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< img src = "../logo.svg" class = "logo" alt = "" > < h1 > Determine Bug-Drug Combinations< / h1 >
< small class = "dont-index" > Source: < a href = "https://github.com/msberends/AMR/blob/HEAD/R/bug_drug_combinations.R" class = "external-link" > < code > R/bug_drug_combinations.R< / code > < / a > < / small >
< div class = "d-none name" > < code > bug_drug_combinations.Rd< / code > < / div >
< / div >
< div class = "ref-description section level2" >
< p > Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use < code > < a href = "https://rdrr.io/r/base/format.html" class = "external-link" > format()< / a > < / code > on the result to prettify it to a publishable/printable format, see < em > Examples< / em > .< / p >
< / div >
< div class = "section level2" >
< h2 id = "ref-usage" > Usage< a class = "anchor" aria-label = "anchor" href = "#ref-usage" > < / a > < / h2 >
< div class = "sourceCode" > < pre class = "sourceCode r" > < code > < span > < span class = "fu" > bug_drug_combinations< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > , col_mo < span class = "op" > =< / span > < span class = "cn" > NULL< / span > , FUN < span class = "op" > =< / span > < span class = "va" > mo_shortname< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span > < / span >
< span > < / span >
< span > < span class = "co" > # S3 method for bug_drug_combinations< / span > < / span >
< span > < span class = "fu" > < a href = "https://rdrr.io/r/base/format.html" class = "external-link" > format< / a > < / span > < span class = "op" > (< / span > < / span >
< span > < span class = "va" > x< / span > ,< / span >
< span > translate_ab < span class = "op" > =< / span > < span class = "st" > "name (ab, atc)"< / span > ,< / span >
< span > language < span class = "op" > =< / span > < span class = "fu" > < a href = "translate.html" > get_AMR_locale< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > ,< / span >
< span > minimum < span class = "op" > =< / span > < span class = "fl" > 30< / span > ,< / span >
< span > combine_SI < span class = "op" > =< / span > < span class = "cn" > TRUE< / span > ,< / span >
< span > combine_IR < span class = "op" > =< / span > < span class = "cn" > FALSE< / span > ,< / span >
< span > add_ab_group < span class = "op" > =< / span > < span class = "cn" > TRUE< / span > ,< / span >
< span > remove_intrinsic_resistant < span class = "op" > =< / span > < span class = "cn" > FALSE< / span > ,< / span >
< span > decimal.mark < span class = "op" > =< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/options.html" class = "external-link" > getOption< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "OutDec"< / span > < span class = "op" > )< / span > ,< / span >
< span > big.mark < span class = "op" > =< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/ifelse.html" class = "external-link" > ifelse< / a > < / span > < span class = "op" > (< / span > < span class = "va" > decimal.mark< / span > < span class = "op" > ==< / span > < span class = "st" > ","< / span > , < span class = "st" > "."< / span > , < span class = "st" > ","< / span > < span class = "op" > )< / span > ,< / span >
< span > < span class = "va" > ...< / span > < / span >
< span > < span class = "op" > )< / span > < / span > < / code > < / pre > < / div >
< / div >
< div class = "section level2" >
< h2 id = "source" > Source< a class = "anchor" aria-label = "anchor" href = "#source" > < / a > < / h2 >
< p > < strong > M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition< / strong > , 2014, < em > Clinical and Laboratory Standards Institute (CLSI)< / em > . < a href = "https://clsi.org/standards/products/microbiology/documents/m39/" class = "external-link" > https://clsi.org/standards/products/microbiology/documents/m39/< / a > .< / p >
< / div >
< div class = "section level2" >
< h2 id = "arguments" > Arguments< a class = "anchor" aria-label = "anchor" href = "#arguments" > < / a > < / h2 >
< dl > < dt > x< / dt >
< dd > < p > data with antibiotic columns, such as < code > amox< / code > , < code > AMX< / code > and < code > AMC< / code > < / p > < / dd >
< dt > col_mo< / dt >
< dd > < 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 > < a href = "as.mo.html" > mo< / a > < / code > . Values will be coerced using < code > < a href = "as.mo.html" > as.mo()< / a > < / code > .< / p > < / dd >
< dt > FUN< / dt >
< dd > < p > the function to call on the < code > mo< / code > column to transform the microorganism codes, defaults to < code > < a href = "mo_property.html" > mo_shortname()< / a > < / code > < / p > < / dd >
< dt > ...< / dt >
< dd > < p > arguments passed on to < code > FUN< / code > < / p > < / dd >
< dt > translate_ab< / dt >
< dd > < p > a < a href = "https://rdrr.io/r/base/character.html" class = "external-link" > character< / a > of length 1 containing column names of the < a href = "antibiotics.html" > antibiotics< / a > data set< / p > < / dd >
< dt > language< / dt >
< dd > < p > language of the returned text, defaults to system language (see < code > < a href = "translate.html" > get_AMR_locale()< / a > < / code > ) and can also be set with < code > getOption("AMR_locale")< / code > . Use < code > language = NULL< / code > or < code > language = ""< / code > to prevent translation.< / p > < / dd >
< dt > minimum< / dt >
< dd > < p > the minimum allowed number of available (tested) isolates. Any isolate count lower than < code > minimum< / code > will return < code > NA< / code > with a warning. The default number of < code > 30< / code > isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see < em > Source< / em > .< / p > < / dd >
< dt > combine_SI< / dt >
< dd > < p > a < a href = "https://rdrr.io/r/base/logical.html" class = "external-link" > logical< / a > to indicate whether all values of S and I must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the argument < code > combine_IR< / code > , but this now follows the redefinition by EUCAST about the interpretation of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. Default is < code > TRUE< / code > .< / p > < / dd >
< dt > combine_IR< / dt >
< dd > < p > a < a href = "https://rdrr.io/r/base/logical.html" class = "external-link" > logical< / a > to indicate whether values R and I should be summed< / p > < / dd >
< dt > add_ab_group< / dt >
< dd > < p > a < a href = "https://rdrr.io/r/base/logical.html" class = "external-link" > logical< / a > to indicate where the group of the antimicrobials must be included as a first column< / p > < / dd >
< dt > remove_intrinsic_resistant< / dt >
< dd > < p > < a href = "https://rdrr.io/r/base/logical.html" class = "external-link" > logical< / a > to indicate that rows and columns with 100% resistance for all tested antimicrobials must be removed from the table< / p > < / dd >
< dt > decimal.mark< / dt >
< dd > < p > the character to be used to indicate the numeric
decimal point.< / p > < / dd >
< dt > big.mark< / dt >
< dd > < p > character; if not empty used as mark between every
< code > big.interval< / code > decimals < em > before< / em > (hence < code > big< / code > ) the
decimal point.< / p > < / dd >
< / dl > < / div >
< div class = "section level2" >
< h2 id = "value" > Value< a class = "anchor" aria-label = "anchor" href = "#value" > < / a > < / h2 >
< p > The function < code > bug_drug_combinations()< / code > returns a < a href = "https://rdrr.io/r/base/data.frame.html" class = "external-link" > data.frame< / a > with columns "mo", "ab", "S", "I", "R" and "total".< / p >
< / div >
< div class = "section level2" >
< h2 id = "details" > Details< a class = "anchor" aria-label = "anchor" href = "#details" > < / a > < / h2 >
< p > The function < code > < a href = "https://rdrr.io/r/base/format.html" class = "external-link" > format()< / a > < / code > calculates the resistance per bug-drug combination. Use < code > combine_IR = FALSE< / code > (default) to test R vs. S+I and < code > combine_IR = TRUE< / code > to test R+I vs. S.< / p >
< / div >
< div class = "section level2" >
< h2 id = "ref-examples" > Examples< a class = "anchor" aria-label = "anchor" href = "#ref-examples" > < / a > < / h2 >
< div class = "sourceCode" > < pre class = "sourceCode r" > < code > < span class = "r-in" > < span > < span class = "co" > # \donttest{< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > x< / span > < span class = "op" > < -< / span > < span class = "fu" > bug_drug_combinations< / span > < span class = "op" > (< / span > < span class = "va" > example_isolates< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > ℹ < / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://rdrr.io/r/utils/head.html" class = "external-link" > head< / a > < / span > < span class = "op" > (< / span > < span class = "va" > x< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > mo ab S I R total< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 1 (unknown species) PEN 14 0 1 15< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 2 (unknown species) OXA 0 0 1 1< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 3 (unknown species) FLC 0 0 0 0< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 4 (unknown species) AMX 15 0 1 16< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 5 (unknown species) AMC 15 0 0 15< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 6 (unknown species) AMP 15 0 1 16< / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > Use 'format()' on this result to get a publishable/printable format.< / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://rdrr.io/r/base/format.html" class = "external-link" > format< / a > < / span > < span class = "op" > (< / span > < span class = "va" > x< / span > , translate_ab < span class = "op" > =< / span > < span class = "st" > "name (atc)"< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > Group Drug< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 1 Aminoglycosides Amikacin (J01GB06)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 2 Gentamicin (J01GB03)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 3 Kanamycin (J01GB04)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 4 Tobramycin (J01GB01)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 5 Amphenicols Chloramphenicol (J01BA01)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 6 Antimycobacterials Rifampicin (J04AB02)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 7 Beta-lactams/penicillins Amoxicillin (J01CA04)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 8 Amoxicillin/clavulanic acid (J01CR02)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 9 Ampicillin (J01CA01)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 10 Benzylpenicillin (J01CE01)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 11 Flucloxacillin (J01CF05)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 12 Oxacillin (J01CF04)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 13 Piperacillin/tazobactam (J01CR05)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 14 Carbapenems Imipenem (J01DH51)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 15 Meropenem (J01DH02)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 16 Cephalosporins (1st gen.) Cefazolin (J01DB04)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 17 Cephalosporins (2nd gen.) Cefoxitin (J01DC01)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 18 Cefuroxime (J01DC02)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 19 Cephalosporins (3rd gen.) Cefotaxime (J01DD01)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 20 Ceftazidime (J01DD02)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 21 Ceftriaxone (J01DD04)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 22 Cephalosporins (4th gen.) Cefepime (J01DE01)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 23 Glycopeptides Teicoplanin (J01XA02)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 24 Vancomycin (J01XA01)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 25 Macrolides/lincosamides Azithromycin (J01FA10)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 26 Clindamycin (J01FF01)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 27 Erythromycin (J01FA01)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 28 Other antibacterials Fosfomycin (J01XX01)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 29 Mupirocin (D06AX09)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 30 Nitrofurantoin (J01XE01)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 31 Oxazolidinones Linezolid (J01XX08)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 32 Polymyxins Colistin (J01XB01)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 33 Quinolones Ciprofloxacin (J01MA02)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 34 Moxifloxacin (J01MA14)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 35 Tetracyclines Doxycycline (J01AA02)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 36 Tetracycline (J01AA07)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 37 Tigecycline (J01AA12)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 38 Trimethoprims Trimethoprim (J01EA01)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 39 Trimethoprim/sulfamethoxazole (J01EE01)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > CoNS E. coli E. faecalis K. pneumoniae< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 1 100.0% (43/43) 0.0% (0/171) 100.0% (39/39) < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 2 13.6% (42/309) 2.0% (9/460) 100.0% (39/39) 10.3% (6/58)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 3 100.0% (43/43) 100.0% (39/39) < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 4 78.2% (43/55) 2.6% (12/462) 100.0% (39/39) 10.3% (6/58)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 5 < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 6 100.0% (467/467) 100.0% (58/58)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 7 93.0% (132/142) 50.0% (196/392) 100.0% (58/58)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 8 42.6% (132/310) 13.1% (61/467) 10.3% (6/58)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 9 93.0% (132/142) 50.0% (196/392) 100.0% (58/58)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 10 77.6% (228/294) 100.0% (467/467) 100.0% (58/58)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 11 42.8% (134/313) < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 12 54.8% (34/62) < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 13 69.7% (23/33) 5.5% (23/416) 11.3% (6/53)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 14 47.9% (23/48) 0.0% (0/422) 0.0% (0/38) 0.0% (0/51)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 15 47.9% (23/48) 0.0% (0/418) 0.0% (0/53)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 16 47.9% (23/48) 2.4% (2/82) 100.0% (39/39) < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 17 47.9% (23/48) 6.9% (26/377) 100.0% (39/39) 2.2% (1/46)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 18 42.6% (133/312) 5.4% (25/465) 100.0% (39/39) 10.3% (6/58)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 19 47.9% (23/48) 2.4% (11/459) 100.0% (39/39) 5.2% (3/58)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 20 100.0% (313/313) 2.4% (11/460) 100.0% (39/39) 5.2% (3/58)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 21 47.9% (23/48) 2.4% (11/459) 100.0% (39/39) 5.2% (3/58)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 22 47.9% (23/48) 2.8% (9/317) 100.0% (39/39) 5.3% (2/38)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 23 100.0% (467/467) 100.0% (58/58)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 24 0.3% (1/304) 100.0% (467/467) 0.0% (0/39) 100.0% (58/58)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 25 44.1% (138/313) 100.0% (467/467) 100.0% (39/39) 100.0% (58/58)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 26 33.5% (59/176) 100.0% (467/467) 100.0% (39/39) 100.0% (58/58)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 27 44.1% (138/313) 100.0% (467/467) 100.0% (39/39) 100.0% (58/58)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 28 0.0% (0/61) < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 29 < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 30 2.8% (13/458) 19.0% (11/58)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 31 100.0% (467/467) 100.0% (58/58)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 32 100.0% (313/313) 0.0% (0/240) 100.0% (39/39) 5.9% (2/34)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 33 27.4% (69/252) 12.5% (57/456) 3.6% (2/55)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 34 100.0% (57/57) < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 35 22.2% (67/302) < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 36 22.5% (59/262) < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 37 0.0% (0/195) 0.0% (0/68) < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 38 41.4% (126/304) 39.1% (155/396) 100.0% (39/39) 18.4% (9/49)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 39 12.2% (30/246) 31.6% (147/465) 100.0% (39/39) 10.3% (6/58)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > P. aeruginosa P. mirabilis S. aureus S. epidermidis< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 1 100.0% (44/44)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 2 0.0% (0/30) 5.9% (2/34) 0.9% (2/233) 21.5% (35/163)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 3 100.0% (30/30) 100.0% (44/44)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 4 0.0% (0/30) 5.9% (2/34) 2.3% (2/86) 49.4% (44/89)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 5 100.0% (30/30) 0.0% (0/46) 3.1% (1/32)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 6 100.0% (30/30) 100.0% (36/36) 0.0% (0/108) 2.7% (2/73)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 7 100.0% (30/30) 93.9% (123/131) 98.9% (90/91)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 8 100.0% (30/30) 2.8% (1/36) 0.4% (1/235) 54.5% (90/165)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 9 100.0% (30/30) 93.9% (123/131) 98.9% (90/91)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 10 100.0% (30/30) 100.0% (36/36) 80.9% (123/152) 89.4% (93/104)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 11 0.4% (1/235) 55.7% (97/174)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 12 0.0% (0/99) 50.0% (37/74)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 13 < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 14 6.3% (2/32) < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 15 < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 16 100.0% (30/30) < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 17 100.0% (30/30) < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 18 100.0% (30/30) 0.0% (0/36) 0.4% (1/235) 56.1% (97/173)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 19 100.0% (30/30) 0.0% (0/36) < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 20 3.3% (1/30) 0.0% (0/36) 100.0% (235/235) 100.0% (174/174)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 21 100.0% (30/30) 0.0% (0/36) < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 22 < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 23 100.0% (30/30) 100.0% (36/36) 0.0% (0/80) 64.1% (25/39)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 24 100.0% (30/30) 100.0% (36/36) 0.0% (0/232) 0.0% (0/171)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 25 100.0% (30/30) 100.0% (36/36) 8.9% (21/235) 53.8% (93/173)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 26 100.0% (30/30) 100.0% (36/36) 6.0% (9/151) 37.5% (42/112)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 27 100.0% (30/30) 100.0% (36/36) 8.9% (21/235) 53.8% (93/173)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 28 0.0% (0/80) 21.9% (14/64)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 29 0.0% (0/84) 8.7% (6/69)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 30 100.0% (36/36) < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 31 100.0% (30/30) 100.0% (36/36) 0.0% (0/82) 0.0% (0/68)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 32 100.0% (36/36) 100.0% (235/235) 100.0% (174/174)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 33 0.0% (0/30) 5.6% (2/36) 10.5% (20/191) 36.0% (49/136)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 34 2.2% (1/46) 0.0% (0/31)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 35 100.0% (30/30) 100.0% (36/36) 3.0% (7/231) 32.4% (55/170)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 36 100.0% (30/30) 100.0% (36/36) 3.2% (7/217) 32.9% (55/167)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 37 100.0% (30/30) 100.0% (36/36) 0.0% (0/209) 0.0% (0/109)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 38 100.0% (30/30) 36.4% (12/33) 8.4% (13/155) 58.5% (69/118)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 39 100.0% (30/30) 25.0% (9/36) 3.9% (9/231) 17.5% (24/137)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > S. hominis S. pneumoniae< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 1 100.0% (117/117)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 2 7.5% (6/80) 100.0% (117/117)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 3 100.0% (117/117)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 4 14.5% (9/62) 100.0% (117/117)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 5 6.5% (2/31) < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 6 0.0% (0/61) < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 7 0.0% (0/112)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 8 35.0% (28/80) 0.0% (0/112)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 9 0.0% (0/112)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 10 0.0% (0/117)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 11 34.6% (28/81) < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 12 39.7% (23/58) < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 13 0.0% (0/112)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 14 < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 15 < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 16 < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 17 < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 18 33.3% (27/81) 0.0% (0/61)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 19 < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 20 100.0% (81/81) 100.0% (117/117)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 21 < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 22 < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 23 6.8% (4/59) < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 24 0.0% (0/81) 0.0% (0/94)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 25 40.7% (33/81) 7.8% (9/116)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 26 29.4% (20/68) 6.5% (4/62)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 27 40.7% (33/81) 7.8% (9/116)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 28 100.0% (59/59) < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 29 1.6% (1/61) < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 30 < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 31 0.0% (0/60) < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 32 100.0% (81/81) 100.0% (117/117)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 33 20.0% (14/70) < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 34 0.0% (0/32) < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 35 55.0% (44/80) 4.5% (5/112)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 36 54.3% (44/81) 4.7% (5/106)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 37 0.0% (0/36) < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 38 57.9% (22/38) 17.9% (17/95)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 39 24.7% (20/81) 7.3% (8/109)< / span >
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # Use FUN to change to transformation of microorganism codes< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > bug_drug_combinations< / span > < span class = "op" > (< / span > < span class = "va" > example_isolates< / span > , < / span > < / span >
< span class = "r-in" > < span > FUN < span class = "op" > =< / span > < span class = "va" > mo_gramstain< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > ℹ < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > mo ab S I R total< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 1 Gram-negative PEN 8 0 717 725< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 2 Gram-negative OXA 6 0 0 6< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 3 Gram-negative FLC 6 0 0 6< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 4 Gram-negative AMX 226 0 405 631< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 5 Gram-negative AMC 463 89 174 726< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 6 Gram-negative AMP 226 0 405 631< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 7 Gram-negative TZP 554 11 76 641< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 8 Gram-negative CZO 94 2 110 206< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 9 Gram-negative FEP 470 1 14 485< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 10 Gram-negative CXM 539 22 142 703< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 11 Gram-negative FOX 435 8 135 578< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 12 Gram-negative CTX 578 1 57 636< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 13 Gram-negative CAZ 607 0 27 634< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 14 Gram-negative CRO 578 1 57 636< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 15 Gram-negative GEN 651 8 25 684< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 16 Gram-negative TOB 651 7 28 686< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 17 Gram-negative AMK 251 0 5 256< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 18 Gram-negative KAN 0 0 35 35< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 19 Gram-negative TMP 364 1 223 588< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 20 Gram-negative SXT 506 0 197 703< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 21 Gram-negative NIT 491 51 122 664< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 22 Gram-negative FOS 71 0 7 78< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 23 Gram-negative LNZ 0 0 707 707< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 24 Gram-negative CIP 610 11 63 684< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 25 Gram-negative MFX 0 0 63 63< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 26 Gram-negative VAN 0 0 707 707< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 27 Gram-negative TEC 0 0 707 707< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 28 Gram-negative TCY 15 1 110 126< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 29 Gram-negative TGC 87 0 101 188< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 30 Gram-negative DOX 10 0 108 118< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 31 Gram-negative ERY 1 2 696 699< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 32 Gram-negative CLI 18 1 709 728< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 33 Gram-negative AZM 1 2 696 699< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 34 Gram-negative IPM 616 10 5 631< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 35 Gram-negative MEM 624 0 2 626< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 36 Gram-negative MTR 21 0 2 23< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 37 Gram-negative CHL 1 0 30 31< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 38 Gram-negative COL 309 0 78 387< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 39 Gram-negative MUP 0 0 0 0< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 40 Gram-negative RIF 1 0 695 696< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 41 Gram-positive PEN 395 11 483 889< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 42 Gram-positive OXA 245 0 113 358< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 43 Gram-positive FLC 659 0 278 937< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 44 Gram-positive AMX 302 3 398 703< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 45 Gram-positive AMC 864 2 272 1138< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 46 Gram-positive AMP 302 3 398 703< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 47 Gram-positive TZP 294 2 49 345< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 48 Gram-positive CZO 151 0 89 240< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 49 Gram-positive FEP 150 0 89 239< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 50 Gram-positive CXM 756 0 328 1084< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 51 Gram-positive FOX 151 0 89 240< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 52 Gram-positive CTX 218 0 89 307< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 53 Gram-positive CAZ 0 0 1177 1177< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 54 Gram-positive CRO 218 0 89 307< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 55 Gram-positive GEN 721 19 430 1170< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 56 Gram-positive TOB 228 0 437 665< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 57 Gram-positive AMK 0 0 436 436< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 58 Gram-positive KAN 0 0 436 436< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 59 Gram-positive TMP 553 9 343 905< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 60 Gram-positive SXT 883 6 163 1052< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 61 Gram-positive NIT 73 0 5 78< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 62 Gram-positive FOS 132 0 141 273< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 63 Gram-positive LNZ 312 0 2 314< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 64 Gram-positive CIP 502 58 164 724< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 65 Gram-positive MFX 136 4 8 148< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 66 Gram-positive VAN 1141 0 5 1146< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 67 Gram-positive TEC 237 0 32 269< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 68 Gram-positive TCY 800 22 245 1067< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 69 Gram-positive TGC 610 0 0 610< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 70 Gram-positive DOX 802 7 206 1015< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 71 Gram-positive ERY 797 7 385 1189< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 72 Gram-positive CLI 556 3 220 779< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 73 Gram-positive AZM 797 7 385 1189< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 74 Gram-positive IPM 207 0 50 257< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 75 Gram-positive MEM 156 0 47 203< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 76 Gram-positive MTR 1 0 2 3< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 77 Gram-positive CHL 120 0 3 123< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 78 Gram-positive COL 0 0 1237 1237< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 79 Gram-positive MUP 251 3 16 270< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 80 Gram-positive RIF 301 2 3 306< / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > Use 'format()' on this result to get a publishable/printable format.< / span >
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > bug_drug_combinations< / span > < span class = "op" > (< / span > < span class = "va" > example_isolates< / span > ,< / span > < / span >
< span class = "r-in" > < span > FUN < span class = "op" > =< / span > < span class = "kw" > function< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > < span class = "op" > )< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/ifelse.html" class = "external-link" > ifelse< / a > < / span > < span class = "op" > (< / span > < span class = "va" > x< / span > < span class = "op" > ==< / span > < span class = "fu" > < a href = "as.mo.html" > as.mo< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "E. coli"< / span > < span class = "op" > )< / span > ,< / span > < / span >
< span class = "r-in" > < span > < span class = "st" > "E. coli"< / span > ,< / span > < / span >
< span class = "r-in" > < span > < span class = "st" > "Others"< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > ℹ < / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > ℹ < / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > coli). Run `mo_uncertainties()` to review this.< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > mo ab S I R total< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 1 E. coli PEN 0 0 467 467< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 2 E. coli OXA 0 0 0 0< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 3 E. coli FLC 0 0 0 0< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 4 E. coli AMX 196 0 196 392< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 5 E. coli AMC 332 74 61 467< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 6 E. coli AMP 196 0 196 392< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 7 E. coli TZP 388 5 23 416< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 8 E. coli CZO 79 1 2 82< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 9 E. coli FEP 308 0 9 317< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 10 E. coli CXM 425 15 25 465< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 11 E. coli FOX 347 4 26 377< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 12 E. coli CTX 448 0 11 459< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 13 E. coli CAZ 449 0 11 460< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 14 E. coli CRO 448 0 11 459< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 15 E. coli GEN 451 0 9 460< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 16 E. coli TOB 450 0 12 462< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 17 E. coli AMK 171 0 0 171< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 18 E. coli KAN 0 0 0 0< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 19 E. coli TMP 241 0 155 396< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 20 E. coli SXT 318 0 147 465< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 21 E. coli NIT 429 16 13 458< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 22 E. coli FOS 61 0 0 61< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 23 E. coli LNZ 0 0 467 467< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 24 E. coli CIP 398 1 57 456< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 25 E. coli MFX 0 0 57 57< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 26 E. coli VAN 0 0 467 467< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 27 E. coli TEC 0 0 467 467< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 28 E. coli TCY 1 0 2 3< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 29 E. coli TGC 68 0 0 68< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 30 E. coli DOX 0 0 0 0< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 31 E. coli ERY 0 0 467 467< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 32 E. coli CLI 0 0 467 467< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 33 E. coli AZM 0 0 467 467< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 34 E. coli IPM 422 0 0 422< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 35 E. coli MEM 418 0 0 418< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 36 E. coli MTR 2 0 0 2< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 37 E. coli CHL 0 0 0 0< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 38 E. coli COL 240 0 0 240< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 39 E. coli MUP 0 0 0 0< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 40 E. coli RIF 0 0 467 467< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 41 Others PEN 417 11 734 1162< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 42 Others OXA 251 0 114 365< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 43 Others FLC 665 0 278 943< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 44 Others AMX 347 3 608 958< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 45 Others AMC 1010 17 385 1412< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 46 Others AMP 347 3 608 958< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 47 Others TZP 474 8 103 585< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 48 Others CZO 166 1 197 364< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 49 Others FEP 312 1 94 407< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 50 Others CXM 872 7 445 1324< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 51 Others FOX 239 4 198 441< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 52 Others CTX 348 1 135 484< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 53 Others CAZ 158 0 1193 1351< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 54 Others CRO 348 1 135 484< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 55 Others GEN 921 27 447 1395< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 56 Others TOB 429 7 453 889< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 57 Others AMK 80 0 441 521< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 58 Others KAN 0 0 471 471< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 59 Others TMP 677 10 416 1103< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 60 Others SXT 1074 6 214 1294< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 61 Others NIT 136 35 114 285< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 62 Others FOS 142 0 148 290< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 63 Others LNZ 314 0 242 556< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 64 Others CIP 714 68 171 953< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 65 Others MFX 136 4 14 154< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 66 Others VAN 1149 0 245 1394< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 67 Others TEC 237 0 272 509< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 68 Others TCY 819 23 355 1197< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 69 Others TGC 629 0 101 730< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 70 Others DOX 814 7 315 1136< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 71 Others ERY 801 9 617 1427< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 72 Others CLI 586 4 463 1053< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 73 Others AZM 801 9 617 1427< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 74 Others IPM 402 10 55 467< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 75 Others MEM 362 0 49 411< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 76 Others MTR 27 0 5 32< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 77 Others CHL 121 0 33 154< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 78 Others COL 69 0 1331 1400< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 79 Others MUP 251 3 16 270< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 80 Others RIF 303 2 231 536< / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > Use 'format()' on this result to get a publishable/printable format.< / span >
< span class = "r-in" > < span > < span class = "co" > # }< / span > < / span > < / span >
< / code > < / pre > < / div >
< / div >
< / main > < aside class = "col-md-3" > < nav id = "toc" > < h2 > On this page< / h2 >
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< footer > < div class = "pkgdown-footer-left" >
< p > < / p > < p > < code > AMR< / code > (for R). Developed at the < a target = "_blank" href = "https://www.rug.nl" class = "external-link" > University of Groningen< / a > in collaboration with non-profit organisations< br > < a target = "_blank" href = "https://www.certe.nl" class = "external-link" > Certe Medical Diagnostics and Advice Foundation< / a > and < a target = "_blank" href = "https://www.umcg.nl" class = "external-link" > University Medical Center Groningen< / a > .< / p >
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