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< title > Determine multidrug-resistant organisms (MDRO) — mdro • AMR (for R)< / title >
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Conduct AMR analysis
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Predict antimicrobial resistance
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Apply EUCAST rules
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Get properties of a microorganism
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Get properties of an antibiotic
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< h1 > Determine multidrug-resistant organisms (MDRO)< / h1 >
< div class = "hidden name" > < code > mdro.Rd< / code > < / div >
< / div >
< div class = "ref-description" >
< p > Determine which isolates are multidrug-resistant organisms (MDRO) according to country-specific guidelines.< / p >
< / div >
< pre class = "usage" > < span class = 'fu' > mdro< / span > (< span class = 'no' > tbl< / span > , < span class = 'kw' > country< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > , < span class = 'kw' > col_mo< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > , < span class = 'kw' > info< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > ,
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< span class = 'kw' > amcl< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > amik< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > amox< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > ampi< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > azit< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > aztr< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > cefa< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > cfra< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > cfep< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > cfot< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > cfox< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > cfta< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > cftr< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > cfur< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > chlo< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > cipr< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > clar< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > clin< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > clox< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > coli< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > czol< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > dapt< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > doxy< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > erta< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > eryt< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > fosf< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > fusi< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > gent< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > imip< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > kana< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > levo< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > linc< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > line< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > mero< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > metr< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > mino< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > moxi< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > nali< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > neom< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > neti< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > nitr< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > novo< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > norf< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > oflo< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > peni< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > pipe< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > pita< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > poly< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > qida< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > rifa< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > roxi< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > siso< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > teic< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > tetr< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > tica< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > tige< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > tobr< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > trim< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > trsu< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > vanc< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > ())
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< span class = 'fu' > brmo< / span > (< span class = 'no' > ...< / span > , < span class = 'kw' > country< / span > < span class = 'kw' > =< / span > < span class = 'st' > "nl"< / span > )
< span class = 'fu' > mrgn< / span > (< span class = 'no' > tbl< / span > , < span class = 'kw' > country< / span > < span class = 'kw' > =< / span > < span class = 'st' > "de"< / span > , < span class = 'no' > ...< / span > )
< span class = 'fu' > eucast_exceptional_phenotypes< / span > (< span class = 'no' > tbl< / span > , < span class = 'kw' > country< / span > < span class = 'kw' > =< / span > < span class = 'st' > "EUCAST"< / span > , < span class = 'no' > ...< / span > )< / pre >
< 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 > tbl< / th >
< td > < p > table with antibiotic columns, like e.g. < code > amox< / code > and < code > amcl< / code > < / p > < / td >
< / tr >
< tr >
< th > country< / th >
< td > < p > country code to determine guidelines. EUCAST rules will be used when left empty, see Details. Should be or a code from the < a href = 'https://en.wikipedia.org/wiki/ISO_3166-1_alpha-2#Officially_assigned_code_elements' > list of ISO 3166-1 alpha-2 country codes< / a > . Case-insensitive. Currently supported are < code > de< / code > (Germany) and < code > nl< / code > (the Netherlands).< / p > < / td >
< / tr >
< tr >
< th > col_mo< / th >
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< td > < p > column name of the unique IDs of the microorganisms (see < code > < a href = 'as.mo.html' > 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 >
2018-12-29 22:24:19 +01:00
< / tr >
< tr >
< th > info< / th >
< td > < p > print progress< / p > < / td >
< / tr >
< tr >
< th > amcl< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > amik< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > amox< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > ampi< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > azit< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > aztr< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > cefa< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > cfra< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > cfep< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > cfot< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > cfox< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > cfta< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > cftr< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > cfur< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > chlo< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > cipr< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > clar< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > clin< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > clox< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > coli< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > czol< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > dapt< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > doxy< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > erta< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > eryt< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > fosf< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > fusi< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > gent< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > imip< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > kana< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > levo< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > linc< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > line< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > mero< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > metr< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > mino< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > moxi< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > nali< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > neom< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > neti< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > nitr< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > novo< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > norf< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > oflo< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > peni< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > pipe< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > pita< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > poly< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > qida< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > rifa< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > roxi< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > siso< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > teic< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > tetr< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > tica< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > tige< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > tobr< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > trim< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > trsu< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > vanc< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > ...< / th >
< td > < p > parameters that are passed on to methods< / p > < / td >
< / tr >
< / table >
< h2 class = "hasAnchor" id = "value" > < a class = "anchor" href = "#value" > < / a > Value< / h2 >
< p > Ordered factor with levels < code > Negative < Positive, unconfirmed < Positive< / code > .< / p >
< h2 class = "hasAnchor" id = "details" > < a class = "anchor" href = "#details" > < / a > Details< / h2 >
< p > When < code > country< / code > will be left blank, guidelines will be taken from EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (< a href = 'http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf' > http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf< / a > ).< / p >
< h2 class = "hasAnchor" id = "antibiotics" > < a class = "anchor" href = "#antibiotics" > < / a > Antibiotics< / h2 >
2019-01-11 20:37:23 +01:00
< p > To define antibiotics column names, leave as it is to determine it automatically with < code > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / code > or input a text (case-insensitive) or use < code > NULL< / code > to skip a column (e.g. < code > tica = NULL< / code > ). Non-existing columns will anyway be skipped with a warning.< / p >
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< p > Abbrevations of the column containing antibiotics in the form: < strong > abbreviation< / strong > : generic name (< em > ATC code< / em > )< / p >
2019-01-08 16:23:45 +01:00
< p > < strong > amcl< / strong > : amoxicillin+clavulanic acid (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01CR02' > J01CR02< / a > ),
< strong > amik< / strong > : amikacin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01GB06' > J01GB06< / a > ),
< strong > amox< / strong > : amoxicillin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01CA04' > J01CA04< / a > ),
< strong > ampi< / strong > : ampicillin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01CA01' > J01CA01< / a > ),
< strong > azit< / strong > : azithromycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01FA10' > J01FA10< / a > ),
< strong > azlo< / strong > : azlocillin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01CA09' > J01CA09< / a > ),
< strong > aztr< / strong > : aztreonam (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DF01' > J01DF01< / a > ),
< strong > cefa< / strong > : cefaloridine (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DB02' > J01DB02< / a > ),
< strong > cfep< / strong > : cefepime (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DE01' > J01DE01< / a > ),
< strong > cfot< / strong > : cefotaxime (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DD01' > J01DD01< / a > ),
< strong > cfox< / strong > : cefoxitin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DC01' > J01DC01< / a > ),
< strong > cfra< / strong > : cefradine (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DB09' > J01DB09< / a > ),
< strong > cfta< / strong > : ceftazidime (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DD02' > J01DD02< / a > ),
< strong > cftr< / strong > : ceftriaxone (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DD04' > J01DD04< / a > ),
< strong > cfur< / strong > : cefuroxime (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DC02' > J01DC02< / a > ),
< strong > chlo< / strong > : chloramphenicol (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01BA01' > J01BA01< / a > ),
< strong > cipr< / strong > : ciprofloxacin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01MA02' > J01MA02< / a > ),
< strong > clar< / strong > : clarithromycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01FA09' > J01FA09< / a > ),
< strong > clin< / strong > : clindamycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01FF01' > J01FF01< / a > ),
< strong > clox< / strong > : flucloxacillin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01CF05' > J01CF05< / a > ),
< strong > coli< / strong > : colistin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01XB01' > J01XB01< / a > ),
< strong > czol< / strong > : cefazolin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DB04' > J01DB04< / a > ),
< strong > dapt< / strong > : daptomycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01XX09' > J01XX09< / a > ),
< strong > doxy< / strong > : doxycycline (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01AA02' > J01AA02< / a > ),
< strong > erta< / strong > : ertapenem (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DH03' > J01DH03< / a > ),
< strong > eryt< / strong > : erythromycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01FA01' > J01FA01< / a > ),
< strong > fosf< / strong > : fosfomycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01XX01' > J01XX01< / a > ),
< strong > fusi< / strong > : fusidic acid (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01XC01' > J01XC01< / a > ),
< strong > gent< / strong > : gentamicin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01GB03' > J01GB03< / a > ),
< strong > imip< / strong > : imipenem (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DH51' > J01DH51< / a > ),
< strong > kana< / strong > : kanamycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01GB04' > J01GB04< / a > ),
< strong > levo< / strong > : levofloxacin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01MA12' > J01MA12< / a > ),
< strong > linc< / strong > : lincomycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01FF02' > J01FF02< / a > ),
< strong > line< / strong > : linezolid (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01XX08' > J01XX08< / a > ),
< strong > mero< / strong > : meropenem (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DH02' > J01DH02< / a > ),
< strong > mezl< / strong > : mezlocillin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01CA10' > J01CA10< / a > ),
< strong > mino< / strong > : minocycline (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01AA08' > J01AA08< / a > ),
< strong > moxi< / strong > : moxifloxacin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01MA14' > J01MA14< / a > ),
< strong > nali< / strong > : nalidixic acid (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01MB02' > J01MB02< / a > ),
< strong > neom< / strong > : neomycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01GB05' > J01GB05< / a > ),
< strong > neti< / strong > : netilmicin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01GB07' > J01GB07< / a > ),
< strong > nitr< / strong > : nitrofurantoin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01XE01' > J01XE01< / a > ),
< strong > norf< / strong > : norfloxacin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01MA06' > J01MA06< / a > ),
< strong > novo< / strong > : novobiocin (an ATCvet code: < a href = 'https://www.whocc.no/atc_ddd_index/?code=QJ01XX95' > QJ01XX95< / a > ),
< strong > oflo< / strong > : ofloxacin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01MA01' > J01MA01< / a > ),
< strong > peni< / strong > : (benzyl)penicillin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01CE01' > J01CE01< / a > ),
< strong > pipe< / strong > : piperacillin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01CA12' > J01CA12< / a > ),
< strong > pita< / strong > : piperacillin+tazobactam (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01CR05' > J01CR05< / a > ),
< strong > poly< / strong > : polymyxin B (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01XB02' > J01XB02< / a > ),
< strong > pris< / strong > : pristinamycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01FG01' > J01FG01< / a > ),
< strong > qida< / strong > : quinupristin/dalfopristin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01FG02' > J01FG02< / a > ),
< strong > rifa< / strong > : rifampicin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J04AB02' > J04AB02< / a > ),
< strong > roxi< / strong > : roxithromycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01FA06' > J01FA06< / a > ),
< strong > siso< / strong > : sisomicin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01GB08' > J01GB08< / a > ),
< strong > teic< / strong > : teicoplanin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01XA02' > J01XA02< / a > ),
< strong > tetr< / strong > : tetracycline (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01AA07' > J01AA07< / a > ),
< strong > tica< / strong > : ticarcillin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01CA13' > J01CA13< / a > ),
< strong > tige< / strong > : tigecycline (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01AA12' > J01AA12< / a > ),
< strong > tobr< / strong > : tobramycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01GB01' > J01GB01< / a > ),
< strong > trim< / strong > : trimethoprim (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01EA01' > J01EA01< / a > ),
< strong > trsu< / strong > : sulfamethoxazole and trimethoprim (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01EE01' > J01EE01< / a > ),
< strong > vanc< / strong > : vancomycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01XA01' > J01XA01< / a > ).< / p >
2018-12-29 22:24:19 +01:00
2019-01-02 23:24:07 +01:00
< 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 >
< p > < img src = 'figures/logo.png' height = 40px style = margin-bottom:5px / > < br / >
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 omprehensive tutorial< / a > about how to conduct AMR analysis and find < a href = 'https://msberends.gitlab.io/AMR/reference' > the complete documentation of all functions< / a > , which reads a lot easier than in R.< / p >
2018-12-29 22:24:19 +01:00
< h2 class = "hasAnchor" id = "examples" > < a class = "anchor" href = "#examples" > < / a > Examples< / h2 >
2019-01-02 23:24:07 +01:00
< pre class = "examples" > < span class = 'co' > # NOT RUN {< / span >
< span class = 'fu' > < a href = 'https://www.rdocumentation.org/packages/base/topics/library' > library< / a > < / span > (< span class = 'no' > dplyr< / span > )
2018-12-29 22:24:19 +01:00
< span class = 'no' > septic_patients< / span > < span class = 'kw' > %> %< / span >
2019-01-06 20:23:49 +01:00
< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/mutate.html' > mutate< / a > < / span > (< span class = 'kw' > EUCAST< / span > < span class = 'kw' > =< / span > < span class = 'fu' > mdro< / span > (< span class = 'no' > .< / span > ),
2019-01-02 23:24:07 +01:00
< span class = 'kw' > BRMO< / span > < span class = 'kw' > =< / span > < span class = 'fu' > brmo< / span > (< span class = 'no' > .< / span > ))
< span class = 'co' > # }< / span > < / pre >
2018-12-29 22:24:19 +01:00
< / div >
< div class = "col-md-3 hidden-xs hidden-sm" id = "sidebar" >
< h2 > Contents< / h2 >
< ul class = "nav nav-pills nav-stacked" >
< li > < a href = "#arguments" > Arguments< / a > < / li >
< li > < a href = "#value" > Value< / a > < / li >
< li > < a href = "#details" > Details< / a > < / li >
< li > < a href = "#antibiotics" > Antibiotics< / a > < / li >
2019-01-02 23:24:07 +01:00
< li > < a href = "#read-more-on-our-website-" > Read more on our website!< / a > < / li >
2018-12-29 22:24:19 +01:00
< li > < a href = "#examples" > Examples< / a > < / li >
< / ul >
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< footer >
< div class = "copyright" >
< 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/c.glasner/' > Corinna Glasner< / a > , < a href = 'https://www.rug.nl/staff/a.w.friedrich/' > Alex W. Friedrich< / a > , < a href = 'https://www.rug.nl/staff/b.sinha/' > Bhanu N. M. Sinha< / a > .< / p >
< / div >
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