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< img src = "../logo.svg" class = "logo" alt = "" > < h1 > Generate Antibiogram: Traditional, Combined, Syndromic, or Weighted-Incidence Syndromic Combination (WISCA)< / h1 >
< small class = "dont-index" > Source: < a href = "https://github.com/msberends/AMR/blob/HEAD/R/antibiogram.R" class = "external-link" > < code > R/antibiogram.R< / code > < / a > < / small >
< div class = "d-none name" > < code > antibiogram.Rd< / code > < / div >
< / div >
< div class = "ref-description section level2" >
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< p > Generate an antibiogram, and communicate the results in plots or tables. These functions follow the logic of Klinker < em > et al.< / em > and Barbieri < em > et al.< / em > (see < em > Source< / em > ), and allow reporting in e.g. R Markdown and Quarto as well.< / p >
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< / div >
< div class = "section level2" >
< h2 id = "ref-usage" > Usage< a class = "anchor" aria-label = "anchor" href = "#ref-usage" > < / a > < / h2 >
< div class = "sourceCode" > < pre class = "sourceCode r" > < code > < span > < span class = "fu" > antibiogram< / span > < span class = "op" > (< / span > < / span >
< span > < span class = "va" > x< / span > ,< / span >
< span > antibiotics < span class = "op" > =< / span > < span class = "fu" > < a href = "https://tidyselect.r-lib.org/reference/where.html" class = "external-link" > where< / a > < / span > < span class = "op" > (< / span > < span class = "va" > is.sir< / span > < span class = "op" > )< / span > ,< / span >
< span > mo_transform < span class = "op" > =< / span > < span class = "st" > "shortname"< / span > ,< / span >
< span > ab_transform < span class = "op" > =< / span > < span class = "cn" > NULL< / span > ,< / span >
< span > syndromic_group < span class = "op" > =< / span > < span class = "cn" > NULL< / span > ,< / span >
< span > add_total_n < span class = "op" > =< / span > < span class = "cn" > TRUE< / span > ,< / span >
< span > only_all_tested < span class = "op" > =< / span > < span class = "cn" > FALSE< / span > ,< / span >
< span > digits < span class = "op" > =< / span > < span class = "fl" > 0< / span > ,< / span >
< span > col_mo < span class = "op" > =< / span > < span class = "cn" > NULL< / span > ,< / span >
< span > language < span class = "op" > =< / span > < span class = "fu" > < a href = "translate.html" > get_AMR_locale< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > ,< / span >
< span > minimum < span class = "op" > =< / span > < span class = "fl" > 30< / span > ,< / span >
< span > combine_SI < span class = "op" > =< / span > < span class = "cn" > TRUE< / span > ,< / span >
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< span > sep < span class = "op" > =< / span > < span class = "st" > " + "< / span > ,< / span >
< span > info < span class = "op" > =< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/interactive.html" class = "external-link" > interactive< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < / span >
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< span > < span class = "op" > )< / span > < / span >
< span > < / span >
< span > < span class = "co" > # S3 method for antibiogram< / span > < / span >
< span > < span class = "fu" > < a href = "plot.html" > plot< / a > < / span > < span class = "op" > (< / span > < span class = "va" > x< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span > < / span >
< span > < / span >
< span > < span class = "co" > # S3 method for antibiogram< / span > < / span >
< span > < span class = "fu" > < a href = "https://ggplot2.tidyverse.org/reference/autoplot.html" class = "external-link" > autoplot< / a > < / span > < span class = "op" > (< / span > < span class = "va" > object< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span > < / span >
< span > < / span >
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< span > < span class = "co" > # S3 method for antibiogram< / span > < / span >
< span > < span class = "fu" > knit_print< / span > < span class = "op" > (< / span > < / span >
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< span > < span class = "va" > x< / span > ,< / span >
< span > italicise < span class = "op" > =< / span > < span class = "cn" > TRUE< / span > ,< / span >
< span > na < span class = "op" > =< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/options.html" class = "external-link" > getOption< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "knitr.kable.NA"< / span > , default < span class = "op" > =< / span > < span class = "st" > ""< / span > < span class = "op" > )< / span > ,< / span >
< span > < span class = "va" > ...< / span > < / span >
< span > < span class = "op" > )< / span > < / span > < / code > < / pre > < / div >
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< / div >
< div class = "section level2" >
< h2 id = "source" > Source< a class = "anchor" aria-label = "anchor" href = "#source" > < / a > < / h2 >
< ul > < li > < p > Klinker KP < em > et al.< / em > (2021). < strong > Antimicrobial stewardship and antibiograms: importance of moving beyond traditional antibiograms< / strong > . < em > Therapeutic Advances in Infectious Disease< / em > , May 5;8:20499361211011373; < a href = "https://doi.org/10.1177/20499361211011373" class = "external-link" > doi:10.1177/20499361211011373< / a > < / p > < / li >
< li > < p > Barbieri E < em > et al.< / em > (2021). < strong > Development of a Weighted-Incidence Syndromic Combination Antibiogram (WISCA) to guide the choice of the empiric antibiotic treatment for urinary tract infection in paediatric patients: a Bayesian approach< / strong > < em > Antimicrobial Resistance & Infection Control< / em > May 1;10(1):74; < a href = "https://doi.org/10.1186/s13756-021-00939-2" class = "external-link" > doi:10.1186/s13756-021-00939-2< / a > < / p > < / li >
< li > < p > < strong > M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 5th Edition< / strong > , 2022, < em > Clinical and Laboratory Standards Institute (CLSI)< / em > . < a href = "https://clsi.org/standards/products/microbiology/documents/m39/" class = "external-link" > https://clsi.org/standards/products/microbiology/documents/m39/< / a > .< / p > < / li >
< / ul > < / div >
< div class = "section level2" >
< h2 id = "arguments" > Arguments< a class = "anchor" aria-label = "anchor" href = "#arguments" > < / a > < / h2 >
< dl > < dt > x< / dt >
< dd > < p > a < a href = "https://rdrr.io/r/base/data.frame.html" class = "external-link" > data.frame< / a > containing at least a column with microorganisms and columns with antibiotic results (class 'sir', see < code > < a href = "as.sir.html" > as.sir()< / a > < / code > )< / p > < / dd >
< dt > antibiotics< / dt >
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< dd > < p > vector of any antibiotic name or code (will be evaluated with < code > < a href = "as.ab.html" > as.ab()< / a > < / code > , column name of < code > x< / code > , or (any combinations of) < a href = "antibiotic_class_selectors.html" > antibiotic selectors< / a > such as < code > < a href = "antibiotic_class_selectors.html" > aminoglycosides()< / a > < / code > or < code > < a href = "antibiotic_class_selectors.html" > carbapenems()< / a > < / code > . For combination antibiograms, this can also be set to values separated with < code > "+"< / code > , such as "TZP+TOB" or "cipro + genta", given that columns resembling such antibiotics exist in < code > x< / code > . See < em > Examples< / em > .< / p > < / dd >
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< dt > mo_transform< / dt >
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< dd > < p > a character to transform microorganism input - must be "name", "shortname", "gramstain", or one of the column names of the < a href = "microorganisms.html" > microorganisms< / a > data set: "mo", "fullname", "status", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "oxygen_tolerance", "source", "lpsn", "lpsn_parent", "lpsn_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence", or "snomed". Can also be < code > NULL< / code > to not transform the input.< / p > < / dd >
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< dt > ab_transform< / dt >
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< dd > < p > a character to transform antibiotic input - must be one of the column names of the < a href = "antibiotics.html" > antibiotics< / a > data set: "ab", "cid", "name", "group", "atc", "atc_group1", "atc_group2", "abbreviations", "synonyms", "oral_ddd", "oral_units", "iv_ddd", "iv_units", or "loinc". Can also be < code > NULL< / code > to not transform the input.< / p > < / dd >
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< dt > syndromic_group< / dt >
< dd > < p > a column name of < code > x< / code > , or values calculated to split rows of < code > x< / code > , e.g. by using < code > < a href = "https://rdrr.io/r/base/ifelse.html" class = "external-link" > ifelse()< / a > < / code > or < code > < a href = "https://dplyr.tidyverse.org/reference/case_when.html" class = "external-link" > case_when()< / a > < / code > . See < em > Examples< / em > .< / p > < / dd >
< dt > add_total_n< / dt >
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< dd > < p > a < a href = "https://rdrr.io/r/base/logical.html" class = "external-link" > logical< / a > to indicate whether total available numbers per pathogen should be added to the table (default is < code > TRUE< / code > ). This will add the lowest and highest number of available isolate per antibiotic (e.g, if for < em > E. coli< / em > 200 isolates are available for ciprofloxacin and 150 for amoxicillin, the returned number will be "150-200").< / p > < / dd >
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< dt > only_all_tested< / dt >
< dd > < p > (for combination antibiograms): a < a href = "https://rdrr.io/r/base/logical.html" class = "external-link" > logical< / a > to indicate that isolates must be tested for all antibiotics, see < em > Details< / em > < / p > < / dd >
< dt > digits< / dt >
< dd > < p > number of digits to use for rounding< / p > < / dd >
< dt > col_mo< / dt >
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< dd > < p > column name of the names or codes of the microorganisms (see < code > < a href = "as.mo.html" > as.mo()< / a > < / code > ) - the default is 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 > < / dd >
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< dt > language< / dt >
< dd > < p > language to translate text, which defaults to the system language (see < code > < a href = "translate.html" > get_AMR_locale()< / a > < / code > )< / p > < / dd >
< dt > minimum< / dt >
< dd > < 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 < em > Source< / em > .< / p > < / dd >
< dt > combine_SI< / dt >
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< dd > < p > a < a href = "https://rdrr.io/r/base/logical.html" class = "external-link" > logical< / a > to indicate whether all susceptibility should be determined by results of either S or I, instead of only S (default is < code > TRUE< / code > )< / p > < / dd >
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< dt > sep< / dt >
< dd > < p > a separating character for antibiotic columns in combination antibiograms< / p > < / dd >
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< dt > info< / dt >
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< dd > < p > a < a href = "https://rdrr.io/r/base/logical.html" class = "external-link" > logical< / a > to indicate info should be printed - the default is < code > TRUE< / code > only in interactive mode< / p > < / dd >
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< dt > ...< / dt >
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< dd > < p > when used in < a href = "https://rdrr.io/pkg/knitr/man/kable.html" class = "external-link" > R Markdown or Quarto< / a > : arguments passed on to < code > < a href = "https://rdrr.io/pkg/knitr/man/kable.html" class = "external-link" > knitr::kable()< / a > < / code > (otherwise, has no use)< / p > < / dd >
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< dt > object< / dt >
< dd > < p > an < code > antibiogram()< / code > object< / p > < / dd >
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< dt > italicise< / dt >
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< dd > < p > a < a href = "https://rdrr.io/r/base/logical.html" class = "external-link" > logical< / a > to indicate whether the microorganism names in the < a href = "https://rdrr.io/pkg/knitr/man/kable.html" class = "external-link" > knitr< / a > table should be made italic, using < code > < a href = "italicise_taxonomy.html" > italicise_taxonomy()< / a > < / code > .< / p > < / dd >
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< dt > na< / dt >
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< dd > < p > character to use for showing < code > NA< / code > values< / p > < / dd >
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< / dl > < / div >
< div class = "section level2" >
< h2 id = "details" > Details< a class = "anchor" aria-label = "anchor" href = "#details" > < / a > < / h2 >
< p > This function returns a table with values between 0 and 100 for < em > susceptibility< / em > , not resistance.< / p >
< p > < strong > Remember that you should filter your data to let it contain only first isolates!< / strong > This is needed to exclude duplicates and to reduce selection bias. Use < code > < a href = "first_isolate.html" > first_isolate()< / a > < / code > to determine them in your data set with one of the four available algorithms.< / p >
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< p > All types of antibiograms as listed below can be plotted (using < code > < a href = "https://ggplot2.tidyverse.org/reference/autoplot.html" class = "external-link" > ggplot2::autoplot()< / a > < / code > or base < span style = "R" > R< / span > < code > < a href = "plot.html" > plot()< / a > < / code > /< code > < a href = "https://rdrr.io/r/graphics/barplot.html" class = "external-link" > barplot()< / a > < / code > ). The < code > antibiogram< / code > object can also be used directly in R Markdown / Quarto (i.e., < code > knitr< / code > ) for reports. In this case, < code > < a href = "https://rdrr.io/pkg/knitr/man/kable.html" class = "external-link" > knitr::kable()< / a > < / code > will be applied automatically and microorganism names will even be printed in italics at default (see argument < code > italicise< / code > ). You can also use functions from specific 'table reporting' packages to transform the output of < code > antibiogram()< / code > to your needs, e.g. with < code > flextable::as_flextable()< / code > or < code > gt::gt()< / code > .< / p > < div class = "section" >
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< h3 id = "antibiogram-types" > Antibiogram Types< a class = "anchor" aria-label = "anchor" href = "#antibiogram-types" > < / a > < / h3 >
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< p > There are four antibiogram types, as proposed by Klinker < em > et al.< / em > (2021, < a href = "https://doi.org/10.1177/20499361211011373" class = "external-link" > doi:10.1177/20499361211011373< / a >
), and they are all supported by < code > antibiogram()< / code > :< / p > < ol > < li > < p > < strong > Traditional Antibiogram< / strong > < / p >
< p > Case example: Susceptibility of < em > Pseudomonas aeruginosa< / em > to piperacillin/tazobactam (TZP)< / p >
< p > Code example:< / p >
< p > < / p > < div class = "sourceCode r" > < pre > < code > < span > < span class = "fu" > < a href = "../reference/antibiogram.html" > antibiogram< / a > < / span > < span class = "op" > (< / span > < span class = "va" > your_data< / span > ,< / span >
< span > antibiotics < span class = "op" > =< / span > < span class = "st" > "TZP"< / span > < span class = "op" > )< / span > < / span > < / code > < / pre > < p > < / p > < / div > < / li >
< li > < p > < strong > Combination Antibiogram< / strong > < / p >
< p > Case example: Additional susceptibility of < em > Pseudomonas aeruginosa< / em > to TZP + tobramycin versus TZP alone< / p >
< p > Code example:< / p >
< p > < / p > < div class = "sourceCode r" > < pre > < code > < span > < span class = "fu" > < a href = "../reference/antibiogram.html" > antibiogram< / a > < / span > < span class = "op" > (< / span > < span class = "va" > your_data< / span > ,< / span >
< span > antibiotics < span class = "op" > =< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/c.html" class = "external-link" > c< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "TZP"< / span > , < span class = "st" > "TZP+TOB"< / span > , < span class = "st" > "TZP+GEN"< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < / span > < / code > < / pre > < p > < / p > < / div > < / li >
< li > < p > < strong > Syndromic Antibiogram< / strong > < / p >
< p > Case example: Susceptibility of < em > Pseudomonas aeruginosa< / em > to TZP among respiratory specimens (obtained among ICU patients only)< / p >
< p > Code example:< / p >
< p > < / p > < div class = "sourceCode r" > < pre > < code > < span > < span class = "fu" > < a href = "../reference/antibiogram.html" > antibiogram< / a > < / span > < span class = "op" > (< / span > < span class = "va" > your_data< / span > ,< / span >
< span > antibiotics < span class = "op" > =< / span > < span class = "fu" > < a href = "../reference/antibiotic_class_selectors.html" > penicillins< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > ,< / span >
< span > syndromic_group < span class = "op" > =< / span > < span class = "st" > "ward"< / span > < span class = "op" > )< / span > < / span > < / code > < / pre > < p > < / p > < / div > < / li >
< li > < p > < strong > Weighted-Incidence Syndromic Combination Antibiogram (WISCA)< / strong > < / p >
< p > Case example: Susceptibility of < em > Pseudomonas aeruginosa< / em > to TZP among respiratory specimens (obtained among ICU patients only) for male patients age > =65 years with heart failure< / p >
< p > Code example:< / p >
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< p > < / p > < div class = "sourceCode r" > < pre > < code > < span > < span class = "kw" > < a href = "https://rdrr.io/r/base/library.html" class = "external-link" > library< / a > < / span > < span class = "op" > (< / span > < span class = "va" > < a href = "https://dplyr.tidyverse.org" class = "external-link" > dplyr< / a > < / span > < span class = "op" > )< / span > < / span >
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< span > < span class = "va" > your_data< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span >
< span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/filter.html" class = "external-link" > filter< / a > < / span > < span class = "op" > (< / span > < span class = "va" > ward< / span > < span class = "op" > ==< / span > < span class = "st" > "ICU"< / span > < span class = "op" > & < / span > < span class = "va" > specimen_type< / span > < span class = "op" > ==< / span > < span class = "st" > "Respiratory"< / span > < span class = "op" > )< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span >
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< span > < span class = "fu" > < a href = "../reference/antibiogram.html" > antibiogram< / a > < / span > < span class = "op" > (< / span > antibiotics < span class = "op" > =< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/c.html" class = "external-link" > c< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "TZP"< / span > , < span class = "st" > "TZP+TOB"< / span > , < span class = "st" > "TZP+GEN"< / span > < span class = "op" > )< / span > ,< / span >
< span > syndromic_group < span class = "op" > =< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/ifelse.html" class = "external-link" > ifelse< / a > < / span > < span class = "op" > (< / span > < span class = "va" > .< / span > < span class = "op" > $< / span > < span class = "va" > age< / span > < span class = "op" > > =< / span > < span class = "fl" > 65< / span > < span class = "op" > & < / span > < / span >
< span > < span class = "va" > .< / span > < span class = "op" > $< / span > < span class = "va" > gender< / span > < span class = "op" > ==< / span > < span class = "st" > "Male"< / span > < span class = "op" > & < / span > < / span >
< span > < span class = "va" > .< / span > < span class = "op" > $< / span > < span class = "va" > condition< / span > < span class = "op" > ==< / span > < span class = "st" > "Heart Disease"< / span > ,< / span >
< span > < span class = "st" > "Study Group"< / span > , < span class = "st" > "Control Group"< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < / span > < / code > < / pre > < p > < / p > < / div > < / li >
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< / ol > < p > Note that for combination antibiograms, it is important to realise that susceptibility can be calculated in two ways, which can be set with the < code > only_all_tested< / code > argument (default is < code > FALSE< / code > ). See this example for two antibiotics, Drug A and Drug B, about how < code > antibiogram()< / code > works to calculate the %SI:< / p >
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< p > < / p > < div class = "sourceCode" > < pre > < code > < span id = "cb1-1" > < a href = "#cb1-1" aria-hidden = "true" tabindex = "-1" > < / a > < span class = "sc" > --------------------------------------------------------------------< / span > < / span >
< span id = "cb1-2" > < a href = "#cb1-2" aria-hidden = "true" tabindex = "-1" > < / a > only_all_tested < span class = "ot" > =< / span > < span class = "cn" > FALSE< / span > only_all_tested < span class = "ot" > =< / span > < span class = "cn" > TRUE< / span > < / span >
< span id = "cb1-3" > < a href = "#cb1-3" aria-hidden = "true" tabindex = "-1" > < / a > < span class = "sc" > -----------------------< / span > < span class = "sc" > -----------------------< / span > < / span >
< span id = "cb1-4" > < a href = "#cb1-4" aria-hidden = "true" tabindex = "-1" > < / a > Drug A Drug B include as include as include as include as< / span >
< span id = "cb1-5" > < a href = "#cb1-5" aria-hidden = "true" tabindex = "-1" > < / a > numerator denominator numerator denominator< / span >
< span id = "cb1-6" > < a href = "#cb1-6" aria-hidden = "true" tabindex = "-1" > < / a > < span class = "sc" > --------< / span > < span class = "sc" > --------< / span > < span class = "sc" > ----------< / span > < span class = "sc" > -----------< / span > < span class = "sc" > ----------< / span > < span class = "sc" > -----------< / span > < / span >
< span id = "cb1-7" > < a href = "#cb1-7" aria-hidden = "true" tabindex = "-1" > < / a > S or I S or I X X X X< / span >
< span id = "cb1-8" > < a href = "#cb1-8" aria-hidden = "true" tabindex = "-1" > < / a > R S or I X X X X< / span >
< span id = "cb1-9" > < a href = "#cb1-9" aria-hidden = "true" tabindex = "-1" > < / a > < span class = "sc" > < < / span > < span class = "cn" > NA< / span > < span class = "sc" > > < / span > S or I X X < span class = "sc" > -< / span > < span class = "sc" > -< / span > < / span >
< span id = "cb1-10" > < a href = "#cb1-10" aria-hidden = "true" tabindex = "-1" > < / a > S or I R X X X X< / span >
< span id = "cb1-11" > < a href = "#cb1-11" aria-hidden = "true" tabindex = "-1" > < / a > R R < span class = "sc" > -< / span > X < span class = "sc" > -< / span > X< / span >
< span id = "cb1-12" > < a href = "#cb1-12" aria-hidden = "true" tabindex = "-1" > < / a > < span class = "sc" > < < / span > < span class = "cn" > NA< / span > < span class = "sc" > > < / span > R < span class = "sc" > -< / span > < span class = "sc" > -< / span > < span class = "sc" > -< / span > < span class = "sc" > -< / span > < / span >
< span id = "cb1-13" > < a href = "#cb1-13" aria-hidden = "true" tabindex = "-1" > < / a > S or I < span class = "sc" > < < / span > < span class = "cn" > NA< / span > < span class = "sc" > > < / span > X X < span class = "sc" > -< / span > < span class = "sc" > -< / span > < / span >
< span id = "cb1-14" > < a href = "#cb1-14" aria-hidden = "true" tabindex = "-1" > < / a > R < span class = "sc" > < < / span > < span class = "cn" > NA< / span > < span class = "sc" > > < / span > < span class = "sc" > -< / span > < span class = "sc" > -< / span > < span class = "sc" > -< / span > < span class = "sc" > -< / span > < / span >
< span id = "cb1-15" > < a href = "#cb1-15" aria-hidden = "true" tabindex = "-1" > < / a > < span class = "er" > < < / span > < span class = "cn" > NA< / span > < span class = "sc" > > < / span > < span class = "er" > < < / span > < span class = "cn" > NA< / span > < span class = "sc" > > < / span > < span class = "sc" > -< / span > < span class = "sc" > -< / span > < span class = "sc" > -< / span > < span class = "sc" > -< / span > < / span >
< span id = "cb1-16" > < a href = "#cb1-16" aria-hidden = "true" tabindex = "-1" > < / a > < span class = "sc" > --------------------------------------------------------------------< / span > < / span > < / code > < / pre > < p > < / p > < / div >
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< / div >
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< / div >
< div class = "section level2" >
< h2 id = "ref-examples" > Examples< a class = "anchor" aria-label = "anchor" href = "#ref-examples" > < / a > < / h2 >
< div class = "sourceCode" > < pre class = "sourceCode r" > < code > < span class = "r-in" > < span > < span class = "co" > # example_isolates is a data set available in the AMR package.< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # run ?example_isolates for more info.< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > example_isolates< / span > < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # A tibble: 2,000 × < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > date patient age gender ward mo PEN OXA FLC AMX < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494; font-style: italic;" > < date> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < dbl> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < mo> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 1< / span > 2002-01-02 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 2< / span > 2002-01-03 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 3< / span > 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 4< / span > 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 5< / span > 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 6< / span > 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 7< / span > 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 8< / span > 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 9< / span > 2002-01-16 067927 45 F ICU B_STPHY_EPDR R NA R NA < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 10< / span > 2002-01-17 858515 79 F ICU B_STPHY_EPDR R NA S NA < / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # ℹ < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # ℹ < sir> , AMP < sir> , TZP < sir> , CZO < sir> , FEP < sir> ,< / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # CXM < sir> , FOX < sir> , CTX < sir> , CAZ < sir> , CRO < sir> , GEN < sir> ,< / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # TOB < sir> , AMK < sir> , KAN < sir> , TMP < sir> , SXT < sir> , NIT < sir> ,< / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # FOS < sir> , LNZ < sir> , CIP < sir> , MFX < sir> , VAN < sir> , TEC < sir> ,< / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # TCY < sir> , TGC < sir> , DOX < sir> , ERY < sir> , CLI < sir> , AZM < sir> ,< / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # IPM < sir> , MEM < sir> , MTR < sir> , CHL < sir> , COL < sir> , MUP < sir> , …< / span > < / span >
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< span class = "r-in" > < span > < / span > < / span >
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< span class = "r-in" > < span > < span class = "co" > # \donttest{< / span > < / span > < / span >
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< span class = "r-in" > < span > < span class = "co" > # Traditional antibiogram ----------------------------------------------< / span > < / span > < / span >
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > antibiogram< / span > < span class = "op" > (< / span > < span class = "va" > example_isolates< / span > ,< / span > < / span >
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< span class = "r-in" > < span > antibiotics < span class = "op" > =< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/c.html" class = "external-link" > c< / a > < / 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 = "fu" > < a href = "antibiotic_class_selectors.html" > carbapenems< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "op" > )< / span > < / span > < / span >
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< span class = "r-msg co" > < span class = "r-pr" > #> < / span > ℹ < / span >
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< span class = "r-msg co" > < span class = "r-pr" > #> < / span > (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)< / span >
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< span class = "r-msg co" > < span class = "r-pr" > #> < / span > ℹ < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # A tibble: 10 × < / span > < / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > `Pathogen (N min-max)` AMK GEN IPM KAN MEM TOB< / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > *< / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < dbl> < / span > < span style = "color: #949494; font-style: italic;" > < dbl> < / span > < span style = "color: #949494; font-style: italic;" > < dbl> < / span > < span style = "color: #949494; font-style: italic;" > < dbl> < / span > < span style = "color: #949494; font-style: italic;" > < dbl> < / span > < span style = "color: #949494; font-style: italic;" > < dbl> < / span > < / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 1< / span > CoNS (43-309) 0 86 52 0 52 22< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 2< / span > E. coli (0-462) 100 98 100 < span style = "color: #BB0000;" > NA< / span > 100 97< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 3< / span > E. faecalis (0-39) 0 0 100 0 < span style = "color: #BB0000;" > NA< / span > 0< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 4< / span > K. pneumoniae (0-58) < span style = "color: #BB0000;" > NA< / span > 90 100 < span style = "color: #BB0000;" > NA< / span > 100 90< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 5< / span > P. aeruginosa (17-30) < span style = "color: #BB0000;" > NA< / span > 100 < span style = "color: #BB0000;" > NA< / span > 0 < span style = "color: #BB0000;" > NA< / span > 100< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 6< / span > P. mirabilis (0-34) < span style = "color: #BB0000;" > NA< / span > 94 94 < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > 94< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 7< / span > S. aureus (2-233) < span style = "color: #BB0000;" > NA< / span > 99 < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > 98< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 8< / span > S. epidermidis (8-163) 0 79 < span style = "color: #BB0000;" > NA< / span > 0 < span style = "color: #BB0000;" > NA< / span > 51< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 9< / span > S. hominis (3-80) < span style = "color: #BB0000;" > NA< / span > 92 < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > 85< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 10< / span > S. pneumoniae (11-117) 0 0 < span style = "color: #BB0000;" > NA< / span > 0 < span style = "color: #BB0000;" > NA< / span > 0< / span >
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< span class = "r-in" > < span > < / span > < / span >
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< span class = "r-in" > < span > < span class = "fu" > antibiogram< / span > < span class = "op" > (< / span > < span class = "va" > example_isolates< / span > ,< / span > < / span >
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< span class = "r-in" > < span > antibiotics < 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 > < / span >
< span class = "r-in" > < span > ab_transform < span class = "op" > =< / span > < span class = "st" > "atc"< / span > ,< / span > < / span >
< span class = "r-in" > < span > mo_transform < span class = "op" > =< / span > < span class = "st" > "gramstain"< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "op" > )< / span > < / span > < / span >
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< span class = "r-msg co" > < span class = "r-pr" > #> < / span > ℹ < / span >
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< span class = "r-msg co" > < span class = "r-pr" > #> < / span > (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)< / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # A tibble: 2 × < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > `Pathogen (N min-max)` J01GB01 J01GB03 J01GB04 J01GB06< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > *< / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < dbl> < / span > < span style = "color: #949494; font-style: italic;" > < dbl> < / span > < span style = "color: #949494; font-style: italic;" > < dbl> < / span > < span style = "color: #949494; font-style: italic;" > < dbl> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 1< / span > Gram-negative (35-686) 96 96 0 98< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 2< / span > Gram-positive (436-1170) 34 63 0 0< / span >
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< span class = "r-in" > < span > < / span > < / span >
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< span class = "r-in" > < span > < span class = "fu" > antibiogram< / span > < span class = "op" > (< / span > < span class = "va" > example_isolates< / span > ,< / span > < / span >
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< span class = "r-in" > < span > antibiotics < 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 > < / span >
< span class = "r-in" > < span > ab_transform < span class = "op" > =< / span > < span class = "st" > "name"< / span > ,< / span > < / span >
< span class = "r-in" > < span > mo_transform < span class = "op" > =< / span > < span class = "st" > "name"< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "op" > )< / span > < / span > < / span >
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< span class = "r-msg co" > < span class = "r-pr" > #> < / span > ℹ < / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # A tibble: 5 × < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > `Pathogen (N min-max)` Imipenem Meropenem< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > *< / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < dbl> < / span > < span style = "color: #949494; font-style: italic;" > < dbl> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 1< / span > Coagulase-negative Staphylococcus (CoNS) (48-48) 52 52< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 2< / span > Enterococcus faecalis (0-38) 100 < span style = "color: #BB0000;" > NA< / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 3< / span > Escherichia coli (418-422) 100 100< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 4< / span > Klebsiella pneumoniae (51-53) 100 100< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 5< / span > Proteus mirabilis (27-32) 94 < span style = "color: #BB0000;" > NA< / span > < / span >
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< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # Combined antibiogram -------------------------------------------------< / span > < / span > < / span >
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # combined antibiotics yield higher empiric coverage< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > antibiogram< / span > < span class = "op" > (< / span > < span class = "va" > example_isolates< / span > ,< / span > < / span >
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< span class = "r-in" > < span > antibiotics < span class = "op" > =< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/c.html" class = "external-link" > c< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "TZP"< / span > , < span class = "st" > "TZP+TOB"< / span > , < span class = "st" > "TZP+GEN"< / span > < span class = "op" > )< / span > ,< / span > < / span >
< span class = "r-in" > < span > mo_transform < span class = "op" > =< / span > < span class = "st" > "gramstain"< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "op" > )< / span > < / span > < / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # A tibble: 2 × < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > `Pathogen (N min-max)` TZP `TZP + GEN` `TZP + TOB`< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > *< / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < dbl> < / span > < span style = "color: #949494; font-style: italic;" > < dbl> < / span > < span style = "color: #949494; font-style: italic;" > < dbl> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 1< / span > Gram-negative (641-693) 88 99 98< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 2< / span > Gram-positive (345-1044) 86 98 95< / span >
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< span class = "r-in" > < span > < / span > < / span >
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< span class = "r-in" > < span > < span class = "co" > # names of antibiotics do not need to resemble columns exactly:< / span > < / span > < / span >
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< span class = "r-in" > < span > < span class = "fu" > antibiogram< / span > < span class = "op" > (< / span > < span class = "va" > example_isolates< / span > ,< / span > < / span >
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< span class = "r-in" > < span > antibiotics < span class = "op" > =< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/c.html" class = "external-link" > c< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "Cipro"< / span > , < span class = "st" > "cipro + genta"< / span > < span class = "op" > )< / span > ,< / span > < / span >
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< span class = "r-in" > < span > mo_transform < span class = "op" > =< / span > < span class = "st" > "gramstain"< / span > ,< / span > < / span >
< span class = "r-in" > < span > ab_transform < span class = "op" > =< / span > < span class = "st" > "name"< / span > ,< / span > < / span >
< span class = "r-in" > < span > sep < span class = "op" > =< / span > < span class = "st" > " & "< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "op" > )< / span > < / span > < / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # A tibble: 2 × < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > `Pathogen (N min-max)` Ciprofloxacin `Ciprofloxacin & Gentamicin`< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > *< / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < dbl> < / span > < span style = "color: #949494; font-style: italic;" > < dbl> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 1< / span > Gram-negative (684-694) 91 99< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 2< / span > Gram-positive (724-847) 77 93< / span >
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< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # Syndromic antibiogram ------------------------------------------------< / span > < / span > < / span >
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # the data set could contain a filter for e.g. respiratory specimens< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > antibiogram< / span > < span class = "op" > (< / span > < span class = "va" > example_isolates< / span > ,< / span > < / span >
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< span class = "r-in" > < span > antibiotics < span class = "op" > =< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/c.html" class = "external-link" > c< / a > < / 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 = "fu" > < a href = "antibiotic_class_selectors.html" > carbapenems< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > ,< / span > < / span >
< span class = "r-in" > < span > syndromic_group < span class = "op" > =< / span > < span class = "st" > "ward"< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "op" > )< / span > < / span > < / span >
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< span class = "r-msg co" > < span class = "r-pr" > #> < / span > ℹ < / span >
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< span class = "r-msg co" > < span class = "r-pr" > #> < / span > (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)< / span >
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< span class = "r-msg co" > < span class = "r-pr" > #> < / span > ℹ < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # A tibble: 14 × < / span > < / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > `Syndromic Group` `Pathogen (N min-max)` AMK GEN IPM KAN MEM TOB< / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > *< / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < dbl> < / span > < span style = "color: #949494; font-style: italic;" > < dbl> < / span > < span style = "color: #949494; font-style: italic;" > < dbl> < / span > < span style = "color: #949494; font-style: italic;" > < dbl> < / span > < span style = "color: #949494; font-style: italic;" > < dbl> < / span > < span style = "color: #949494; font-style: italic;" > < dbl> < / span > < / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 1< / span > Clinical CoNS (23-205) < span style = "color: #BB0000;" > NA< / span > 89 57 < span style = "color: #BB0000;" > NA< / span > 57 26< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 2< / span > ICU CoNS (10-73) < span style = "color: #BB0000;" > NA< / span > 79 < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 3< / span > Outpatient CoNS (3-31) < span style = "color: #BB0000;" > NA< / span > 84 < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 4< / span > Clinical E. coli (0-299) 100 98 100 < span style = "color: #BB0000;" > NA< / span > 100 98< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 5< / span > ICU E. coli (0-137) 100 99 100 < span style = "color: #BB0000;" > NA< / span > 100 96< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 6< / span > Clinical K. pneumoniae (0-51) < span style = "color: #BB0000;" > NA< / span > 92 100 < span style = "color: #BB0000;" > NA< / span > 100 92< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 7< / span > Clinical P. mirabilis (0-30) < span style = "color: #BB0000;" > NA< / span > 100 < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > 100< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 8< / span > Clinical S. aureus (2-150) < span style = "color: #BB0000;" > NA< / span > 99 < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > 97< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 9< / span > ICU S. aureus (0-66) < span style = "color: #BB0000;" > NA< / span > 100 < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 10< / span > Clinical S. epidermidis (4-79) < span style = "color: #BB0000;" > NA< / span > 82 < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > 55< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 11< / span > ICU S. epidermidis (4-75) < span style = "color: #BB0000;" > NA< / span > 72 < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > 41< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 12< / span > Clinical S. hominis (1-45) < span style = "color: #BB0000;" > NA< / span > 96 < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > 94< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 13< / span > Clinical S. pneumoniae (5-78) 0 0 < span style = "color: #BB0000;" > NA< / span > 0 < span style = "color: #BB0000;" > NA< / span > 0< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 14< / span > ICU S. pneumoniae (5-30) 0 0 < span style = "color: #BB0000;" > NA< / span > 0 < span style = "color: #BB0000;" > NA< / span > 0< / span >
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< span class = "r-in" > < span > < / span > < / span >
2023-02-10 16:26:36 +01:00
< span class = "r-in" > < span > < span class = "co" > # now define a data set with only E. coli< / span > < / span > < / span >
2023-02-08 17:01:47 +01:00
< span class = "r-in" > < span > < span class = "va" > ex1< / span > < span class = "op" > < -< / span > < span class = "va" > example_isolates< / span > < span class = "op" > [< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/which.html" class = "external-link" > which< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "mo_property.html" > mo_genus< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > ==< / span > < span class = "st" > "Escherichia"< / span > < span class = "op" > )< / span > , < span class = "op" > ]< / span > < / span > < / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > ℹ < / span >
2023-02-10 16:26:36 +01:00
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # with a custom language, though this will be determined automatically< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # (i.e., this table will be in Spanish on Spanish systems)< / span > < / span > < / span >
2023-02-08 17:01:47 +01:00
< span class = "r-in" > < span > < span class = "fu" > antibiogram< / span > < span class = "op" > (< / span > < span class = "va" > ex1< / span > ,< / span > < / span >
2023-03-11 14:32:27 +01:00
< span class = "r-in" > < span > antibiotics < 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 > < / span >
< span class = "r-in" > < span > ab_transform < span class = "op" > =< / span > < span class = "st" > "name"< / span > ,< / span > < / span >
< span class = "r-in" > < span > syndromic_group < span class = "op" > =< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/ifelse.html" class = "external-link" > ifelse< / a > < / span > < span class = "op" > (< / span > < span class = "va" > ex1< / span > < span class = "op" > $< / span > < span class = "va" > ward< / span > < span class = "op" > ==< / span > < span class = "st" > "ICU"< / span > ,< / span > < / span >
< span class = "r-in" > < span > < span class = "st" > "UCI"< / span > , < span class = "st" > "No UCI"< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "op" > )< / span > ,< / span > < / span >
< span class = "r-in" > < span > language < span class = "op" > =< / span > < span class = "st" > "es"< / span > < / span > < / span >
2023-02-12 17:20:08 +01:00
< span class = "r-in" > < span > < span class = "op" > )< / span > < / span > < / span >
2023-02-08 17:01:47 +01:00
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > ℹ < / span >
2023-02-22 14:47:35 +01:00
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)< / span >
2023-02-12 11:30:57 +01:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # A tibble: 2 × < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > `Grupo sindrómico` `Patógeno (N min-max)` Amikacina Gentamicina Tobramicina< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > *< / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < dbl> < / span > < span style = "color: #949494; font-style: italic;" > < dbl> < / span > < span style = "color: #949494; font-style: italic;" > < dbl> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 1< / span > No UCI E. coli (0-325) 100 98 98< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 2< / span > UCI E. coli (0-137) 100 99 96< / span >
2023-02-08 17:01:47 +01:00
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # Weighted-incidence syndromic combination antibiogram (WISCA) ---------< / span > < / span > < / span >
< span class = "r-in" > < span > < / span > < / span >
2023-02-13 10:34:26 +01:00
< span class = "r-in" > < span > < span class = "co" > # the data set could contain a filter for e.g. respiratory specimens/ICU< / span > < / span > < / span >
2023-02-08 17:01:47 +01:00
< span class = "r-in" > < span > < span class = "fu" > antibiogram< / span > < span class = "op" > (< / span > < span class = "va" > example_isolates< / span > ,< / span > < / span >
2023-03-11 14:32:27 +01:00
< span class = "r-in" > < span > antibiotics < span class = "op" > =< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/c.html" class = "external-link" > c< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "AMC"< / span > , < span class = "st" > "AMC+CIP"< / span > , < span class = "st" > "TZP"< / span > , < span class = "st" > "TZP+TOB"< / span > < span class = "op" > )< / span > ,< / span > < / span >
< span class = "r-in" > < span > mo_transform < span class = "op" > =< / span > < span class = "st" > "gramstain"< / span > ,< / span > < / span >
< span class = "r-in" > < span > minimum < span class = "op" > =< / span > < span class = "fl" > 10< / span > , < span class = "co" > # this should be > =30, but now just as example< / span > < / span > < / span >
< span class = "r-in" > < span > syndromic_group < span class = "op" > =< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/ifelse.html" class = "external-link" > ifelse< / a > < / span > < span class = "op" > (< / span > < span class = "va" > example_isolates< / span > < span class = "op" > $< / span > < span class = "va" > age< / span > < span class = "op" > > =< / span > < span class = "fl" > 65< / span > < span class = "op" > & < / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > example_isolates< / span > < span class = "op" > $< / span > < span class = "va" > gender< / span > < span class = "op" > ==< / span > < span class = "st" > "M"< / span > ,< / span > < / span >
< span class = "r-in" > < span > < span class = "st" > "WISCA Group 1"< / span > , < span class = "st" > "WISCA Group 2"< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "op" > )< / span > < / span > < / span >
2023-02-12 17:20:08 +01:00
< span class = "r-in" > < span > < span class = "op" > )< / span > < / span > < / span >
2023-02-22 15:50:02 +01:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # A tibble: 4 × < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > `Syndromic Group` `Pathogen (N min-max)` AMC `AMC + CIP` TZP `TZP + TOB`< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > *< / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < dbl> < / span > < span style = "color: #949494; font-style: italic;" > < dbl> < / span > < span style = "color: #949494; font-style: italic;" > < dbl> < / span > < span style = "color: #949494; font-style: italic;" > < dbl> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 1< / span > WISCA Group 1 Gram-negative (261-285) 76 95 89 99< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 2< / span > WISCA Group 2 Gram-negative (380-442) 76 98 88 98< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 3< / span > WISCA Group 1 Gram-positive (123-406) 76 89 81 95< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 4< / span > WISCA Group 2 Gram-positive (222-732) 76 89 88 95< / span >
2023-02-08 17:01:47 +01:00
< span class = "r-in" > < span > < / span > < / span >
2023-02-24 09:51:48 +01:00
< span class = "r-in" > < span > < / span > < / span >
2023-02-17 09:54:21 +01:00
< span class = "r-in" > < span > < span class = "co" > # Print the output for R Markdown / Quarto -----------------------------< / span > < / span > < / span >
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > ureido< / span > < span class = "op" > < -< / span > < span class = "fu" > antibiogram< / span > < span class = "op" > (< / span > < span class = "va" > example_isolates< / span > ,< / span > < / span >
2023-03-11 14:32:27 +01:00
< span class = "r-in" > < span > antibiotics < span class = "op" > =< / span > < span class = "fu" > < a href = "antibiotic_class_selectors.html" > ureidopenicillins< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > ,< / span > < / span >
< span class = "r-in" > < span > ab_transform < span class = "op" > =< / span > < span class = "st" > "name"< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "op" > )< / span > < / span > < / span >
2023-02-17 09:54:21 +01:00
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > ℹ < / span >
< span class = "r-in" > < span > < / span > < / span >
2023-02-23 16:36:44 +01:00
< span class = "r-in" > < span > < span class = "co" > # in an Rmd file, you would just need to return `ureido` in a chunk,< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # but to be explicit here:< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "kw" > if< / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/ns-load.html" class = "external-link" > requireNamespace< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "knitr"< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < span class = "op" > {< / span > < / span > < / span >
2023-03-20 22:10:09 +01:00
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://rdrr.io/r/base/cat.html" class = "external-link" > cat< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > knitr< / span > < span class = "fu" > ::< / span > < span class = "fu" > < a href = "https://rdrr.io/pkg/knitr/man/knit_print.html" class = "external-link" > knit_print< / a > < / span > < span class = "op" > (< / span > < span class = "va" > ureido< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < / span > < / span >
2023-02-23 16:36:44 +01:00
< span class = "r-in" > < span > < span class = "op" > }< / span > < / span > < / span >
2023-03-20 22:10:09 +01:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > |Pathogen (N) | Piperacillin/tazobactam|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > |:---------------------|-----------------------:|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > |CoNS (33) | 30|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > |*E. coli* (416) | 94|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > |*K. pneumoniae* (53) | 89|< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > |*S. pneumoniae* (112) | 100|< / span >
2023-02-17 09:54:21 +01:00
< span class = "r-in" > < span > < / span > < / span >
2023-02-08 17:01:47 +01:00
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # Generate plots with ggplot2 or base R --------------------------------< / span > < / span > < / span >
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > ab1< / span > < span class = "op" > < -< / span > < span class = "fu" > antibiogram< / span > < span class = "op" > (< / span > < span class = "va" > example_isolates< / span > ,< / span > < / span >
2023-02-12 17:20:08 +01:00
< span class = "r-in" > < span > antibiotics < span class = "op" > =< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/c.html" class = "external-link" > c< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "AMC"< / span > , < span class = "st" > "CIP"< / span > , < span class = "st" > "TZP"< / span > , < span class = "st" > "TZP+TOB"< / span > < span class = "op" > )< / span > ,< / span > < / span >
< span class = "r-in" > < span > mo_transform < span class = "op" > =< / span > < span class = "st" > "gramstain"< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "op" > )< / span > < / span > < / span >
2023-02-08 17:01:47 +01:00
< span class = "r-in" > < span > < span class = "va" > ab2< / span > < span class = "op" > < -< / span > < span class = "fu" > antibiogram< / span > < span class = "op" > (< / span > < span class = "va" > example_isolates< / span > ,< / span > < / span >
2023-02-12 17:20:08 +01:00
< span class = "r-in" > < span > antibiotics < span class = "op" > =< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/c.html" class = "external-link" > c< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "AMC"< / span > , < span class = "st" > "CIP"< / span > , < span class = "st" > "TZP"< / span > , < span class = "st" > "TZP+TOB"< / span > < span class = "op" > )< / span > ,< / span > < / span >
< span class = "r-in" > < span > mo_transform < span class = "op" > =< / span > < span class = "st" > "gramstain"< / span > ,< / span > < / span >
< span class = "r-in" > < span > syndromic_group < span class = "op" > =< / span > < span class = "st" > "ward"< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < / span > < / span >
2023-02-08 17:01:47 +01:00
< span class = "r-in" > < span > < span class = "kw" > if< / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/ns-load.html" class = "external-link" > requireNamespace< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "ggplot2"< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < span class = "op" > {< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > ggplot2< / span > < span class = "fu" > ::< / span > < span class = "fu" > < a href = "https://ggplot2.tidyverse.org/reference/autoplot.html" class = "external-link" > autoplot< / a > < / span > < span class = "op" > (< / span > < span class = "va" > ab1< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "op" > }< / span > < / span > < / span >
2023-02-22 15:50:02 +01:00
< span class = "r-plt img" > < img src = "antibiogram-1.png" alt = "" width = "700" height = "433" > < / span >
2023-02-08 17:01:47 +01:00
< span class = "r-in" > < span > < span class = "kw" > if< / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/ns-load.html" class = "external-link" > requireNamespace< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "ggplot2"< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < span class = "op" > {< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > ggplot2< / span > < span class = "fu" > ::< / span > < span class = "fu" > < a href = "https://ggplot2.tidyverse.org/reference/autoplot.html" class = "external-link" > autoplot< / a > < / span > < span class = "op" > (< / span > < span class = "va" > ab2< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "op" > }< / span > < / span > < / span >
2023-02-22 15:50:02 +01:00
< span class = "r-plt img" > < img src = "antibiogram-2.png" alt = "" width = "700" height = "433" > < / span >
2023-02-17 09:54:21 +01:00
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "plot.html" > plot< / a > < / span > < span class = "op" > (< / span > < span class = "va" > ab1< / span > < span class = "op" > )< / span > < / span > < / span >
2023-02-22 15:50:02 +01:00
< span class = "r-plt img" > < img src = "antibiogram-3.png" alt = "" width = "700" height = "433" > < / span >
2023-02-17 09:54:21 +01:00
< span class = "r-in" > < span > < span class = "fu" > < a href = "plot.html" > plot< / a > < / span > < span class = "op" > (< / span > < span class = "va" > ab2< / span > < span class = "op" > )< / span > < / span > < / span >
2023-02-22 15:50:02 +01:00
< span class = "r-plt img" > < img src = "antibiogram-4.png" alt = "" width = "700" height = "433" > < / span >
2023-02-13 17:04:12 +01:00
< span class = "r-in" > < span > < span class = "co" > # }< / span > < / span > < / span >
2023-02-08 17:01:47 +01:00
< / code > < / pre > < / div >
< / div >
< / main > < aside class = "col-md-3" > < nav id = "toc" > < h2 > On this page< / h2 >
< / nav > < / aside > < / div >
< footer > < div class = "pkgdown-footer-left" >
< p > < / p > < p > < code > AMR< / code > (for R). Free and open-source, licenced under the < a target = "_blank" href = "https://github.com/msberends/AMR/blob/main/LICENSE" class = "external-link" > GNU General Public License version 2.0 (GPL-2)< / a > .< br > Developed at the < a target = "_blank" href = "https://www.rug.nl" class = "external-link" > University of Groningen< / a > and < a target = "_blank" href = "https://www.umcg.nl" class = "external-link" > University Medical Center Groningen< / a > in The Netherlands.< / p >
< / div >
< div class = "pkgdown-footer-right" >
< p > < / p > < p > < a target = "_blank" href = "https://www.rug.nl" class = "external-link" > < img src = "https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_rug.svg" style = "max-width: 150px;" > < / a > < a target = "_blank" href = "https://www.umcg.nl" class = "external-link" > < img src = "https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_umcg.svg" style = "max-width: 150px;" > < / a > < / p >
< / div >
< / footer > < / div >
< / body > < / html >
