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< meta property = "og:description" content = "Apply susceptibility rules as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, http://eucast.org), see Source. This includes (1) expert rules, (2) intrinsic resistance and (3) inferred resistance as defined in their breakpoint tables." / >
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< h1 > EUCAST rules< / h1 >
< div class = "hidden name" > < code > eucast_rules.Rd< / code > < / div >
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< p > Apply susceptibility rules as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, < a href = 'http://eucast.org' > http://eucast.org< / a > ), see < em > Source< / em > . This includes (1) expert rules, (2) intrinsic resistance and (3) inferred resistance as defined in their breakpoint tables.< / p >
< / div >
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< pre class = "usage" > < span class = 'fu' > eucast_rules< / span > (< span class = 'no' > x< / 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' > rules< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'https://rdrr.io/r/base/c.html' > c< / a > < / span > (< span class = 'st' > "breakpoints"< / span > ,
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< span class = 'st' > "expert"< / span > , < span class = 'st' > "other"< / span > , < span class = 'st' > "all"< / span > ), < span class = 'kw' > verbose< / span > < span class = 'kw' > =< / span > < span class = 'fl' > FALSE< / 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 >
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< td > < p > data with antibiotic columns, like e.g. < code > AMX< / code > and < code > AMC< / code > < / 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 >
< tr >
< th > rules< / th >
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< td > < p > a character vector that specifies which rules should be applied - one or more of < code > < a href = 'https://rdrr.io/r/base/c.html' > c("breakpoints", "expert", "other", "all")< / a > < / code > < / p > < / td >
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< / tr >
< tr >
< th > verbose< / th >
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< td > < p > a logical to turn Verbose mode on and off (default is off). In Verbose mode, the function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way.< / p > < / td >
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< / tr >
< 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 >
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< ul >
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< li > < p > EUCAST Expert Rules. Version 2.0, 2012. < br / >
Leclercq et al. < strong > EUCAST expert rules in antimicrobial susceptibility testing.< / strong > < em > Clin Microbiol Infect.< / em > 2013;19(2):141-60. < br / >
< a href = 'https://doi.org/10.1111/j.1469-0691.2011.03703.x' > https://doi.org/10.1111/j.1469-0691.2011.03703.x< / a > < / p > < / li >
< li > < p > EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016. < br / >
< a href = 'http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf' > http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf< / a > < / p > < / li >
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< li > < p > EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019. < br / >
< a href = 'http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx' > http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx< / a > < / p > < / li >
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< h2 class = "hasAnchor" id = "value" > < a class = "anchor" href = "#value" > < / a > Value< / h2 >
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< p > The input of < code > x< / code > , possibly with edited values of antibiotics. Or, if < code > verbose = TRUE< / code > , a < code > data.frame< / code > with all original and new values of the affected bug-drug combinations.< / p >
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< h2 class = "hasAnchor" id = "details" > < a class = "anchor" href = "#details" > < / a > Details< / h2 >
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< p > < strong > Note:< / strong > This function does not translate MIC values to RSI values. Use < code > < a href = 'as.rsi.html' > as.rsi< / a > < / code > for that. < br / >
< strong > Note:< / strong > When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance.< / p >
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< p > The file containing all EUCAST rules is located here: < a href = 'https://gitlab.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv' > https://gitlab.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv< / 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 > eucast_rules< / code > and < code > < a href = 'mdro.html' > mdro< / a > < / 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 >
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< 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 = 'no' > a< / span > < span class = 'kw' > < -< / span > < span class = 'fu' > < a href = 'https://rdrr.io/r/base/data.frame.html' > data.frame< / a > < / span > (< span class = 'kw' > mo< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'https://rdrr.io/r/base/c.html' > c< / a > < / span > (< span class = 'st' > "Staphylococcus aureus"< / span > ,
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< span class = 'st' > "Enterococcus faecalis"< / span > ,
< span class = 'st' > "Escherichia coli"< / span > ,
< span class = 'st' > "Klebsiella pneumoniae"< / span > ,
< span class = 'st' > "Pseudomonas aeruginosa"< / span > ),
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< span class = 'kw' > VAN< / span > < span class = 'kw' > =< / span > < span class = 'st' > "-"< / span > , < span class = 'co' > # Vancomycin< / span >
< span class = 'kw' > AMX< / span > < span class = 'kw' > =< / span > < span class = 'st' > "-"< / span > , < span class = 'co' > # Amoxicillin< / span >
< span class = 'kw' > COL< / span > < span class = 'kw' > =< / span > < span class = 'st' > "-"< / span > , < span class = 'co' > # Colistin< / span >
< span class = 'kw' > CAZ< / span > < span class = 'kw' > =< / span > < span class = 'st' > "-"< / span > , < span class = 'co' > # Ceftazidime< / span >
< span class = 'kw' > CXM< / span > < span class = 'kw' > =< / span > < span class = 'st' > "-"< / span > , < span class = 'co' > # Cefuroxime< / span >
< span class = 'kw' > PEN< / span > < span class = 'kw' > =< / span > < span class = 'st' > "S"< / span > , < span class = 'co' > # Penicillin G< / span >
< span class = 'kw' > FOX< / span > < span class = 'kw' > =< / span > < span class = 'st' > "S"< / span > , < span class = 'co' > # Cefoxitin< / span >
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< span class = 'kw' > stringsAsFactors< / span > < span class = 'kw' > =< / span > < span class = 'fl' > FALSE< / span > )
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< span class = 'no' > a< / span >
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< span class = 'co' > # mo VAN AMX COL CAZ CXM PEN FOX< / span >
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< span class = 'co' > # 1 Staphylococcus aureus - - - - - S S< / span >
< span class = 'co' > # 2 Enterococcus faecalis - - - - - S S< / span >
< span class = 'co' > # 3 Escherichia coli - - - - - S S< / span >
< span class = 'co' > # 4 Klebsiella pneumoniae - - - - - S S< / span >
< span class = 'co' > # 5 Pseudomonas aeruginosa - - - - - S S< / span >
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< span class = 'co' > # apply EUCAST rules: 18 results are forced as R or S< / span >
< span class = 'no' > b< / span > < span class = 'kw' > < -< / span > < span class = 'fu' > eucast_rules< / span > (< span class = 'no' > a< / span > )
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< span class = 'no' > b< / span >
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< span class = 'co' > # mo VAN AMX COL CAZ CXM PEN FOX< / span >
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< span class = 'co' > # 1 Staphylococcus aureus - S R R S S S< / span >
< span class = 'co' > # 2 Enterococcus faecalis - - R R R S R< / span >
< span class = 'co' > # 3 Escherichia coli R - - - - R S< / span >
< span class = 'co' > # 4 Klebsiella pneumoniae R R - - - R S< / span >
< span class = 'co' > # 5 Pseudomonas aeruginosa R R - - R R R< / span >
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< span class = 'co' > # \donttest{< / span >
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< span class = 'co' > # do not apply EUCAST rules, but rather get a data.frame< / span >
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< span class = 'co' > # with 18 rows, containing all details about the transformations:< / span >
< span class = 'no' > c< / span > < span class = 'kw' > < -< / span > < span class = 'fu' > eucast_rules< / span > (< span class = 'no' > a< / span > , < span class = 'kw' > verbose< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > )
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< span class = 'co' > # }< / span > < / pre >
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< / div >
< div class = "col-md-3 hidden-xs hidden-sm" id = "sidebar" >
< h2 > Contents< / h2 >
< ul class = "nav nav-pills nav-stacked" >
< li > < a href = "#arguments" > Arguments< / a > < / li >
< li > < a href = "#source" > Source< / a > < / li >
< li > < a href = "#value" > Value< / a > < / li >
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< li > < a href = "#details" > Details< / a > < / li >
2018-12-23 21:26:21 +01:00
< 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 >
2018-12-23 21:26:21 +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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