J01FA09< / a > ),
< strong > CLI< / strong > : clindamycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01FF01' > J01FF01< / a > ),
< strong > COL< / strong > : colistin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01XB01' > J01XB01< / a > ),
< strong > DAP< / strong > : daptomycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01XX09' > J01XX09< / a > ),
< strong > DOX< / strong > : doxycycline (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01AA02' > J01AA02< / a > ),
< strong > ETP< / strong > : ertapenem (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DH03' > J01DH03< / a > ),
< strong > ERY< / strong > : erythromycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01FA01' > J01FA01< / a > ),
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< strong > ETH< / strong > : ethambutol (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J04AK02' > J04AK02< / a > ),
< strong > FLC< / strong > : flucloxacillin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01CF05' > J01CF05< / a > ),
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< strong > FOS< / strong > : fosfomycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01XX01' > J01XX01< / a > ),
< strong > FUS< / strong > : fusidic acid (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01XC01' > J01XC01< / a > ),
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< strong > GAT< / strong > : gatifloxacin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01MA16' > J01MA16< / a > ),
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< strong > GEN< / strong > : gentamicin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01GB03' > J01GB03< / a > ),
< strong > IPM< / strong > : imipenem (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DH51' > J01DH51< / a > ),
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< strong > INH< / strong > : isoniazid (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J04AC01' > J04AC01< / a > ),
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< strong > KAN< / strong > : kanamycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01GB04' > J01GB04< / a > ),
< strong > LVX< / strong > : levofloxacin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01MA12' > J01MA12< / a > ),
< strong > LIN< / strong > : lincomycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01FF02' > J01FF02< / a > ),
< strong > LNZ< / strong > : linezolid (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01XX08' > J01XX08< / a > ),
< strong > MEM< / strong > : meropenem (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DH02' > J01DH02< / a > ),
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< strong > MTR< / strong > : metronidazole (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01XD01' > J01XD01< / a > ),
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< strong > MEZ< / strong > : mezlocillin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01CA10' > J01CA10< / a > ),
< strong > MNO< / strong > : minocycline (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01AA08' > J01AA08< / a > ),
< strong > MFX< / strong > : moxifloxacin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01MA14' > J01MA14< / a > ),
< strong > NAL< / strong > : nalidixic acid (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01MB02' > J01MB02< / a > ),
< strong > NEO< / strong > : neomycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01GB05' > J01GB05< / a > ),
< strong > NET< / strong > : netilmicin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01GB07' > J01GB07< / a > ),
< strong > NIT< / strong > : nitrofurantoin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01XE01' > J01XE01< / a > ),
< strong > NOR< / strong > : norfloxacin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01MA06' > J01MA06< / a > ),
< strong > NOV< / strong > : novobiocin (an ATCvet code: < a href = 'https://www.whocc.no/atc_ddd_index/?code=QJ01XX95' > QJ01XX95< / a > ),
< strong > OFX< / strong > : ofloxacin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01MA01' > J01MA01< / a > ),
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< strong > OXA< / strong > : oxacillin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01CF04' > J01CF04< / a > ),
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< strong > PEN< / strong > : penicillin G (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01CE01' > J01CE01< / a > ),
< strong > PIP< / strong > : piperacillin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01CA12' > J01CA12< / a > ),
< strong > TZP< / strong > : piperacillin/tazobactam (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01CR05' > J01CR05< / a > ),
< strong > PLB< / strong > : polymyxin B (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01XB02' > J01XB02< / a > ),
< strong > PRI< / strong > : pristinamycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01FG01' > J01FG01< / a > ),
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< strong > PZA< / strong > : pyrazinamide (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J04AK01' > J04AK01< / a > ),
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< strong > QDA< / strong > : quinupristin/dalfopristin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01FG02' > J01FG02< / a > ),
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< strong > RIB< / strong > : rifabutin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J04AB04' > J04AB04< / a > ),
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< strong > RIF< / strong > : rifampicin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J04AB02' > J04AB02< / a > ),
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< strong > RIF< / strong > : rifampin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J04AB02' > J04AB02< / a > ),
< strong > RFP< / strong > : rifapentine (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J04AB05' > J04AB05< / a > ),
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< strong > RXT< / strong > : roxithromycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01FA06' > J01FA06< / a > ),
< strong > SIS< / strong > : sisomicin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01GB08' > J01GB08< / a > ),
< strong > TEC< / strong > : teicoplanin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01XA02' > J01XA02< / a > ),
< strong > TCY< / strong > : tetracycline (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01AA07' > J01AA07< / a > ),
< strong > TIC< / strong > : ticarcillin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01CA13' > J01CA13< / a > ),
< strong > TGC< / strong > : tigecycline (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01AA12' > J01AA12< / a > ),
< strong > TOB< / strong > : tobramycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01GB01' > J01GB01< / a > ),
< strong > TMP< / strong > : trimethoprim (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01EA01' > J01EA01< / a > ),
< strong > SXT< / strong > : trimethoprim/sulfamethoxazole (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01EE01' > J01EE01< / a > ),
< strong > VAN< / strong > : vancomycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01XA01' > J01XA01< / a > ).< / p >
2019-01-02 23:24:07 +01:00
< h2 class = "hasAnchor" id = "read-more-on-our-website-" > < a class = "anchor" href = "#read-more-on-our-website-" > < / a > Read more on our website!< / h2 >
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< p > On our website < a href = 'https://msberends.gitlab.io/AMR' > https://msberends.gitlab.io/AMR< / a > you can find < a href = 'https://msberends.gitlab.io/AMR/articles/AMR.html' > a tutorial< / a > about how to conduct AMR analysis, the < a href = 'https://msberends.gitlab.io/AMR/reference' > complete documentation of all functions< / a > (which reads a lot easier than here in R) and < a href = 'https://msberends.gitlab.io/AMR/articles/WHONET.html' > an example analysis using WHONET data< / a > .< / p >
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< h2 class = "hasAnchor" id = "examples" > < a class = "anchor" href = "#examples" > < / a > Examples< / h2 >
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< pre class = "examples" > < span class = 'fu' > < a href = 'https://rdrr.io/r/base/library.html' > library< / a > < / span > (< span class = 'no' > dplyr< / span > )
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< span class = 'no' > example_isolates< / span > < span class = 'kw' > %> %< / span >
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< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/mutate.html' > mutate< / a > < / span > (< span class = 'kw' > EUCAST< / span > < span class = 'kw' > =< / span > < span class = 'fu' > mdro< / span > (< span class = 'no' > .< / span > ),
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< span class = 'kw' > BRMO< / span > < span class = 'kw' > =< / span > < span class = 'fu' > brmo< / span > (< span class = 'no' > .< / span > ),
< span class = 'kw' > MRGN< / span > < span class = 'kw' > =< / span > < span class = 'fu' > mrgn< / span > (< span class = 'no' > .< / span > ))
< span class = 'no' > example_isolates< / span > < span class = 'kw' > %> %< / span >
2019-10-07 14:57:27 +02:00
< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/select.html' > rename< / a > < / span > (< span class = 'kw' > PIP< / span > < span class = 'kw' > =< / span > < span class = 'no' > TZP< / span > ) < span class = 'kw' > %> %< / span > < span class = 'co' > # no piperacillin, so take piperacillin/tazobactam< / span >
< span class = 'fu' > mrgn< / span > () < span class = 'kw' > %> %< / span > < span class = 'co' > # check German guideline< / span >
< span class = 'fu' > < a href = 'https://rdrr.io/pkg/clean/man/freq.html' > freq< / a > < / span > () < span class = 'co' > # check frequencies< / span > < / pre >
2018-12-29 22:24:19 +01:00
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< h2 > Contents< / h2 >
< ul class = "nav nav-pills nav-stacked" >
< li > < a href = "#arguments" > Arguments< / a > < / li >
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< li > < a href = "#source" > Source< / a > < / li >
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< li > < a href = "#value" > Value< / a > < / li >
< li > < a href = "#details" > Details< / a > < / li >
< li > < a href = "#antibiotics" > Antibiotics< / a > < / li >
2019-01-02 23:24:07 +01:00
< li > < a href = "#read-more-on-our-website-" > Read more on our website!< / a > < / li >
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< li > < a href = "#examples" > Examples< / a > < / li >
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< p > Developed by < a href = 'https://www.rug.nl/staff/m.s.berends/' > Matthijs S. Berends< / a > , < a href = 'https://www.rug.nl/staff/c.f.luz/' > Christian F. Luz< / a > , < a href = 'https://www.rug.nl/staff/a.w.friedrich/' > Alex W. Friedrich< / a > , < a href = 'https://www.rug.nl/staff/b.sinha/' > Bhanu N. M. Sinha< / a > , < a href = 'https://www.rug.nl/staff/c.j.albers/' > Casper J. Albers< / a > , < a href = 'https://www.rug.nl/staff/c.glasner/' > Corinna Glasner< / a > .< / p >
2018-12-29 22:24:19 +01:00
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< p > Site built with < a href = "https://pkgdown.r-lib.org/" > pkgdown< / a > 1.4.1.< / p >
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