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< h1 > Determine first (weighted) isolates< / h1 >
< div class = "hidden name" > < code > first_isolate.Rd< / code > < / div >
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< p > Determine first (weighted) isolates of all microorganisms of every patient per episode and (if needed) per specimen type.< / p >
< / div >
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< pre class = "usage" > < span class = 'fu' > first_isolate< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > col_date< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > , < span class = 'kw' > col_patient_id< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > ,
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< span class = 'kw' > col_mo< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > , < span class = 'kw' > col_testcode< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > , < span class = 'kw' > col_specimen< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > ,
< span class = 'kw' > col_icu< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > , < span class = 'kw' > col_keyantibiotics< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > , < span class = 'kw' > episode_days< / span > < span class = 'kw' > =< / span > < span class = 'fl' > 365< / span > ,
< span class = 'kw' > testcodes_exclude< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > , < span class = 'kw' > icu_exclude< / span > < span class = 'kw' > =< / span > < span class = 'fl' > FALSE< / span > ,
< span class = 'kw' > specimen_group< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > , < span class = 'kw' > type< / span > < span class = 'kw' > =< / span > < span class = 'st' > "keyantibiotics"< / span > , < span class = 'kw' > ignore_I< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > ,
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< span class = 'kw' > points_threshold< / span > < span class = 'kw' > =< / span > < span class = 'fl' > 2< / span > , < span class = 'kw' > info< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > , < span class = 'kw' > include_unknown< / span > < span class = 'kw' > =< / span > < span class = 'fl' > FALSE< / span > , < span class = 'no' > ...< / span > )
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< span class = 'fu' > filter_first_isolate< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > col_date< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > , < span class = 'kw' > col_patient_id< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > ,
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< span class = 'kw' > col_mo< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > , < span class = 'no' > ...< / span > )
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< span class = 'fu' > filter_first_weighted_isolate< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > col_date< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > ,
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< span class = 'kw' > col_patient_id< / 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' > col_keyantibiotics< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / 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 >
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< th > x< / th >
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< td > < p > a < code > data.frame< / code > containing isolates.< / p > < / td >
< / tr >
< tr >
< th > col_date< / th >
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< td > < p > column name of the result date (or date that is was received on the lab), defaults to the first column of with a date class< / p > < / td >
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< / tr >
< tr >
< th > col_patient_id< / th >
< td > < p > column name of the unique IDs of the patients, defaults to the first column that starts with 'patient' or 'patid' (case insensitive)< / 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 >
< tr >
< th > col_testcode< / th >
< td > < p > column name of the test codes. Use < code > col_testcode = NULL< / code > to < strong > not< / strong > exclude certain test codes (like test codes for screening). In that case < code > testcodes_exclude< / code > will be ignored.< / p > < / td >
< / tr >
< tr >
< th > col_specimen< / th >
< td > < p > column name of the specimen type or group< / p > < / td >
< / tr >
< tr >
< th > col_icu< / th >
< td > < p > column name of the logicals (< code > TRUE< / code > /< code > FALSE< / code > ) whether a ward or department is an Intensive Care Unit (ICU)< / p > < / td >
< / tr >
< tr >
< th > col_keyantibiotics< / th >
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< td > < p > column name of the key antibiotics to determine first < em > weighted< / em > isolates, see < code > < a href = 'key_antibiotics.html' > key_antibiotics< / a > < / code > . Defaults to the first column that starts with 'key' followed by 'ab' or 'antibiotics' (case insensitive). Use < code > col_keyantibiotics = FALSE< / code > to prevent this.< / p > < / td >
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< / tr >
< tr >
< th > episode_days< / th >
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< td > < p > episode in days after which a genus/species combination will be determined as 'first isolate' again. The default of 365 days is based on the guideline by CLSI, see Source.< / p > < / td >
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< / tr >
< tr >
< th > testcodes_exclude< / th >
< td > < p > character vector with test codes that should be excluded (case-insensitive)< / p > < / td >
< / tr >
< tr >
< th > icu_exclude< / th >
< td > < p > logical whether ICU isolates should be excluded (rows with value < code > TRUE< / code > in column < code > col_icu< / code > )< / p > < / td >
< / tr >
< tr >
< th > specimen_group< / th >
< td > < p > value in column < code > col_specimen< / code > to filter on< / p > < / td >
< / tr >
< tr >
< th > type< / th >
< td > < p > type to determine weighed isolates; can be < code > "keyantibiotics"< / code > or < code > "points"< / code > , see Details< / p > < / td >
< / tr >
< tr >
< th > ignore_I< / th >
< td > < p > logical to determine whether antibiotic interpretations with < code > "I"< / code > will be ignored when < code > type = "keyantibiotics"< / code > , see Details< / p > < / td >
< / tr >
< tr >
< th > points_threshold< / th >
< td > < p > points until the comparison of key antibiotics will lead to inclusion of an isolate when < code > type = "points"< / code > , see Details< / p > < / td >
< / tr >
< tr >
< th > info< / th >
< td > < p > print progress< / p > < / td >
< / tr >
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< tr >
< th > include_unknown< / th >
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< td > < p > logical to determine whether 'unknown' microorganisms should be included too, i.e. microbial code < code > "UNKNOWN"< / code > , which defaults to < code > FALSE< / code > . For WHONET users, this means that all records with organism code < code > "con"< / code > (< em > contamination< / em > ) will be excluded at default. Isolates with a microbial ID of < code > NA< / code > will always be excluded as first isolate.< / p > < / td >
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< / tr >
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< tr >
< th > ...< / th >
< td > < p > parameters passed on to the < code > first_isolate< / code > function< / p > < / td >
< / tr >
< / table >
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< h2 class = "hasAnchor" id = "source" > < a class = "anchor" href = "#source" > < / a > Source< / h2 >
< p > Methodology of this function is based on: < 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 >
< h2 class = "hasAnchor" id = "value" > < a class = "anchor" href = "#value" > < / a > Value< / h2 >
< p > Logical vector< / p >
< h2 class = "hasAnchor" id = "details" > < a class = "anchor" href = "#details" > < / a > Details< / h2 >
< p > < strong > WHY THIS IS SO IMPORTANT< / strong > < br / >
To conduct an analysis of antimicrobial resistance, you should only include the first isolate of every patient per episode < a href = 'https://www.ncbi.nlm.nih.gov/pubmed/17304462' > [1]< / a > . If you would not do this, you could easily get an overestimate or underestimate of the resistance of an antibiotic. Imagine that a patient was admitted with an MRSA and that it was found in 5 different blood cultures the following week. The resistance percentage of oxacillin of all < em > S. aureus< / em > isolates would be overestimated, because you included this MRSA more than once. It would be < a href = 'https://en.wikipedia.org/wiki/Selection_bias' > selection bias< / a > .< / p >
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< p > All isolates with a microbial ID of < code > NA< / code > will be excluded as first isolate.< / p >
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< p > The functions < code > filter_first_isolate< / code > and < code > filter_first_weighted_isolate< / code > are helper functions to quickly filter on first isolates. The function < code > filter_first_isolate< / code > is essentially equal to:< / p > < pre >
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x %> %
mutate(only_firsts = first_isolate(x, ...)) %> %
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filter(only_firsts == TRUE) %> %
select(-only_firsts)
< / pre > < p > The function < code > filter_first_weighted_isolate< / code > is essentially equal to:< / p > < pre >
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x %> %
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mutate(keyab = key_antibiotics(.)) %> %
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mutate(only_weighted_firsts = first_isolate(x,
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col_keyantibiotics = "keyab", ...)) %> %
filter(only_weighted_firsts == TRUE) %> %
select(-only_weighted_firsts)
< / pre >
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< h2 class = "hasAnchor" id = "key-antibiotics" > < a class = "anchor" href = "#key-antibiotics" > < / a > Key antibiotics< / h2 >
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< p > There are two ways to determine whether isolates can be included as first < em > weighted< / em > isolates which will give generally the same results: < br / > < / p >
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< p > < strong > 1. Using< / strong > < code > type = "keyantibiotics"< / code > < strong > and parameter< / strong > < code > ignore_I< / code > < br / >
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Any difference from S to R (or vice versa) will (re)select an isolate as a first weighted isolate. With < code > ignore_I = FALSE< / code > , also differences from I to S|R (or vice versa) will lead to this. This is a reliable method and 30-35 times faster than method 2. Read more about this in the < code > < a href = 'key_antibiotics.html' > key_antibiotics< / a > < / code > function. < br / > < / p >
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< p > < strong > 2. Using< / strong > < code > type = "points"< / code > < strong > and parameter< / strong > < code > points_threshold< / code > < br / >
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A difference from I to S|R (or vice versa) means 0.5 points, a difference from S to R (or vice versa) means 1 point. When the sum of points exceeds < code > points_threshold< / code > , which default to < code > 2< / code > , an isolate will be (re)selected as a first weighted isolate.< / 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 = "see-also" > < a class = "anchor" href = "#see-also" > < / a > See also< / h2 >
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< div class = 'dont-index' > < p > < code > < a href = 'key_antibiotics.html' > key_antibiotics< / a > < / code > < / p > < / div >
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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' > # `example_isolates` is a dataset available in the AMR package.< / span >
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< span class = 'co' > # See ?example_isolates.< / span >
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< span class = 'fu' > < a href = 'https://rdrr.io/r/base/library.html' > library< / a > < / span > (< span class = 'no' > dplyr< / span > )
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< span class = 'co' > # Filter on first isolates:< / span >
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< span class = 'no' > example_isolates< / span > < span class = 'kw' > %> %< / span >
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< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/mutate.html' > mutate< / a > < / span > (< span class = 'kw' > first_isolate< / span > < span class = 'kw' > =< / span > < span class = 'fu' > first_isolate< / span > (< span class = 'no' > .< / span > ,
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< span class = 'kw' > col_date< / span > < span class = 'kw' > =< / span > < span class = 'st' > "date"< / span > ,
< span class = 'kw' > col_patient_id< / span > < span class = 'kw' > =< / span > < span class = 'st' > "patient_id"< / span > ,
< span class = 'kw' > col_mo< / span > < span class = 'kw' > =< / span > < span class = 'st' > "mo"< / span > )) < span class = 'kw' > %> %< / span >
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< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/filter.html' > filter< / a > < / span > (< span class = 'no' > first_isolate< / span > < span class = 'kw' > ==< / span > < span class = 'fl' > TRUE< / span > )
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< span class = 'co' > # Which can be shortened to:< / span >
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< span class = 'no' > example_isolates< / span > < span class = 'kw' > %> %< / span >
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< span class = 'fu' > filter_first_isolate< / span > ()
< span class = 'co' > # or for first weighted isolates:< / span >
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< span class = 'no' > example_isolates< / span > < span class = 'kw' > %> %< / span >
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< span class = 'fu' > filter_first_weighted_isolate< / span > ()
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< span class = 'co' > # Now let's see if first isolates matter:< / span >
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< span class = 'no' > A< / span > < span class = 'kw' > < -< / span > < span class = 'no' > example_isolates< / span > < span class = 'kw' > %> %< / span >
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< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/group_by.html' > group_by< / a > < / span > (< span class = 'no' > hospital_id< / span > ) < span class = 'kw' > %> %< / span >
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< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/summarise.html' > summarise< / a > < / span > (< span class = 'kw' > count< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'count.html' > n_rsi< / a > < / span > (< span class = 'no' > GEN< / span > ), < span class = 'co' > # gentamicin availability< / span >
< span class = 'kw' > resistance< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'portion.html' > portion_IR< / a > < / span > (< span class = 'no' > GEN< / span > )) < span class = 'co' > # gentamicin resistance< / span >
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< span class = 'no' > B< / span > < span class = 'kw' > < -< / span > < span class = 'no' > example_isolates< / span > < span class = 'kw' > %> %< / span >
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< span class = 'fu' > filter_first_weighted_isolate< / span > () < span class = 'kw' > %> %< / span > < span class = 'co' > # the 1st isolate filter< / span >
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< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/group_by.html' > group_by< / a > < / span > (< span class = 'no' > hospital_id< / span > ) < span class = 'kw' > %> %< / span >
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< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/summarise.html' > summarise< / a > < / span > (< span class = 'kw' > count< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'count.html' > n_rsi< / a > < / span > (< span class = 'no' > GEN< / span > ), < span class = 'co' > # gentamicin availability< / span >
< span class = 'kw' > resistance< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'portion.html' > portion_IR< / a > < / span > (< span class = 'no' > GEN< / span > )) < span class = 'co' > # gentamicin resistance< / span >
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< span class = 'co' > # Have a look at A and B.< / span >
< span class = 'co' > # B is more reliable because every isolate is only counted once.< / span >
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< span class = 'co' > # Gentamicin resitance in hospital D appears to be 3.1% higher than< / span >
< span class = 'co' > # when you (erroneously) would have used all isolates for analysis.< / span >
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< span class = 'co' > ## OTHER EXAMPLES:< / span >
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< span class = 'kw' > if< / span > (< span class = 'fl' > FALSE< / span > ) {
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< span class = 'co' > # set key antibiotics to a new variable< / span >
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< span class = 'no' > x< / span > $< span class = 'no' > keyab< / span > < span class = 'kw' > < -< / span > < span class = 'fu' > < a href = 'key_antibiotics.html' > key_antibiotics< / a > < / span > (< span class = 'no' > x< / span > )
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< span class = 'no' > x< / span > $< span class = 'no' > first_isolate< / span > < span class = 'kw' > < -< / span > < span class = 'fu' > first_isolate< / span > (< span class = 'no' > x< / span > )
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< span class = 'no' > x< / span > $< span class = 'no' > first_isolate_weighed< / span > < span class = 'kw' > < -< / span > < span class = 'fu' > first_isolate< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > col_keyantibiotics< / span > < span class = 'kw' > =< / span > < span class = 'st' > 'keyab'< / span > )
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< span class = 'no' > x< / span > $< span class = 'no' > first_blood_isolate< / span > < span class = 'kw' > < -< / span > < span class = 'fu' > first_isolate< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > specimen_group< / span > < span class = 'kw' > =< / span > < span class = 'st' > "Blood"< / span > )
}< / pre >
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< / div >
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< h2 > Contents< / h2 >
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< li > < a href = "#arguments" > Arguments< / a > < / li >
< li > < a href = "#source" > Source< / a > < / li >
< li > < a href = "#value" > Value< / a > < / li >
< li > < a href = "#details" > Details< / a > < / li >
< li > < a href = "#key-antibiotics" > Key antibiotics< / a > < / li >
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< li > < a href = "#read-more-on-our-website-" > Read more on our website!< / a > < / li >
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< li > < a href = "#see-also" > See also< / a > < / li >
< li > < a href = "#examples" > Examples< / a > < / li >
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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/' > Alex 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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< p > Site built with < a href = "https://pkgdown.r-lib.org/" > pkgdown< / a > 1.4.1.< / p >
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