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< title > Calculate resistance of isolates — portion • AMR (for R)< / title >
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portion_R and portion_IR can be used to calculate resistance, portion_S and portion_SI can be used to calculate susceptibility." />
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< h1 > Calculate resistance of isolates< / h1 >
< div class = "hidden name" > < code > portion.Rd< / code > < / div >
< / div >
< div class = "ref-description" >
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< p > These functions can be used to calculate the (co-)resistance of microbial isolates (i.e. percentage S, SI, I, IR or R). All functions support quasiquotation with pipes, can be used in < code > dplyr< / code > s < code > < a href = 'https://dplyr.tidyverse.org/reference/summarise.html' > summarise< / a > < / code > and support grouped variables, see < em > Examples< / em > .< / p >
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< p > < code > portion_R< / code > and < code > portion_IR< / code > can be used to calculate resistance, < code > portion_S< / code > and < code > portion_SI< / code > can be used to calculate susceptibility.< br / > < / p >
< / div >
< pre class = "usage" > < span class = 'fu' > portion_R< / span > (< span class = 'no' > ...< / span > , < span class = 'kw' > minimum< / span > < span class = 'kw' > =< / span > < span class = 'fl' > 30< / span > , < span class = 'kw' > as_percent< / span > < span class = 'kw' > =< / span > < span class = 'fl' > FALSE< / span > ,
< span class = 'kw' > also_single_tested< / span > < span class = 'kw' > =< / span > < span class = 'fl' > FALSE< / span > )
< span class = 'fu' > portion_IR< / span > (< span class = 'no' > ...< / span > , < span class = 'kw' > minimum< / span > < span class = 'kw' > =< / span > < span class = 'fl' > 30< / span > , < span class = 'kw' > as_percent< / span > < span class = 'kw' > =< / span > < span class = 'fl' > FALSE< / span > ,
< span class = 'kw' > also_single_tested< / span > < span class = 'kw' > =< / span > < span class = 'fl' > FALSE< / span > )
< span class = 'fu' > portion_I< / span > (< span class = 'no' > ...< / span > , < span class = 'kw' > minimum< / span > < span class = 'kw' > =< / span > < span class = 'fl' > 30< / span > , < span class = 'kw' > as_percent< / span > < span class = 'kw' > =< / span > < span class = 'fl' > FALSE< / span > ,
< span class = 'kw' > also_single_tested< / span > < span class = 'kw' > =< / span > < span class = 'fl' > FALSE< / span > )
< span class = 'fu' > portion_SI< / span > (< span class = 'no' > ...< / span > , < span class = 'kw' > minimum< / span > < span class = 'kw' > =< / span > < span class = 'fl' > 30< / span > , < span class = 'kw' > as_percent< / span > < span class = 'kw' > =< / span > < span class = 'fl' > FALSE< / span > ,
< span class = 'kw' > also_single_tested< / span > < span class = 'kw' > =< / span > < span class = 'fl' > FALSE< / span > )
< span class = 'fu' > portion_S< / span > (< span class = 'no' > ...< / span > , < span class = 'kw' > minimum< / span > < span class = 'kw' > =< / span > < span class = 'fl' > 30< / span > , < span class = 'kw' > as_percent< / span > < span class = 'kw' > =< / span > < span class = 'fl' > FALSE< / span > ,
< span class = 'kw' > also_single_tested< / span > < span class = 'kw' > =< / span > < span class = 'fl' > FALSE< / span > )
< span class = 'fu' > portion_df< / span > (< span class = 'no' > data< / span > , < span class = 'kw' > translate_ab< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'https://www.rdocumentation.org/packages/base/topics/options' > getOption< / a > < / span > (< span class = 'st' > "get_antibiotic_names"< / span > ,
< span class = 'st' > "official"< / span > ), < span class = 'kw' > minimum< / span > < span class = 'kw' > =< / span > < span class = 'fl' > 30< / span > , < span class = 'kw' > as_percent< / span > < span class = 'kw' > =< / span > < span class = 'fl' > FALSE< / span > , < span class = 'kw' > combine_IR< / span > < span class = 'kw' > =< / span > < span class = 'fl' > FALSE< / 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 > ...< / th >
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< td > < p > one or more vectors (or columns) with antibiotic interpretations. They will be transformed internally with < code > < a href = 'as.rsi.html' > as.rsi< / a > < / code > if needed. Use multiple columns to calculate (the lack of) co-resistance: the probability where one of two drugs have a resistant or susceptible result. See Examples.< / p > < / td >
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< / tr >
< tr >
< th > minimum< / th >
< td > < p > the minimal amount of available isolates. Any number 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 >
< tr >
< th > as_percent< / th >
< td > < p > a logical to indicate whether the output must be returned as a hundred fold with % sign (a character). A value of < code > 0.123456< / code > will then be returned as < code > "12.3%"< / code > .< / p > < / td >
< / tr >
< tr >
< th > also_single_tested< / th >
< td > < p > a logical to indicate whether (in combination therapies) also observations should be included where not all antibiotics were tested, but at least one of the tested antibiotics contains a target interpretation (e.g. S in case of < code > portion_S< / code > and R in case of < code > portion_R< / code > ). < strong > This would lead to selection bias in almost all cases.< / strong > < / p > < / td >
< / tr >
< tr >
< th > data< / th >
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< td > < p > a < code > data.frame< / code > containing columns with class < code > rsi< / code > (see < code > < a href = 'as.rsi.html' > as.rsi< / a > < / code > )< / p > < / td >
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< / tr >
< tr >
< th > translate_ab< / th >
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< td > < p > a column name of the < code > < a href = 'antibiotics.html' > antibiotics< / a > < / code > data set to translate the antibiotic abbreviations to, using < code > < a href = 'abname.html' > abname< / a > < / code > . This can be set with < code > < a href = 'https://www.rdocumentation.org/packages/base/topics/options' > getOption< / a > ("get_antibiotic_names")< / code > .< / p > < / td >
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< / tr >
< tr >
< th > combine_IR< / th >
< td > < p > a logical to indicate whether all values of I and R must be merged into one, so the output only consists of S vs. IR (susceptible vs. non-susceptible)< / p > < / td >
< / tr >
< / table >
< 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 >
< p > Wickham H. < strong > Tidy Data.< / strong > The Journal of Statistical Software, vol. 59, 2014. < a href = 'http://vita.had.co.nz/papers/tidy-data.html' > http://vita.had.co.nz/papers/tidy-data.html< / a > < / p >
< h2 class = "hasAnchor" id = "value" > < a class = "anchor" href = "#value" > < / a > Value< / h2 >
< p > Double or, when < code > as_percent = TRUE< / code > , a character.< / p >
< h2 class = "hasAnchor" id = "details" > < a class = "anchor" href = "#details" > < / a > Details< / h2 >
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< p > < strong > Remember that you should filter your table to let it contain only first isolates!< / strong > Use < code > < a href = 'first_isolate.html' > first_isolate< / a > < / code > to determine them in your data set.< / p >
< p > These functions are not meant to count isolates, but to calculate the portion of resistance/susceptibility. Use the < code > < a href = 'count.html' > count< / a > < / code > functions to count isolates. < em > Low counts can infuence the outcome - these < code > portion< / code > functions may camouflage this, since they only return the portion albeit being dependent on the < code > minimum< / code > parameter.< / em > < / p >
< p > < code > portion_df< / code > takes any variable from < code > data< / code > that has an < code > "rsi"< / code > class (created with < code > < a href = 'as.rsi.html' > as.rsi< / a > < / code > ) and calculates the portions R, I and S. The resulting < em > tidy data< / em > (see Source) < code > data.frame< / code > will have three rows (S/I/R) and a column for each variable with class < code > "rsi"< / code > .< / p >
< p > The old < code > < a href = 'rsi.html' > rsi< / a > < / code > function is still available for backwards compatibility but is deprecated.
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< br / > < br / >
To calculate the probability (< em > p< / em > ) of susceptibility of one antibiotic, we use this formula:
< div style = "text-align: center" > < img src = 'figures/mono_therapy.png' alt = '' / > < / div >
To calculate the probability (< em > p< / em > ) of susceptibility of more antibiotics (i.e. combination therapy), we need to check whether one of them has a susceptible result (as numerator) and count all cases where all antibiotics were tested (as denominator). < br / >
< br / >
For two antibiotics:
< div style = "text-align: center" > < img src = 'figures/combi_therapy_2.png' alt = '' / > < / div >
< br / >
For three antibiotics:
< div style = "text-align: center" > < img src = 'figures/combi_therapy_3.png' alt = '' / > < / div >
< br / >
And so on.< / 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 comprehensive 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 = 'count.html' > count< / a > _*< / code > to count resistant and susceptible isolates.< / 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' > # NOT RUN {< / span >
< span class = 'co' > # septic_patients is a data set available in the AMR package. It is true, genuine data.< / span >
?< span class = 'no' > septic_patients< / span >
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< span class = 'co' > # Calculate resistance< / span >
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< span class = 'fu' > portion_R< / span > (< span class = 'no' > septic_patients< / span > $< span class = 'no' > amox< / span > )
< span class = 'fu' > portion_IR< / span > (< span class = 'no' > septic_patients< / span > $< span class = 'no' > amox< / span > )
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< span class = 'co' > # Or susceptibility< / span >
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< span class = 'fu' > portion_S< / span > (< span class = 'no' > septic_patients< / span > $< span class = 'no' > amox< / span > )
< span class = 'fu' > portion_SI< / span > (< span class = 'no' > septic_patients< / span > $< span class = 'no' > amox< / span > )
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< span class = 'co' > # Do the above with pipes:< / span >
< span class = 'fu' > < a href = 'https://www.rdocumentation.org/packages/base/topics/library' > library< / a > < / span > (< span class = 'no' > dplyr< / span > )
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< span class = 'no' > septic_patients< / span > < span class = 'kw' > %> %< / span > < span class = 'fu' > portion_R< / span > (< span class = 'no' > amox< / span > )
< span class = 'no' > septic_patients< / span > < span class = 'kw' > %> %< / span > < span class = 'fu' > portion_IR< / span > (< span class = 'no' > amox< / span > )
< span class = 'no' > septic_patients< / span > < span class = 'kw' > %> %< / span > < span class = 'fu' > portion_S< / span > (< span class = 'no' > amox< / span > )
< span class = 'no' > septic_patients< / span > < span class = 'kw' > %> %< / span > < span class = 'fu' > portion_SI< / span > (< span class = 'no' > amox< / span > )
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< span class = 'no' > septic_patients< / 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 >
< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/summarise.html' > summarise< / a > < / span > (< span class = 'kw' > p< / span > < span class = 'kw' > =< / span > < span class = 'fu' > portion_S< / span > (< span class = 'no' > cipr< / span > ),
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< span class = 'kw' > n< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'count.html' > n_rsi< / a > < / span > (< span class = 'no' > cipr< / span > )) < span class = 'co' > # n_rsi works like n_distinct in dplyr< / span >
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< span class = 'no' > septic_patients< / 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 >
< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/summarise.html' > summarise< / a > < / span > (< span class = 'kw' > R< / span > < span class = 'kw' > =< / span > < span class = 'fu' > portion_R< / span > (< span class = 'no' > cipr< / span > , < span class = 'kw' > as_percent< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > ),
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< span class = 'kw' > I< / span > < span class = 'kw' > =< / span > < span class = 'fu' > portion_I< / span > (< span class = 'no' > cipr< / span > , < span class = 'kw' > as_percent< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > ),
< span class = 'kw' > S< / span > < span class = 'kw' > =< / span > < span class = 'fu' > portion_S< / span > (< span class = 'no' > cipr< / span > , < span class = 'kw' > as_percent< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > ),
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< span class = 'kw' > n< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'count.html' > n_rsi< / a > < / span > (< span class = 'no' > cipr< / span > ), < span class = 'co' > # works like n_distinct in dplyr< / span >
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< span class = 'kw' > total< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/n.html' > n< / a > < / span > ()) < span class = 'co' > # NOT the amount of tested isolates!< / span >
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< span class = 'co' > # Calculate co-resistance between amoxicillin/clav acid and gentamicin,< / span >
< span class = 'co' > # so we can see that combination therapy does a lot more than mono therapy:< / span >
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< span class = 'no' > septic_patients< / span > < span class = 'kw' > %> %< / span > < span class = 'fu' > portion_S< / span > (< span class = 'no' > amcl< / span > ) < span class = 'co' > # S = 67.1%< / span >
< span class = 'no' > septic_patients< / span > < span class = 'kw' > %> %< / span > < span class = 'fu' > < a href = 'count.html' > count_all< / a > < / span > (< span class = 'no' > amcl< / span > ) < span class = 'co' > # n = 1576< / span >
< span class = 'no' > septic_patients< / span > < span class = 'kw' > %> %< / span > < span class = 'fu' > portion_S< / span > (< span class = 'no' > gent< / span > ) < span class = 'co' > # S = 74.0%< / span >
< span class = 'no' > septic_patients< / span > < span class = 'kw' > %> %< / span > < span class = 'fu' > < a href = 'count.html' > count_all< / a > < / span > (< span class = 'no' > gent< / span > ) < span class = 'co' > # n = 1855< / span >
< span class = 'no' > septic_patients< / span > < span class = 'kw' > %> %< / span > < span class = 'fu' > portion_S< / span > (< span class = 'no' > amcl< / span > , < span class = 'no' > gent< / span > ) < span class = 'co' > # S = 92.0%< / span >
< span class = 'no' > septic_patients< / span > < span class = 'kw' > %> %< / span > < span class = 'fu' > < a href = 'count.html' > count_all< / a > < / span > (< span class = 'no' > amcl< / span > , < span class = 'no' > gent< / span > ) < span class = 'co' > # n = 1517< / span >
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< span class = 'no' > septic_patients< / 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 >
< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/summarise.html' > summarise< / a > < / span > (< span class = 'kw' > cipro_p< / span > < span class = 'kw' > =< / span > < span class = 'fu' > portion_S< / span > (< span class = 'no' > cipr< / span > , < span class = 'kw' > as_percent< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > ),
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< span class = 'kw' > cipro_n< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'count.html' > count_all< / a > < / span > (< span class = 'no' > cipr< / span > ),
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< span class = 'kw' > genta_p< / span > < span class = 'kw' > =< / span > < span class = 'fu' > portion_S< / span > (< span class = 'no' > gent< / span > , < span class = 'kw' > as_percent< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > ),
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< span class = 'kw' > genta_n< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'count.html' > count_all< / a > < / span > (< span class = 'no' > gent< / span > ),
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< span class = 'kw' > combination_p< / span > < span class = 'kw' > =< / span > < span class = 'fu' > portion_S< / span > (< span class = 'no' > cipr< / span > , < span class = 'no' > gent< / span > , < span class = 'kw' > as_percent< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > ),
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< span class = 'kw' > combination_n< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'count.html' > count_all< / a > < / span > (< span class = 'no' > cipr< / span > , < span class = 'no' > gent< / span > ))
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< span class = 'co' > # Get portions S/I/R immediately of all rsi columns< / span >
< span class = 'no' > septic_patients< / span > < span class = 'kw' > %> %< / span >
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< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/select.html' > select< / a > < / span > (< span class = 'no' > amox< / span > , < span class = 'no' > cipr< / span > ) < span class = 'kw' > %> %< / span >
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< span class = 'fu' > portion_df< / span > (< span class = 'kw' > translate< / span > < span class = 'kw' > =< / span > < span class = 'fl' > FALSE< / span > )
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< span class = 'co' > # It also supports grouping variables< / span >
< span class = 'no' > septic_patients< / span > < span class = 'kw' > %> %< / span >
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< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/select.html' > select< / a > < / span > (< span class = 'no' > hospital_id< / span > , < span class = 'no' > amox< / span > , < span class = 'no' > cipr< / span > ) < span class = 'kw' > %> %< / span >
< 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 >
2019-01-02 23:24:07 +01:00
< span class = 'fu' > portion_df< / span > (< span class = 'kw' > translate< / span > < span class = 'kw' > =< / span > < span class = 'fl' > FALSE< / span > )
< span class = 'co' > # }< / span > < span class = 'co' > # NOT RUN {< / span >
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< span class = 'co' > # calculate current empiric combination therapy of Helicobacter gastritis:< / span >
< span class = 'no' > my_table< / 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 = 'no' > genus< / span > < span class = 'kw' > ==< / span > < span class = 'st' > "Helicobacter"< / 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' > p< / span > < span class = 'kw' > =< / span > < span class = 'fu' > portion_S< / span > (< span class = 'no' > amox< / span > , < span class = 'no' > metr< / span > ), < span class = 'co' > # amoxicillin with metronidazole< / span >
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< span class = 'kw' > n< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'count.html' > count_all< / a > < / span > (< span class = 'no' > amox< / span > , < span class = 'no' > metr< / span > ))
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< span class = 'co' > # }< / span > < / pre >
< / 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 = "#source" > Source< / a > < / li >
< li > < a href = "#value" > Value< / a > < / li >
< li > < a href = "#details" > Details< / 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 >
< / ul >
< / div >
< / div >
< footer >
< div class = "copyright" >
2018-12-29 22:24:19 +01:00
< 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 >
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< / div >
< div class = "pkgdown" >
< p > Site built with < a href = "https://pkgdown.r-lib.org/" > pkgdown< / a > 1.3.0.< / p >
< / div >
< / footer >
< / div >
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< script src = "https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity = "sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin = "anonymous" > < / script >
< script >
docsearch({
apiKey: 'f737050abfd4d726c63938e18f8c496e',
indexName: 'amr',
inputSelector: 'input#search-input.form-control',
transformData: function(hits) {
return hits.map(function (hit) {
hit.url = updateHitURL(hit);
return hit;
});
}
});
< / script >
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< / body >
< / html >
