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< ul class = "dropdown-menu" aria-labelledby = "dropdown-how-to" > < li > < a class = "dropdown-item" href = "../articles/AMR.html" > < span class = "fa fa-directions" > < / span > Conduct AMR Analysis< / a > < / li >
< li > < a class = "dropdown-item" href = "../reference/antibiogram.html" > < span class = "fa fa-file-prescription" > < / span > Generate Antibiogram (Trad./Syndromic/WISCA)< / a > < / li >
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< img src = "../logo.svg" class = "logo" alt = "" > < h1 > Determine Bug-Drug Combinations< / h1 >
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< small class = "dont-index" > Source: < a href = "https://github.com/msberends/AMR/blob/main/R/bug_drug_combinations.R" class = "external-link" > < code > R/bug_drug_combinations.R< / code > < / a > < / small >
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< 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 >
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< span > < span class = "co" > # S3 method for class 'bug_drug_combinations'< / span > < / span >
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< 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 > 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 >
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< 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 >
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< span > < span class = "va" > ...< / span > < / span >
< span > < span class = "op" > )< / span > < / span > < / code > < / pre > < / div >
< / div >
< div class = "section level2" >
< h2 id = "arguments" > Arguments< a class = "anchor" aria-label = "anchor" href = "#arguments" > < / a > < / h2 >
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< dl > < dt id = "arg-x" > x< a class = "anchor" aria-label = "anchor" href = "#arg-x" > < / a > < / dt >
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< dd > < p > a data set with antibiotic columns, such as < code > amox< / code > , < code > AMX< / code > and < code > AMC< / code > < / p > < / dd >
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< dt id = "arg-col-mo" > col_mo< a class = "anchor" aria-label = "anchor" href = "#arg-col-mo" > < / a > < / dt >
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< dd > < p > column name of the names or codes of the microorganisms (see < code > < a href = "as.mo.html" > as.mo()< / a > < / code > ) - the default is 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 >
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< dt id = "arg-fun" > FUN< a class = "anchor" aria-label = "anchor" href = "#arg-fun" > < / a > < / dt >
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< dd > < p > the function to call on the < code > mo< / code > column to transform the microorganism codes - the default is < code > < a href = "mo_property.html" > mo_shortname()< / a > < / code > < / p > < / dd >
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< dt id = "arg--" > ...< a class = "anchor" aria-label = "anchor" href = "#arg--" > < / a > < / dt >
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< dd > < p > arguments passed on to < code > FUN< / code > < / p > < / dd >
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< dt id = "arg-translate-ab" > translate_ab< a class = "anchor" aria-label = "anchor" href = "#arg-translate-ab" > < / a > < / dt >
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< 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 >
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< dt id = "arg-language" > language< a class = "anchor" aria-label = "anchor" href = "#arg-language" > < / a > < / dt >
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< dd > < p > language of the returned text - the default is the current system language (see < code > < a href = "translate.html" > get_AMR_locale()< / a > < / code > ) and can also be set with the package option < code > < a href = "AMR-options.html" > AMR_locale< / a > < / code > . Use < code > language = NULL< / code > or < code > language = ""< / code > to prevent translation.< / p > < / dd >
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< dt id = "arg-minimum" > minimum< a class = "anchor" aria-label = "anchor" href = "#arg-minimum" > < / a > < / dt >
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< 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 >
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< dt id = "arg-combine-si" > combine_SI< a class = "anchor" aria-label = "anchor" href = "#arg-combine-si" > < / a > < / dt >
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< dd > < p > a < a href = "https://rdrr.io/r/base/logical.html" class = "external-link" > logical< / a > to indicate whether values S, SDD, and I should be summed, so resistance will be based on only R - the default is < code > TRUE< / code > < / p > < / dd >
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< dt id = "arg-add-ab-group" > add_ab_group< a class = "anchor" aria-label = "anchor" href = "#arg-add-ab-group" > < / a > < / dt >
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< 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 >
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< dt id = "arg-remove-intrinsic-resistant" > remove_intrinsic_resistant< a class = "anchor" aria-label = "anchor" href = "#arg-remove-intrinsic-resistant" > < / a > < / dt >
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< 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 >
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< dt id = "arg-decimal-mark" > decimal.mark< a class = "anchor" aria-label = "anchor" href = "#arg-decimal-mark" > < / a > < / dt >
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< dd > < p > the character to be used to indicate the numeric
decimal point.< / p > < / dd >
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< dt id = "arg-big-mark" > big.mark< a class = "anchor" aria-label = "anchor" href = "#arg-big-mark" > < / a > < / dt >
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< 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 >
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< 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", "SDD", "I", "R", and "total".< / p >
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< / div >
< div class = "section level2" >
< h2 id = "details" > Details< a class = "anchor" aria-label = "anchor" href = "#details" > < / a > < / h2 >
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< 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 and returns a table ready for reporting/publishing. Use < code > combine_SI = TRUE< / code > (default) to test R vs. S+I and < code > combine_SI = FALSE< / code > to test R+I vs. S. This table can also directly be used in R Markdown / Quarto without the need for e.g. < code > < a href = "https://rdrr.io/pkg/knitr/man/kable.html" class = "external-link" > knitr::kable()< / a > < / code > .< / p >
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< / div >
< div class = "section level2" >
< h2 id = "ref-examples" > Examples< a class = "anchor" aria-label = "anchor" href = "#ref-examples" > < / a > < / h2 >
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< div class = "sourceCode" > < pre class = "sourceCode r" > < code > < span class = "r-in" > < span > < span class = "co" > # example_isolates is a data set available in the AMR package.< / span > < / span > < / span >
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< span class = "r-in" > < span > < span class = "co" > # run ?example_isolates for more info.< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > example_isolates< / span > < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # A tibble: 2,000 × < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > date patient age gender ward mo PEN OXA FLC AMX < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494; font-style: italic;" > < date> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < dbl> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < mo> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 1< / span > 2002-01-02 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 2< / span > 2002-01-03 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 3< / span > 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 4< / span > 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 5< / span > 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 6< / span > 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 7< / span > 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 8< / span > 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 9< / span > 2002-01-16 067927 45 F ICU B_STPHY_EPDR R NA R NA < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 10< / span > 2002-01-17 858515 79 F ICU B_STPHY_EPDR R NA S NA < / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # ℹ < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # ℹ < sir> , AMP < sir> , TZP < sir> , CZO < sir> , FEP < sir> ,< / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # CXM < sir> , FOX < sir> , CTX < sir> , CAZ < sir> , CRO < sir> , GEN < sir> ,< / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # TOB < sir> , AMK < sir> , KAN < sir> , TMP < sir> , SXT < sir> , NIT < sir> ,< / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # FOS < sir> , LNZ < sir> , CIP < sir> , MFX < sir> , VAN < sir> , TEC < sir> ,< / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # TCY < sir> , TGC < sir> , DOX < sir> , ERY < sir> , CLI < sir> , AZM < sir> ,< / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # IPM < sir> , MEM < sir> , MTR < sir> , CHL < sir> , COL < sir> , MUP < sir> , …< / span > < / span >
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< span class = "r-in" > < span > < / span > < / span >
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< span class = "r-in" > < span > < span class = "co" > # \donttest{< / span > < / span > < / span >
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< 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 >
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< 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 >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # A tibble: 6 × < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > mo ab S SDD I R NI total< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < int> < / span > < span style = "color: #949494; font-style: italic;" > < int> < / span > < span style = "color: #949494; font-style: italic;" > < int> < / span > < span style = "color: #949494; font-style: italic;" > < int> < / span > < span style = "color: #949494; font-style: italic;" > < int> < / span > < span style = "color: #949494; font-style: italic;" > < int> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 1< / span > (unknown species) AMC 15 0 0 0 0 15< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 2< / span > (unknown species) AMK 0 0 0 0 0 0< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 3< / span > (unknown species) AMP 15 0 0 1 0 16< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 4< / span > (unknown species) AMX 15 0 0 1 0 16< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 5< / span > (unknown species) AZM 3 0 0 3 0 6< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 6< / span > (unknown species) CAZ 0 0 0 0 0 0< / span >
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< span class = "r-msg co" > < span class = "r-pr" > #> < / span > Use 'format()' on this result to get a publishable/printable format.< / span >
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< 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 >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # A tibble: 39 × < / span > < / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > Group Drug CoNS `E. coli` `E. faecalis` `K. pneumoniae` `P. aeruginosa`< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 1< / span > < span style = "color: #949494;" > "< / span > Aminogl… Amik… < span style = "color: #949494;" > "< / span > 100… < span style = "color: #949494;" > "< / span > 0.0% … < span style = "color: #949494;" > "< / span > 100.0% (39/… < span style = "color: #949494;" > ""< / span > < span style = "color: #949494;" > ""< / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 2< / span > < span style = "color: #949494;" > ""< / span > Gent… < span style = "color: #949494;" > "< / span > 13… < span style = "color: #949494;" > "< / span > 2.0% … < span style = "color: #949494;" > "< / span > 100.0% (39/… < span style = "color: #949494;" > "< / span > 10.3% (6/58)< span style = "color: #949494;" > "< / span > < span style = "color: #949494;" > "< / span > 0.0% (0/30)< span style = "color: #949494;" > "< / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 3< / span > < span style = "color: #949494;" > ""< / span > Kana… < span style = "color: #949494;" > "< / span > 100… < span style = "color: #949494;" > ""< / span > < span style = "color: #949494;" > "< / span > 100.0% (39/… < span style = "color: #949494;" > ""< / span > < span style = "color: #949494;" > "< / span > 100.0% (30/30…< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 4< / span > < span style = "color: #949494;" > ""< / span > Tobr… < span style = "color: #949494;" > "< / span > 78… < span style = "color: #949494;" > "< / span > 2.6% … < span style = "color: #949494;" > "< / span > 100.0% (39/… < span style = "color: #949494;" > "< / span > 10.3% (6/58)< span style = "color: #949494;" > "< / span > < span style = "color: #949494;" > "< / span > 0.0% (0/30)< span style = "color: #949494;" > "< / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 5< / span > < span style = "color: #949494;" > "< / span > Ampheni… Chlo… < span style = "color: #949494;" > ""< / span > < span style = "color: #949494;" > ""< / span > < span style = "color: #949494;" > ""< / span > < span style = "color: #949494;" > ""< / span > < span style = "color: #949494;" > "< / span > 100.0% (30/30…< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 6< / span > < span style = "color: #949494;" > "< / span > Antimyc… Rifa… < span style = "color: #949494;" > ""< / span > < span style = "color: #949494;" > "< / span > 100.0% … < span style = "color: #949494;" > ""< / span > < span style = "color: #949494;" > "< / span > 100.0% (58/58… < span style = "color: #949494;" > "< / span > 100.0% (30/30…< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 7< / span > < span style = "color: #949494;" > "< / span > Beta-la… Amox… < span style = "color: #949494;" > "< / span > 93… < span style = "color: #949494;" > "< / span > 50.0% … < span style = "color: #949494;" > ""< / span > < span style = "color: #949494;" > "< / span > 100.0% (58/58… < span style = "color: #949494;" > "< / span > 100.0% (30/30…< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 8< / span > < span style = "color: #949494;" > ""< / span > Amox… < span style = "color: #949494;" > "< / span > 42… < span style = "color: #949494;" > "< / span > 13.1% … < span style = "color: #949494;" > ""< / span > < span style = "color: #949494;" > "< / span > 10.3% (6/58)< span style = "color: #949494;" > "< / span > < span style = "color: #949494;" > "< / span > 100.0% (30/30…< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 9< / span > < span style = "color: #949494;" > ""< / span > Ampi… < span style = "color: #949494;" > "< / span > 93… < span style = "color: #949494;" > "< / span > 50.0% … < span style = "color: #949494;" > ""< / span > < span style = "color: #949494;" > "< / span > 100.0% (58/58… < span style = "color: #949494;" > "< / span > 100.0% (30/30…< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 10< / span > < span style = "color: #949494;" > ""< / span > Benz… < span style = "color: #949494;" > "< / span > 77… < span style = "color: #949494;" > "< / span > 100.0% … < span style = "color: #949494;" > ""< / span > < span style = "color: #949494;" > "< / span > 100.0% (58/58… < span style = "color: #949494;" > "< / span > 100.0% (30/30…< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # ℹ < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # ℹ < chr> , `S. aureus` < chr> ,< / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # `S. epidermidis` < chr> , `S. hominis` < chr> , `S. pneumoniae` < chr> < / span > < / span >
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< 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 >
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< 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 > < / span >
< span class = "r-in" > < span > < span class = "op" > )< / span > < / span > < / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # A tibble: 80 × < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > mo ab S SDD I R NI total< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > *< / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < int> < / span > < span style = "color: #949494; font-style: italic;" > < int> < / span > < span style = "color: #949494; font-style: italic;" > < int> < / span > < span style = "color: #949494; font-style: italic;" > < int> < / span > < span style = "color: #949494; font-style: italic;" > < int> < / span > < span style = "color: #949494; font-style: italic;" > < int> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 1< / span > Gram-negative AMC 463 0 89 174 0 726< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 2< / span > Gram-negative AMK 251 0 0 5 0 256< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 3< / span > Gram-negative AMP 226 0 0 405 0 631< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 4< / span > Gram-negative AMX 226 0 0 405 0 631< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 5< / span > Gram-negative AZM 1 0 2 696 0 699< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 6< / span > Gram-negative CAZ 607 0 0 27 0 634< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 7< / span > Gram-negative CHL 1 0 0 30 0 31< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 8< / span > Gram-negative CIP 610 0 11 63 0 684< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 9< / span > Gram-negative CLI 18 0 1 709 0 728< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 10< / span > Gram-negative COL 309 0 0 78 0 387< / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # ℹ < / span > < / span >
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< span class = "r-msg co" > < span class = "r-pr" > #> < / span > Use 'format()' on this result to get a publishable/printable format.< / span >
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< span class = "r-in" > < span > < / span > < / span >
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< span class = "r-in" > < span > < span class = "fu" > bug_drug_combinations< / span > < span class = "op" > (< / span > < span class = "va" > example_isolates< / span > ,< / span > < / span >
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< 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 = "op" > {< / span > < / span > < / span >
< span class = "r-in" > < 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" > "Escherichia 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 > < / span >
< span class = "r-in" > < span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "op" > }< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "op" > )< / span > < / span > < / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # A tibble: 80 × < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > mo ab S SDD I R NI total< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > *< / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < int> < / span > < span style = "color: #949494; font-style: italic;" > < int> < / span > < span style = "color: #949494; font-style: italic;" > < int> < / span > < span style = "color: #949494; font-style: italic;" > < int> < / span > < span style = "color: #949494; font-style: italic;" > < int> < / span > < span style = "color: #949494; font-style: italic;" > < int> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 1< / span > E. coli AMC 332 0 74 61 0 467< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 2< / span > E. coli AMK 171 0 0 0 0 171< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 3< / span > E. coli AMP 196 0 0 196 0 392< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 4< / span > E. coli AMX 196 0 0 196 0 392< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 5< / span > E. coli AZM 0 0 0 467 0 467< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 6< / span > E. coli CAZ 449 0 0 11 0 460< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 7< / span > E. coli CHL 0 0 0 0 0 0< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 8< / span > E. coli CIP 398 0 1 57 0 456< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 9< / span > E. coli CLI 0 0 0 467 0 467< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 10< / span > E. coli COL 240 0 0 0 0 240< / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # ℹ < / span > < / span >
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< 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 >
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< / main > < aside class = "col-md-3" > < nav id = "toc" aria-label = "Table of contents" > < h2 > On this page< / h2 >
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< / nav > < / aside > < / div >
< footer > < div class = "pkgdown-footer-left" >
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< p > < code > AMR< / code > (for R). Free and open-source, licenced under the < a target = "_blank" href = "https://github.com/msberends/AMR/blob/main/LICENSE" class = "external-link" > GNU General Public License version 2.0 (GPL-2)< / a > .< br > Developed at the < a target = "_blank" href = "https://www.rug.nl" class = "external-link" > University of Groningen< / a > and < a target = "_blank" href = "https://www.umcg.nl" class = "external-link" > University Medical Center Groningen< / a > in The Netherlands.< / p >
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< / div >
< div class = "pkgdown-footer-right" >
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< p > < a target = "_blank" href = "https://www.rug.nl" class = "external-link" > < img src = "https://github.com/msberends/AMR/raw/main/pkgdown/assets/logo_rug.svg" style = "max-width: 150px;" > < / a > < a target = "_blank" href = "https://www.umcg.nl" class = "external-link" > < img src = "https://github.com/msberends/AMR/raw/main/pkgdown/assets/logo_umcg.svg" style = "max-width: 150px;" > < / a > < / p >
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< / div >
< / footer > < / div >
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< / body > < / html >
