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< title > Create Identifier of an Isolate — isolate_identifier • AMR (for R)< / title >
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< h1 > Create Identifier of an Isolate< / h1 >
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< small class = "dont-index" > Source: < a href = 'https://github.com/msberends/AMR/blob/master/R/isolate_identifier.R' > < code > R/isolate_identifier.R< / code > < / a > < / small >
< div class = "hidden name" > < code > isolate_identifier.Rd< / code > < / div >
< / div >
< div class = "ref-description" >
< p > This function will paste the microorganism code with all antimicrobial results into one string for each row in a data set. This is useful to compare isolates, e.g. between institutions or regions, when there is no genotyping available.< / p >
< / div >
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< pre class = "usage" > < span class = 'fu' > isolate_identifier< / span > < span class = 'op' > (< / span > < span class = 'va' > x< / span > , col_mo < span class = 'op' > =< / span > < span class = 'cn' > NULL< / span > , cols_ab < span class = 'op' > =< / span > < span class = 'cn' > NULL< / span > < span class = 'op' > )< / span >
< span class = 'co' > # S3 method for isolate_identifier< / span >
< span class = 'fu' > < a href = 'https://rdrr.io/r/base/all.equal.html' > all.equal< / a > < / span > < span class = 'op' > (< / span > < span class = 'va' > target< / span > , < span class = 'va' > current< / span > , ignore_empty_results < span class = 'op' > =< / span > < span class = 'cn' > TRUE< / span > , < span class = 'va' > ...< / span > < span class = 'op' > )< / 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, such as < code > amox< / code > , < code > AMX< / code > and < code > AMC< / code > < / p > < / td >
< / tr >
< tr >
< th > col_mo< / th >
< 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 > < a href = 'as.mo.html' > mo< / a > < / code > . Values will be coerced using < code > < a href = 'as.mo.html' > as.mo()< / a > < / code > .< / p > < / td >
< / tr >
< tr >
< th > cols_ab< / th >
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< td > < p > a character vector of column names of < code > x< / code > , or (a combination with) an < a href = '[ab_class()]' > antibiotic selector function< / a > , such as < code > < a href = 'antibiotic_class_selectors.html' > carbapenems()< / a > < / code > and < code > < a href = 'antibiotic_class_selectors.html' > aminoglycosides()< / a > < / code > < / p > < / td >
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< / tr >
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< tr >
< th > target< / th >
< td > < p > < span style = "R" > R< / span > object.< / p > < / td >
< / tr >
< tr >
< th > current< / th >
< td > < p > other < span style = "R" > R< / span > object, to be compared with < code > target< / code > .< / p > < / td >
< / tr >
< tr >
< th > ignore_empty_results< / th >
< td > < p > a logical to indicate whether empty results must be ignored, so that only values R, S and I will be compared< / p > < / td >
< / tr >
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< tr >
< th > ...< / th >
< td > < p > column name of an antibiotic, see section < em > Antibiotics< / em > below< / p > < / td >
< / tr >
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< / table >
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< h2 class = "hasAnchor" id = "experimental-lifecycle" > < a class = "anchor" href = "#experimental-lifecycle" > < / a > Experimental Lifecycle< / h2 >
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< p > < img src = 'figures/lifecycle_experimental.svg' style = margin-bottom:5px / > < br / >
The < a href = 'lifecycle.html' > lifecycle< / a > of this function is < strong > experimental< / strong > . An experimental function is in early stages of development. The unlying code might be changing frequently. Experimental functions might be removed without deprecation, so you are generally best off waiting until a function is more mature before you use it in production code. Experimental functions are only available in development versions of this < code > AMR< / code > package and will thus not be included in releases that are submitted to CRAN, since such functions have not yet matured enough.< / 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.github.io/AMR/' > https://msberends.github.io/AMR/< / a > you can find < a href = 'https://msberends.github.io/AMR/articles/AMR.html' > a comprehensive tutorial< / a > about how to conduct AMR data analysis, the < a href = 'https://msberends.github.io/AMR/reference/' > complete documentation of all functions< / a > and < a href = 'https://msberends.github.io/AMR/articles/WHONET.html' > an example analysis using WHONET data< / a > . As we would like to better understand the backgrounds and needs of our users, please < a href = 'https://msberends.github.io/AMR/survey.html' > participate in our survey< / a > !< / p >
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< h2 class = "hasAnchor" id = "examples" > < a class = "anchor" href = "#examples" > < / a > Examples< / h2 >
< pre class = "examples" > < span class = 'co' > # automatic selection of microorganism and antibiotics (i.e., all < rsi> columns, see ?as.rsi)< / span >
< span class = 'va' > x< / span > < span class = 'op' > < -< / span > < span class = 'fu' > isolate_identifier< / span > < span class = 'op' > (< / span > < span class = 'va' > example_isolates< / span > < span class = 'op' > )< / span >
< span class = 'co' > # ignore microorganism codes, only use antimicrobial results< / span >
< span class = 'va' > x< / span > < span class = 'op' > < -< / span > < span class = 'fu' > isolate_identifier< / span > < span class = 'op' > (< / span > < span class = 'va' > example_isolates< / span > , col_mo < span class = 'op' > =< / span > < span class = 'cn' > FALSE< / span > , cols_ab < span class = 'op' > =< / span > < span class = 'fu' > < a href = 'https://rdrr.io/r/base/c.html' > c< / a > < / span > < span class = 'op' > (< / span > < span class = 'st' > "AMX"< / span > , < span class = 'st' > "TZP"< / span > , < span class = 'st' > "GEN"< / span > , < span class = 'st' > "TOB"< / span > < span class = 'op' > )< / span > < span class = 'op' > )< / span >
< span class = 'co' > # select antibiotics from certain antibiotic classes< / span >
< span class = 'va' > x< / span > < span class = 'op' > < -< / span > < span class = 'fu' > isolate_identifier< / span > < span class = 'op' > (< / span > < span class = 'va' > example_isolates< / span > , cols_ab < span class = 'op' > =< / span > < span class = 'fu' > < a href = 'https://rdrr.io/r/base/c.html' > c< / a > < / span > < span class = 'op' > (< / span > < span class = 'fu' > < a href = 'antibiotic_class_selectors.html' > carbapenems< / a > < / span > < span class = 'op' > (< / span > < span class = 'op' > )< / span > , < span class = 'fu' > < a href = 'antibiotic_class_selectors.html' > aminoglycosides< / a > < / span > < span class = 'op' > (< / span > < span class = 'op' > )< / span > < span class = 'op' > )< / span > < span class = 'op' > )< / span >
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< p > Developed by < a href = 'https://www.rug.nl/staff/m.s.berends/' > Matthijs S. Berends< / a > , < a href = 'https://www.rug.nl/staff/c.f.luz/' > Christian F. Luz< / a > , < a href = 'https://www.rug.nl/staff/a.w.friedrich/' > Alexander W. Friedrich< / a > , < a href = 'https://www.rug.nl/staff/b.sinha/' > Bhanu N. M. Sinha< / a > , < a href = 'https://www.rug.nl/staff/c.j.albers/' > Casper J. Albers< / a > , < a href = 'https://www.rug.nl/staff/c.glasner/' > Corinna Glasner< / a > .< / p >
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