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< h1 > Determine bug-drug combinations< / h1 >
< div class = "hidden name" > < code > bug_drug_combinations.Rd< / code > < / div >
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< 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 > format< / code > on the result to prettify it to a publicable/printable format, see Examples.< / p >
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< / div >
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< pre class = "usage" > < span class = 'fu' > bug_drug_combinations< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > col_mo< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > , < span class = 'kw' > FUN< / span > < span class = 'kw' > =< / span > < span class = 'no' > mo_shortname< / span > , < span class = 'no' > ...< / span > )
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< span class = 'co' > # S3 method for bug_drug_combinations< / span >
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< span class = 'fu' > < a href = 'https://rdrr.io/r/base/format.html' > format< / a > < / span > (< span class = 'no' > x< / span > ,
< span class = 'kw' > translate_ab< / span > < span class = 'kw' > =< / span > < span class = 'st' > "name (ab, atc)"< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'translate.html' > get_locale< / a > < / span > (),
< span class = 'kw' > minimum< / span > < span class = 'kw' > =< / span > < span class = 'fl' > 30< / span > , < span class = 'kw' > combine_SI< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > , < span class = 'kw' > combine_IR< / span > < span class = 'kw' > =< / span > < span class = 'fl' > FALSE< / span > ,
< span class = 'kw' > add_ab_group< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > , < span class = 'kw' > remove_intrinsic_resistant< / span > < span class = 'kw' > =< / span > < span class = 'fl' > FALSE< / span > ,
< span class = 'kw' > decimal.mark< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'https://rdrr.io/r/base/options.html' > getOption< / a > < / span > (< span class = 'st' > "OutDec"< / span > ), < span class = 'kw' > big.mark< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'https://rdrr.io/r/base/ifelse.html' > ifelse< / a > < / span > (< span class = 'no' > decimal.mark< / span > < span class = 'kw' > ==< / span >
< span class = 'st' > ","< / span > , < span class = 'st' > "."< / span > , < span class = 'st' > ","< / 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 >
< th > x< / th >
< td > < p > data with antibiotic columns, like e.g. < code > AMX< / code > and < code > AMC< / code > < / p > < / td >
< / 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 >
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< tr >
< th > FUN< / th >
< td > < p > the function to call on the < code > mo< / code > column to transform the microorganism IDs, defaults to < code > < a href = 'mo_property.html' > mo_shortname< / a > < / code > < / p > < / td >
< / tr >
< tr >
< th > ...< / th >
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< td > < p > arguments passed on to < code > FUN< / code > < / p > < / td >
< / tr >
< tr >
< th > translate_ab< / th >
< td > < p > a character of length 1 containing column names of the < code > < a href = 'antibiotics.html' > antibiotics< / a > < / code > data set< / p > < / td >
< / tr >
< tr >
< th > language< / th >
< td > < p > language of the returned text, defaults to system language (see < code > < a href = 'translate.html' > get_locale< / a > < / code > ) and can also be set with < code > < a href = 'https://rdrr.io/r/base/options.html' > getOption< / a > ("AMR_locale")< / code > . Use < code > language = NULL< / code > or < code > language = ""< / code > to prevent translation.< / p > < / td >
< / tr >
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< tr >
< th > minimum< / th >
< td > < 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 Source.< / p > < / td >
< / tr >
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< tr >
< th > combine_SI< / th >
< td > < p > a logical 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 parameter < code > combine_IR< / code > , but this now follows the redefinition by EUCAST about the interpretion of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. Default is < code > TRUE< / code > .< / p > < / td >
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< / tr >
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< tr >
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< th > combine_IR< / th >
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< td > < p > logical to indicate whether values R and I should be summed< / p > < / td >
< / tr >
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< tr >
< th > add_ab_group< / th >
< td > < p > logical to indicate where the group of the antimicrobials must be included as a first column< / p > < / td >
< / tr >
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< tr >
< th > remove_intrinsic_resistant< / th >
< td > < p > logical to indicate that rows with 100% resistance for all tested antimicrobials must be removed from the table< / p > < / td >
< / tr >
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< tr >
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< th > decimal.mark< / th >
< td > < p > the character to be used to indicate the numeric
decimal point.< / p > < / td >
< / tr >
< tr >
< th > big.mark< / th >
< td > < 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 > < / td >
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< / tr >
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< / table >
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< h2 class = "hasAnchor" id = "source" > < a class = "anchor" href = "#source" > < / a > Source< / 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/' > https://clsi.org/standards/products/microbiology/documents/m39/< / a > .< / p >
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< h2 class = "hasAnchor" id = "value" > < a class = "anchor" href = "#value" > < / a > Value< / h2 >
< p > The function < code > bug_drug_combinations< / code > returns a < code > data.frame< / code > with columns "mo", "ab", "S", "I", "R" and "total".< / p >
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< h2 class = "hasAnchor" id = "details" > < a class = "anchor" href = "#details" > < / a > Details< / h2 >
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< p > The function < code > format< / 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 >
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< p > The language of the output can be overwritten with < code > < a href = 'https://rdrr.io/r/base/options.html' > options(AMR_locale)< / a > < / code > , please see < a href = 'translate.html' > translate< / 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 = 'co' > # \donttest{< / span >
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< span class = 'no' > x< / span > < span class = 'kw' > < -< / span > < span class = 'fu' > bug_drug_combinations< / span > (< span class = 'no' > example_isolates< / span > )
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< span class = 'no' > x< / span >
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< span class = 'fu' > < a href = 'https://rdrr.io/r/base/format.html' > format< / a > < / span > (< span class = 'no' > x< / span > , < span class = 'kw' > translate_ab< / span > < span class = 'kw' > =< / span > < span class = 'st' > "name (atc)"< / span > )
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< span class = 'co' > # Use FUN to change to transformation of microorganism codes< / span >
< span class = 'no' > x< / span > < span class = 'kw' > < -< / span > < span class = 'fu' > bug_drug_combinations< / span > (< span class = 'no' > example_isolates< / span > ,
< span class = 'kw' > FUN< / span > < span class = 'kw' > =< / span > < span class = 'no' > mo_gramstain< / span > )
< span class = 'no' > x< / span > < span class = 'kw' > < -< / span > < span class = 'fu' > bug_drug_combinations< / span > (< span class = 'no' > example_isolates< / span > ,
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< span class = 'kw' > FUN< / span > < span class = 'kw' > =< / span > < span class = 'kw' > function< / span > (< span class = 'no' > x< / span > ) < span class = 'fu' > < a href = 'https://rdrr.io/r/base/ifelse.html' > ifelse< / a > < / span > (< span class = 'no' > x< / span > < span class = 'kw' > ==< / span > < span class = 'st' > "B_ESCHR_COLI"< / span > ,
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< span class = 'st' > "E. coli"< / span > ,
< span class = 'st' > "Others"< / span > ))
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< span class = 'co' > # }< / span > < / pre >
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