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< li > < a class = "dropdown-item" href = "articles/AMR.html" > < span class = "fa fa-directions" > < / span > Conduct AMR Analysis< / a > < / li >
< li > < a class = "dropdown-item" href = "reference/antibiogram.html" > < span class = "fa fa-file-prescription" > < / span > Generate Antibiogram (Trad./Syndromic/WISCA)< / a > < / li >
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< li > < a class = "dropdown-item" href = "articles/PCA.html" > < span class = "fa fa-compress" > < / span > Conduct Principal Component Analysis for AMR< / a > < / li >
< li > < a class = "dropdown-item" href = "articles/MDR.html" > < span class = "fa fa-skull-crossbones" > < / span > Determine Multi-Drug Resistance (MDR)< / a > < / li >
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< li > < a class = "dropdown-item" href = "reference/ab_property.html" > < span class = "fa fa-capsules" > < / span > Get Properties of an Antibiotic Drug< / a > < / li >
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< img src = "logo.svg" class = "logo" alt = "" > < h1 id = "the-amr-package-for-r-" > The < code > AMR< / code > Package for R
< a class = "anchor" aria-label = "anchor" href = "#the-amr-package-for-r-" > < / a >
< / h1 >
< / div >
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< ul >
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< li > Provides an < strong > all-in-one solution< / strong > for antimicrobial resistance (AMR) data analysis in a One Health approach< / li >
< li > Used in over 175 countries, available in 20 languages< / li >
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< li > Generates < strong > antibiograms< / strong > - traditional, combined, syndromic, and even WISCA< / li >
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< li > Provides the < strong > full microbiological taxonomy< / strong > and extensive info on < strong > all antimicrobial drugs< / strong >
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< / li >
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< li > Applies all recent < strong > CLSI< / strong > and < strong > EUCAST< / strong > clinical and veterinary breakpoints for MICs, disk zones and ECOFFs< / li >
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< li > Corrects for duplicate isolates, < strong > calculates< / strong > and < strong > predicts< / strong > AMR per antibiotic class< / li >
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< li > Integrates with < strong > WHONET< / strong > , ATC, < strong > EARS-Net< / strong > , PubChem, < strong > LOINC< / strong > , < strong > SNOMED CT< / strong > , and < strong > NCBI< / strong >
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< / li >
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< li > 100% free of costs and dependencies, highly suitable for places with < strong > limited resources< / strong >
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< / li >
< / ul >
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< p > < a href = "https://chatgpt.com/g/g-M4UNLwFi5-amr-for-r-assistant" class = "external-link" > < img src = "../AMRforRGPT.svg" style = "min-width: 300px; width: 10%;" > < / a > < / p >
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< small > < a href = "https://msberends.github.io/AMR/" > https://msberends.github.io/AMR< / a > < / small >
< / p >
< p style = "text-align:right; width: 50%;" >
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< small > < a href = "https://doi.org/10.18637/jss.v104.i03" target = "_blank" class = "external-link" > https://doi.org/10.18637/jss.v104.i03< / a > < / small >
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< / p >
< / div >
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< p > < a href = "./reference/clinical_breakpoints.html#response-from-clsi-and-eucast" > < img src = "./endorsement_clsi_eucast.jpg" class = "endorse_img" align = "right" height = "120" > < / a > < / p >
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< div class = "section level3" >
< h3 id = "introduction" > Introduction< a class = "anchor" aria-label = "anchor" href = "#introduction" > < / a >
< / h3 >
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< p > The < code > AMR< / code > package is a < a href = "#copyright" > free and open-source< / a > R package with < a href = "https://en.wikipedia.org/wiki/Dependency_hell" class = "external-link" > zero dependencies< / a > to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. < strong > Our aim is to provide a standard< / strong > for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. < a href = "./authors.html" > Many different researchers< / a > from around the globe are continually helping us to make this a successful and durable project!< / p >
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< p > This work was published in the Journal of Statistical Software (Volume 104(3); < a href = "https://doi.org/10.18637/jss.v104.i03" class = "external-link" > DOI 10.18637/jss.v104.i03< / a > ) and formed the basis of two PhD theses (< a href = "https://doi.org/10.33612/diss.177417131" class = "external-link" > DOI 10.33612/diss.177417131< / a > and < a href = "https://doi.org/10.33612/diss.192486375" class = "external-link" > DOI 10.33612/diss.192486375< / a > ).< / p >
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< p > After installing this package, R knows < a href = "./reference/microorganisms.html" > < strong > ~52,000 distinct microbial species< / strong > < / a > (updated December 2022) and all < a href = "./reference/antibiotics.html" > < strong > ~600 antibiotic, antimycotic and antiviral drugs< / strong > < / a > by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). < strong > It was designed to work in any setting, including those with very limited resources< / strong > . It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the < a href = "https://www.rug.nl" class = "external-link" > University of Groningen< / a > , in collaboration with non-profit organisations < a href = "https://www.certe.nl" class = "external-link" > Certe Medical Diagnostics and Advice Foundation< / a > and < a href = "https://www.umcg.nl" class = "external-link" > University Medical Center Groningen< / a > .< / p >
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< div class = "section level5" >
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< h5 id = "used-in-over-175-countries-available-in-20-languages" > Used in over 175 countries, available in 20 languages< a class = "anchor" aria-label = "anchor" href = "#used-in-over-175-countries-available-in-20-languages" > < / a >
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< / h5 >
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< p > < a href = "./countries_large.png" target = "_blank" > < img src = "./countries.png" align = "right" style = "max-width: 300px;" > < / a > < / p >
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< p > Since its first public release in early 2018, this R package has been used in almost all countries in the world. Click the map to enlarge and to see the country names.< / p >
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< p > With the help of contributors from all corners of the world, the < code > AMR< / code > package is available in < img src = "lang_en.svg" style = "height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;" > English, < img src = "lang_cs.svg" style = "height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;" > Czech, < img src = "lang_zh.svg" style = "height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;" > Chinese, < img src = "lang_da.svg" style = "height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;" > Danish, < img src = "lang_nl.svg" style = "height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;" > Dutch, < img src = "lang_fi.svg" style = "height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;" > Finnish, < img src = "lang_fr.svg" style = "height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;" > French, < img src = "lang_de.svg" style = "height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;" > German, < img src = "lang_el.svg" style = "height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;" > Greek, < img src = "lang_it.svg" style = "height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;" > Italian, < img src = "lang_ja.svg" style = "height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;" > Japanese, < img src = "lang_no.svg" style = "height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;" > Norwegian, < img src = "lang_pl.svg" style = "height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;" > Polish, < img src = "lang_pt.svg" style = "height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;" > Portuguese, < img src = "lang_ro.svg" style = "height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;" > Romanian, < img src = "lang_ru.svg" style = "height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;" > Russian, < img src = "lang_es.svg" style = "height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;" > Spanish, < img src = "lang_sv.svg" style = "height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;" > Swedish, < img src = "lang_tr.svg" style = "height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;" > Turkish, and < img src = "lang_uk.svg" style = "height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;" > Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.< / p >
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< / div >
< / div >
< div class = "section level3" >
< h3 id = "practical-examples" > Practical examples< a class = "anchor" aria-label = "anchor" href = "#practical-examples" > < / a >
< / h3 >
< div class = "section level4" >
< h4 id = "filtering-and-selecting-data" > Filtering and selecting data< a class = "anchor" aria-label = "anchor" href = "#filtering-and-selecting-data" > < / a >
< / h4 >
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< p > One of the most powerful functions of this package, aside from calculating and plotting AMR, is selecting and filtering based on antibiotic columns. This can be done using the so-called < a href = "https://msberends.github.io/AMR/reference/antibiotic_class_selectors.html" > antibiotic class selectors< / a > that work in base R, < code > dplyr< / code > and < code > data.table< / code > :< / p >
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< div class = "sourceCode" id = "cb1" > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < span class = "co" > # AMR works great with dplyr, but it's not required or neccesary< / span > < / span >
< 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://msberends.github.io/AMR/" > AMR< / a > < / span > < span class = "op" > )< / span > < / span >
< 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 >
< span > < / span >
< span > < span class = "va" > example_isolates< / 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/mutate.html" class = "external-link" > mutate< / a > < / span > < span class = "op" > (< / span > bacteria < span class = "op" > =< / span > < span class = "fu" > < a href = "reference/mo_property.html" > mo_fullname< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / 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 = "co" > # filtering functions for microorganisms:< / span > < / span >
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< 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 = "fu" > < a href = "reference/mo_property.html" > mo_is_gram_negative< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > ,< / span >
< span > < span class = "fu" > < a href = "reference/mo_property.html" > mo_is_intrinsic_resistant< / a > < / span > < span class = "op" > (< / span > ab < span class = "op" > =< / span > < span class = "st" > "cefotax"< / span > < span class = "op" > )< / 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 = "co" > # antibiotic selectors:< / span > < / span >
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< span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/select.html" class = "external-link" > select< / a > < / span > < span class = "op" > (< / span > < span class = "va" > bacteria< / span > ,< / span >
< span > < span class = "fu" > < a href = "reference/antibiotic_class_selectors.html" > aminoglycosides< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > ,< / span >
< span > < span class = "fu" > < a href = "reference/antibiotic_class_selectors.html" > carbapenems< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < / span > < / code > < / pre > < / div >
< p > With only having defined a row filter on Gram-negative bacteria with intrinsic resistance to cefotaxime (< code > < a href = "reference/mo_property.html" > mo_is_gram_negative()< / a > < / code > and < code > < a href = "reference/mo_property.html" > mo_is_intrinsic_resistant()< / a > < / code > ) and a column selection on two antibiotic groups (< code > < a href = "reference/antibiotic_class_selectors.html" > aminoglycosides()< / a > < / code > and < code > < a href = "reference/antibiotic_class_selectors.html" > carbapenems()< / a > < / code > ), the reference data about < a href = "./reference/microorganisms.html" > all microorganisms< / a > and < a href = "./reference/antibiotics.html" > all antibiotics< / a > in the < code > AMR< / code > package make sure you get what you meant:< / p >
< table class = "table" >
< thead > < tr class = "header" >
< th align = "left" > bacteria< / th >
< th align = "center" > GEN< / th >
< th align = "center" > TOB< / th >
< th align = "center" > AMK< / th >
< th align = "center" > KAN< / th >
< th align = "center" > IPM< / th >
< th align = "center" > MEM< / th >
< / tr > < / thead >
< tbody >
< tr class = "odd" >
< td align = "left" > < em > Pseudomonas aeruginosa< / em > < / td >
< td align = "center" > I< / td >
< td align = "center" > S< / td >
< td align = "center" > < / td >
< td align = "center" > R< / td >
< td align = "center" > S< / td >
< td align = "center" > < / td >
< / tr >
< tr class = "even" >
< td align = "left" > < em > Pseudomonas aeruginosa< / em > < / td >
< td align = "center" > I< / td >
< td align = "center" > S< / td >
< td align = "center" > < / td >
< td align = "center" > R< / td >
< td align = "center" > S< / td >
< td align = "center" > < / td >
< / tr >
< tr class = "odd" >
< td align = "left" > < em > Pseudomonas aeruginosa< / em > < / td >
< td align = "center" > I< / td >
< td align = "center" > S< / td >
< td align = "center" > < / td >
< td align = "center" > R< / td >
< td align = "center" > S< / td >
< td align = "center" > < / td >
< / tr >
< tr class = "even" >
< td align = "left" > < em > Pseudomonas aeruginosa< / em > < / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > R< / td >
< td align = "center" > < / td >
< td align = "center" > S< / td >
< / tr >
< tr class = "odd" >
< td align = "left" > < em > Pseudomonas aeruginosa< / em > < / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > R< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< / tr >
< tr class = "even" >
< td align = "left" > < em > Pseudomonas aeruginosa< / em > < / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > R< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< / tr >
< tr class = "odd" >
< td align = "left" > < em > Stenotrophomonas maltophilia< / em > < / td >
< td align = "center" > R< / td >
< td align = "center" > R< / td >
< td align = "center" > R< / td >
< td align = "center" > R< / td >
< td align = "center" > R< / td >
< td align = "center" > R< / td >
< / tr >
< tr class = "even" >
< td align = "left" > < em > Pseudomonas aeruginosa< / em > < / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > R< / td >
< td align = "center" > < / td >
< td align = "center" > S< / td >
< / tr >
< tr class = "odd" >
< td align = "left" > < em > Pseudomonas aeruginosa< / em > < / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > R< / td >
< td align = "center" > < / td >
< td align = "center" > S< / td >
< / tr >
< tr class = "even" >
< td align = "left" > < em > Pseudomonas aeruginosa< / em > < / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > R< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< / tr >
< / tbody >
< / table >
< p > A base R equivalent would be:< / p >
< div class = "sourceCode" id = "cb2" > < pre class = "downlit sourceCode r" >
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< code class = "sourceCode R" > < 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://msberends.github.io/AMR/" > AMR< / a > < / span > < span class = "op" > )< / span > < / span >
< span > < span class = "va" > example_isolates< / span > < span class = "op" > $< / span > < span class = "va" > bacteria< / span > < span class = "op" > < -< / span > < span class = "fu" > < a href = "reference/mo_property.html" > mo_fullname< / a > < / span > < span class = "op" > (< / span > < span class = "va" > example_isolates< / span > < span class = "op" > $< / span > < span class = "va" > mo< / span > < span class = "op" > )< / span > < / span >
2022-08-21 16:59:35 +02:00
< 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 = "reference/mo_property.html" > mo_is_gram_negative< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > & < / span > < / span >
< span > < span class = "fu" > < a href = "reference/mo_property.html" > mo_is_intrinsic_resistant< / a > < / span > < span class = "op" > (< / span > ab < span class = "op" > =< / span > < span class = "st" > "cefotax"< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > ,< / span >
< 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" > "bacteria"< / span > , < span class = "fu" > < a href = "reference/antibiotic_class_selectors.html" > aminoglycosides< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > , < span class = "fu" > < a href = "reference/antibiotic_class_selectors.html" > carbapenems< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < span class = "op" > ]< / span > < / span > < / code > < / pre > < / div >
2023-03-11 17:02:25 +01:00
< p > This base R code will work in any version of R since April 2013 (R-3.0). Moreover, this code works identically with the < code > data.table< / code > package, only by starting with:< / p >
< div class = "sourceCode" id = "cb3" > < pre class = "downlit sourceCode r" >
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< code class = "sourceCode R" > < span > < span class = "va" > example_isolates< / span > < span class = "op" > < -< / span > < span class = "fu" > data.table< / span > < span class = "fu" > ::< / span > < span class = "fu" > < a href = "https://rdatatable.gitlab.io/data.table/reference/as.data.table.html" class = "external-link" > as.data.table< / a > < / span > < span class = "op" > (< / span > < span class = "va" > example_isolates< / span > < span class = "op" > )< / span > < / span > < / code > < / pre > < / div >
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< / div >
< div class = "section level4" >
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< h4 id = "generating-antibiograms" > Generating antibiograms< a class = "anchor" aria-label = "anchor" href = "#generating-antibiograms" > < / a >
2022-08-21 16:59:35 +02:00
< / h4 >
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< p > The < code > AMR< / code > package supports generating traditional, combined, syndromic, and even weighted-incidence syndromic combination antibiograms (WISCA).< / p >
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< p > If used inside R Markdown or Quarto, the table will be printed in the right output format automatically (such as markdown, LaTeX, HTML, etc.).< / p >
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< div class = "sourceCode" id = "cb4" > < pre class = "downlit sourceCode r" >
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< code class = "sourceCode R" > < span > < span class = "fu" > < a href = "reference/antibiogram.html" > antibiogram< / a > < / span > < span class = "op" > (< / span > < span class = "va" > example_isolates< / 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 = "fu" > < a href = "reference/antibiotic_class_selectors.html" > aminoglycosides< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > , < span class = "fu" > < a href = "reference/antibiotic_class_selectors.html" > carbapenems< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < / span > < / code > < / pre > < / div >
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< table style = "width:100%;" class = "table" >
< colgroup >
< col width = "18%" >
< col width = "13%" >
< col width = "12%" >
< col width = "13%" >
< col width = "13%" >
< col width = "13%" >
< col width = "13%" >
< / colgroup >
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< thead > < tr class = "header" >
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< th align = "left" > Pathogen< / th >
< th align = "center" > Amikacin< / th >
< th align = "center" > Gentamicin< / th >
< th align = "center" > Imipenem< / th >
< th align = "center" > Kanamycin< / th >
< th align = "center" > Meropenem< / th >
< th align = "center" > Tobramycin< / th >
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< / tr > < / thead >
< tbody >
< tr class = "odd" >
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< td align = "left" > CoNS< / td >
< td align = "center" > 0% (0/43)< / td >
< td align = "center" > 86% (267/309)< / td >
< td align = "center" > 52% (25/48)< / td >
< td align = "center" > 0% (0/43)< / td >
< td align = "center" > 52% (25/48)< / td >
< td align = "center" > 22% (12/55)< / td >
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< / tr >
< tr class = "even" >
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< td align = "left" > < em > E. coli< / em > < / td >
< td align = "center" > 100% (171/171)< / td >
< td align = "center" > 98% (451/460)< / td >
< td align = "center" > 100% (422/422)< / td >
< td align = "center" > < / td >
< td align = "center" > 100% (418/418)< / td >
< td align = "center" > 97% (450/462)< / td >
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< / tr >
< tr class = "odd" >
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< td align = "left" > < em > E. faecalis< / em > < / td >
< td align = "center" > 0% (0/39)< / td >
< td align = "center" > 0% (0/39)< / td >
< td align = "center" > 100% (38/38)< / td >
< td align = "center" > 0% (0/39)< / td >
< td align = "center" > < / td >
< td align = "center" > 0% (0/39)< / td >
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< / tr >
< tr class = "even" >
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< td align = "left" > < em > K. pneumoniae< / em > < / td >
< td align = "center" > < / td >
< td align = "center" > 90% (52/58)< / td >
< td align = "center" > 100% (51/51)< / td >
< td align = "center" > < / td >
< td align = "center" > 100% (53/53)< / td >
< td align = "center" > 90% (52/58)< / td >
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< / tr >
< tr class = "odd" >
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< td align = "left" > < em > P. aeruginosa< / em > < / td >
< td align = "center" > < / td >
< td align = "center" > 100% (30/30)< / td >
< td align = "center" > < / td >
< td align = "center" > 0% (0/30)< / td >
< td align = "center" > < / td >
< td align = "center" > 100% (30/30)< / td >
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< / tr >
< tr class = "even" >
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< td align = "left" > < em > P. mirabilis< / em > < / td >
< td align = "center" > < / td >
< td align = "center" > 94% (32/34)< / td >
< td align = "center" > 94% (30/32)< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > 94% (32/34)< / td >
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< / tr >
< tr class = "odd" >
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< td align = "left" > < em > S. aureus< / em > < / td >
< td align = "center" > < / td >
< td align = "center" > 99% (231/233)< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > 98% (84/86)< / td >
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< / tr >
< tr class = "even" >
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< td align = "left" > < em > S. epidermidis< / em > < / td >
< td align = "center" > 0% (0/44)< / td >
< td align = "center" > 79% (128/163)< / td >
< td align = "center" > < / td >
< td align = "center" > 0% (0/44)< / td >
< td align = "center" > < / td >
< td align = "center" > 51% (45/89)< / td >
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< / tr >
< tr class = "odd" >
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< td align = "left" > < em > S. hominis< / em > < / td >
< td align = "center" > < / td >
< td align = "center" > 92% (74/80)< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > 85% (53/62)< / td >
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< / tr >
< tr class = "even" >
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< td align = "left" > < em > S. pneumoniae< / em > < / td >
< td align = "center" > 0% (0/117)< / td >
< td align = "center" > 0% (0/117)< / td >
< td align = "center" > < / td >
< td align = "center" > 0% (0/117)< / td >
< td align = "center" > < / td >
< td align = "center" > 0% (0/117)< / td >
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< / tr >
< / tbody >
< / table >
< p > In combination antibiograms, it is clear that combined antibiotics yield higher empiric coverage:< / p >
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< div class = "sourceCode" id = "cb5" > < pre class = "downlit sourceCode r" >
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< code class = "sourceCode R" > < span > < span class = "fu" > < a href = "reference/antibiogram.html" > antibiogram< / a > < / span > < span class = "op" > (< / span > < span class = "va" > example_isolates< / 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 >
< span > mo_transform < span class = "op" > =< / span > < span class = "st" > "gramstain"< / span > < span class = "op" > )< / span > < / span > < / code > < / pre > < / div >
< table class = "table" >
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< colgroup >
< col width = "12%" >
< col width = "21%" >
< col width = "33%" >
< col width = "32%" >
< / colgroup >
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< thead > < tr class = "header" >
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< th align = "left" > Pathogen< / th >
< th align = "center" > Piperacillin/tazobactam< / th >
< th align = "center" > Piperacillin/tazobactam + Gentamicin< / th >
< th align = "center" > Piperacillin/tazobactam + Tobramycin< / th >
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< / tr > < / thead >
< tbody >
< tr class = "odd" >
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< td align = "left" > Gram-negative< / td >
< td align = "center" > 88% (565/641)< / td >
< td align = "center" > 99% (681/691)< / td >
< td align = "center" > 98% (679/693)< / td >
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< / tr >
< tr class = "even" >
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< td align = "left" > Gram-positive< / td >
< td align = "center" > 86% (296/345)< / td >
< td align = "center" > 98% (1018/1044)< / td >
< td align = "center" > 95% (524/550)< / td >
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< / tr >
< / tbody >
< / table >
2023-02-17 09:54:21 +01:00
< p > Like many other functions in this package, < code > < a href = "reference/antibiogram.html" > antibiogram()< / a > < / code > comes with support for 20 languages that are often detected automatically based on system language:< / p >
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< div class = "sourceCode" id = "cb6" > < pre class = "downlit sourceCode r" >
2023-02-15 19:56:18 +01:00
< code class = "sourceCode R" > < span > < span class = "fu" > < a href = "reference/antibiogram.html" > antibiogram< / a > < / span > < span class = "op" > (< / span > < span class = "va" > example_isolates< / span > ,< / span >
2023-02-22 16:09:09 +01:00
< 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" > "tobra"< / span > , < span class = "st" > "genta"< / span > < span class = "op" > )< / span > , < span class = "co" > # any arbitrary name or code will work< / span > < / span >
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< span > mo_transform < span class = "op" > =< / span > < span class = "st" > "gramstain"< / span > ,< / span >
< span > ab_transform < span class = "op" > =< / span > < span class = "st" > "name"< / span > ,< / span >
< span > language < span class = "op" > =< / span > < span class = "st" > "uk"< / span > < span class = "op" > )< / span > < span class = "co" > # Ukrainian< / span > < / span > < / code > < / pre > < / div >
< table class = "table" >
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< colgroup >
< col width = "20%" >
< col width = "27%" >
< col width = "26%" >
< col width = "25%" >
< / colgroup >
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< thead > < tr class = "header" >
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< th align = "left" > Збудник< / th >
< th align = "center" > Гентаміцин< / th >
< th align = "center" > Тобраміцин< / th >
< th align = "center" > Ципрофлоксацин< / th >
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< / tr > < / thead >
< tbody >
< tr class = "odd" >
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< td align = "left" > Грамнегативні< / td >
< td align = "center" > 96% (659/684)< / td >
< td align = "center" > 96% (658/686)< / td >
< td align = "center" > 91% (621/684)< / td >
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< / tr >
< tr class = "even" >
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< td align = "left" > Грампозитивні< / td >
< td align = "center" > 63% (740/1170)< / td >
< td align = "center" > 34% (228/665)< / td >
< td align = "center" > 77% (560/724)< / td >
2023-02-15 19:56:18 +01:00
< / tr >
< / tbody >
< / table >
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< / div >
< div class = "section level4" >
< h4 id = "calculating-resistance-per-group" > Calculating resistance per group< a class = "anchor" aria-label = "anchor" href = "#calculating-resistance-per-group" > < / a >
< / h4 >
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< p > For a manual approach, you can use the < code > resistance< / code > or < code > < a href = "reference/proportion.html" > susceptibility()< / a > < / code > function:< / p >
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< div class = "sourceCode" id = "cb7" > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < span class = "va" > example_isolates< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span >
< span > < span class = "co" > # group by ward:< / span > < / span >
< span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/group_by.html" class = "external-link" > group_by< / a > < / span > < span class = "op" > (< / span > < span class = "va" > ward< / span > < span class = "op" > )< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span >
< span > < span class = "co" > # calculate AMR using resistance() for gentamicin and tobramycin< / span > < / span >
< span > < span class = "co" > # and get their 95% confidence intervals using sir_confidence_interval():< / span > < / span >
< span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/summarise.html" class = "external-link" > summarise< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/across.html" class = "external-link" > across< / a > < / span > < 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 = "va" > GEN< / span > , < span class = "va" > TOB< / span > < span class = "op" > )< / span > ,< / span >
< span > < span class = "fu" > < a href = "https://rdrr.io/r/base/list.html" class = "external-link" > list< / a > < / span > < span class = "op" > (< / span > total_R < span class = "op" > =< / span > < span class = "va" > resistance< / span > ,< / span >
< span > conf_int < span class = "op" > =< / span > < span class = "kw" > function< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > < span class = "op" > )< / span > < span class = "fu" > < a href = "reference/proportion.html" > sir_confidence_interval< / a > < / span > < span class = "op" > (< / span > < span class = "va" > x< / span > , collapse < span class = "op" > =< / span > < span class = "st" > "-"< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < / span > < / code > < / pre > < / div >
< table class = "table" >
< thead > < tr class = "header" >
< th align = "center" > ward< / th >
< th align = "center" > GEN_total_R< / th >
< th align = "center" > GEN_conf_int< / th >
< th align = "center" > TOB_total_R< / th >
< th align = "center" > TOB_conf_int< / th >
< / tr > < / thead >
< tbody >
< tr class = "odd" >
< td align = "center" > Clinical< / td >
< td align = "center" > 0.229< / td >
< td align = "center" > 0.205-0.254< / td >
< td align = "center" > 0.315< / td >
< td align = "center" > 0.284-0.347< / td >
< / tr >
< tr class = "even" >
< td align = "center" > ICU< / td >
< td align = "center" > 0.290< / td >
< td align = "center" > 0.253-0.330< / td >
< td align = "center" > 0.400< / td >
< td align = "center" > 0.353-0.449< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > Outpatient< / td >
< td align = "center" > 0.200< / td >
< td align = "center" > 0.131-0.285< / td >
< td align = "center" > 0.368< / td >
< td align = "center" > 0.254-0.493< / td >
< / tr >
< / tbody >
< / table >
< p > Or use < a href = "https://msberends.github.io/AMR/reference/antibiotic_class_selectors.html" > antibiotic class selectors< / a > to select a series of antibiotic columns:< / p >
< div class = "sourceCode" id = "cb8" > < pre class = "downlit sourceCode r" >
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< code class = "sourceCode R" > < 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://msberends.github.io/AMR/" > AMR< / a > < / span > < span class = "op" > )< / span > < / span >
< 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 >
< span > < / span >
< span > < span class = "va" > out< / span > < span class = "op" > < -< / span > < span class = "va" > example_isolates< / 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 = "co" > # group by ward:< / span > < / span >
< span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/group_by.html" class = "external-link" > group_by< / a > < / span > < span class = "op" > (< / span > < span class = "va" > ward< / 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 = "co" > # calculate AMR using resistance(), over all aminoglycosides and polymyxins:< / span > < / span >
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< span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/summarise.html" class = "external-link" > summarise< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/across.html" class = "external-link" > across< / a > < / span > < 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 = "reference/antibiotic_class_selectors.html" > aminoglycosides< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > , < span class = "fu" > < a href = "reference/antibiotic_class_selectors.html" > polymyxins< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > ,< / span >
< span > < span class = "va" > resistance< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < / span >
< span > < span class = "va" > out< / span > < / span > < / code > < / pre > < / div >
< table class = "table" >
< thead > < tr class = "header" >
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< th align = "left" > ward< / th >
< th align = "right" > GEN< / th >
< th align = "right" > TOB< / th >
< th align = "right" > AMK< / th >
< th align = "right" > KAN< / th >
< th align = "right" > COL< / th >
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< / tr > < / thead >
< tbody >
< tr class = "odd" >
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< td align = "left" > Clinical< / td >
< td align = "right" > 0.229< / td >
< td align = "right" > 0.315< / td >
< td align = "right" > 0.626< / td >
< td align = "right" > 1< / td >
< td align = "right" > 0.780< / td >
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< / tr >
< tr class = "even" >
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< td align = "left" > ICU< / td >
< td align = "right" > 0.290< / td >
< td align = "right" > 0.400< / td >
< td align = "right" > 0.662< / td >
< td align = "right" > 1< / td >
< td align = "right" > 0.857< / td >
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< / tr >
< tr class = "odd" >
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< td align = "left" > Outpatient< / td >
< td align = "right" > 0.200< / td >
< td align = "right" > 0.368< / td >
< td align = "right" > 0.605< / td >
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< td align = "right" > < / td >
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< td align = "right" > 0.889< / td >
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< / tr >
< / tbody >
< / table >
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< div class = "sourceCode" id = "cb9" > < pre class = "downlit sourceCode r" >
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< code class = "sourceCode R" > < span > < span class = "co" > # transform the antibiotic columns to names:< / span > < / span >
< span > < span class = "va" > out< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < span class = "fu" > < a href = "reference/ab_property.html" > set_ab_names< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < / span > < / code > < / pre > < / div >
< table class = "table" >
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< colgroup >
< col width = "17%" >
< col width = "17%" >
< col width = "17%" >
< col width = "14%" >
< col width = "16%" >
< col width = "16%" >
< / colgroup >
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< thead > < tr class = "header" >
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< th align = "left" > ward< / th >
< th align = "right" > gentamicin< / th >
< th align = "right" > tobramycin< / th >
< th > amikacin< / th >
< th align = "right" > kanamycin< / th >
< th align = "right" > colistin< / th >
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< / tr > < / thead >
< tbody >
< tr class = "odd" >
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< td align = "left" > Clinical< / td >
< td align = "right" > 0.229< / td >
< td align = "right" > 0.315< / td >
< td > 0.626< / td >
< td align = "right" > 1< / td >
< td align = "right" > 0.780< / td >
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< / tr >
< tr class = "even" >
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< td align = "left" > ICU< / td >
< td align = "right" > 0.290< / td >
< td align = "right" > 0.400< / td >
< td > 0.662< / td >
< td align = "right" > 1< / td >
< td align = "right" > 0.857< / td >
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< / tr >
< tr class = "odd" >
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< td align = "left" > Outpatient< / td >
< td align = "right" > 0.200< / td >
< td align = "right" > 0.368< / td >
< td > 0.605< / td >
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< td align = "right" > < / td >
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< td align = "right" > 0.889< / td >
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< / tr >
< / tbody >
< / table >
2023-03-11 17:02:25 +01:00
< div class = "sourceCode" id = "cb10" > < pre class = "downlit sourceCode r" >
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< code class = "sourceCode R" > < span > < span class = "co" > # transform the antibiotic column to ATC codes:< / span > < / span >
< span > < span class = "va" > out< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < span class = "fu" > < a href = "reference/ab_property.html" > set_ab_names< / a > < / span > < span class = "op" > (< / span > property < span class = "op" > =< / span > < span class = "st" > "atc"< / span > < span class = "op" > )< / span > < / span > < / code > < / pre > < / div >
< table class = "table" >
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< colgroup >
< col width = "17%" >
< col width = "17%" >
< col width = "17%" >
< col width = "14%" >
< col width = "16%" >
< col width = "16%" >
< / colgroup >
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< thead > < tr class = "header" >
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< th align = "left" > ward< / th >
< th align = "right" > J01GB03< / th >
< th align = "right" > J01GB01< / th >
< th > J01GB06< / th >
< th align = "right" > J01GB04< / th >
< th align = "right" > J01XB01< / th >
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< / tr > < / thead >
< tbody >
< tr class = "odd" >
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< td align = "left" > Clinical< / td >
< td align = "right" > 0.229< / td >
< td align = "right" > 0.315< / td >
< td > 0.626< / td >
< td align = "right" > 1< / td >
< td align = "right" > 0.780< / td >
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< / tr >
< tr class = "even" >
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< td align = "left" > ICU< / td >
< td align = "right" > 0.290< / td >
< td align = "right" > 0.400< / td >
< td > 0.662< / td >
< td align = "right" > 1< / td >
< td align = "right" > 0.857< / td >
2022-08-21 16:59:35 +02:00
< / tr >
< tr class = "odd" >
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< td align = "left" > Outpatient< / td >
< td align = "right" > 0.200< / td >
< td align = "right" > 0.368< / td >
< td > 0.605< / td >
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< td align = "right" > < / td >
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< td align = "right" > 0.889< / td >
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< / tr >
< / tbody >
< / table >
< / div >
< / div >
< div class = "section level3" >
< h3 id = "what-else-can-you-do-with-this-package" > What else can you do with this package?< a class = "anchor" aria-label = "anchor" href = "#what-else-can-you-do-with-this-package" > < / a >
< / h3 >
< p > This package was intended as a comprehensive toolbox for integrated AMR data analysis. This package can be used for:< / p >
< ul >
2022-10-05 12:32:07 +02:00
< li > Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the List of Prokaryotic names with Standing in Nomenclature (< a href = "(https://lpsn.dsmz.de)" class = "external-link" > LPSN< / a > ) and the Global Biodiversity Information Facility (< a href = "https://www.gbif.org" class = "external-link" > GBIF< / a > ) (< a href = "./reference/mo_property.html" > manual< / a > )< / li >
2023-06-22 15:20:36 +02:00
< li > Interpreting raw MIC and disk diffusion values, based on any CLSI or EUCAST guideline (< a href = "./reference/as.sir.html" > manual< / a > )< / li >
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< li > Retrieving antimicrobial drug names, doses and forms of administration from clinical health care records (< a href = "./reference/ab_from_text.html" > manual< / a > )< / li >
< li > Determining first isolates to be used for AMR data analysis (< a href = "./reference/first_isolate.html" > manual< / a > )< / li >
< li > Calculating antimicrobial resistance (< a href = "./articles/AMR.html" > tutorial< / a > )< / li >
< li > Determining multi-drug resistance (MDR) / multi-drug resistant organisms (MDRO) (< a href = "./articles/MDR.html" > tutorial< / a > )< / li >
< li > Calculating (empirical) susceptibility of both mono therapy and combination therapies (< a href = "./articles/AMR.html" > tutorial< / a > )< / li >
< li > Predicting future antimicrobial resistance using regression models (< a href = "./articles/resistance_predict.html" > tutorial< / a > )< / li >
< li > Getting properties for any microorganism (like Gram stain, species, genus or family) (< a href = "./reference/mo_property.html" > manual< / a > )< / li >
< li > Getting properties for any antibiotic (like name, code of EARS-Net/ATC/LOINC/PubChem, defined daily dose or trade name) (< a href = "./reference/ab_property.html" > manual< / a > )< / li >
< li > Plotting antimicrobial resistance (< a href = "./articles/AMR.html" > tutorial< / a > )< / li >
< li > Applying EUCAST expert rules (< a href = "./reference/eucast_rules.html" > manual< / a > )< / li >
< li > Getting SNOMED codes of a microorganism, or getting properties of a microorganism based on a SNOMED code (< a href = "./reference/mo_property.html" > manual< / a > )< / li >
< li > Getting LOINC codes of an antibiotic, or getting properties of an antibiotic based on a LOINC code (< a href = "./reference/ab_property.html" > manual< / a > )< / li >
2023-01-21 23:53:21 +01:00
< li > Machine reading the EUCAST and CLSI guidelines from 2011-2021 to translate MIC values and disk diffusion diameters to SIR (< a href = "./articles/datasets.html" > link< / a > )< / li >
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< li > Principal component analysis for AMR (< a href = "./articles/PCA.html" > tutorial< / a > )< / li >
< / ul >
< / div >
< div class = "section level3" >
< h3 id = "get-this-package" > Get this package< a class = "anchor" aria-label = "anchor" href = "#get-this-package" > < / a >
< / h3 >
< div class = "section level4" >
< h4 id = "latest-official-version" > Latest official version< a class = "anchor" aria-label = "anchor" href = "#latest-official-version" > < / a >
< / h4 >
< p > < a href = "https://cran.r-project.org/package=AMR" class = "external-link" > < img src = "https://www.r-pkg.org/badges/version-ago/AMR" alt = "CRAN" > < / a > < a href = "https://cran.r-project.org/package=AMR" class = "external-link" > < img src = "https://cranlogs.r-pkg.org/badges/grand-total/AMR" alt = "CRANlogs" > < / a > < / p >
< p > This package is available < a href = "https://cran.r-project.org/package=AMR" class = "external-link" > here on the official R network (CRAN)< / a > . Install this package in R from CRAN by using the command:< / p >
2023-03-11 17:02:25 +01:00
< div class = "sourceCode" id = "cb11" > < pre class = "downlit sourceCode r" >
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< code class = "sourceCode R" > < span > < span class = "fu" > < a href = "https://rdrr.io/r/utils/install.packages.html" class = "external-link" > install.packages< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "AMR"< / span > < span class = "op" > )< / span > < / span > < / code > < / pre > < / div >
< p > It will be downloaded and installed automatically. For RStudio, click on the menu < em > Tools< / em > > < em > Install Packages…< / em > and then type in “AMR” and press < kbd > Install< / kbd > .< / p >
< p > < strong > Note:< / strong > Not all functions on this website may be available in this latest release. To use all functions and data sets mentioned on this website, install the latest development version.< / p >
< / div >
< div class = "section level4" >
< h4 id = "latest-development-version" > Latest development version< a class = "anchor" aria-label = "anchor" href = "#latest-development-version" > < / a >
< / h4 >
2024-06-13 07:43:57 +02:00
< p > < a href = "https://github.com/msberends/AMR/actions/workflows/check-old.yaml?query=branch%3Amain" class = "external-link" > < img src = "https://github.com/msberends/AMR/actions/workflows/check-old.yaml/badge.svg?branch=main" alt = "check-old" > < / a > < a href = "https://github.com/msberends/AMR/actions/workflows/check-recent.yaml?query=branch%3Amain" class = "external-link" > < img src = "https://github.com/msberends/AMR/actions/workflows/check-recent.yaml/badge.svg?branch=main" alt = "check-recent" > < / a > < a href = "https://www.codefactor.io/repository/github/msberends/amr" class = "external-link" > < img src = "https://www.codefactor.io/repository/github/msberends/amr/badge" alt = "CodeFactor" > < / a > < a href = "https://codecov.io/gh/msberends/AMR?branch=main" class = "external-link" > < img src = "https://codecov.io/gh/msberends/AMR/branch/main/graph/badge.svg" alt = "Codecov" > < / a > < / p >
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< p > Please read our < a href = "https://github.com/msberends/AMR/wiki/Developer-Guideline" class = "external-link" > Developer Guideline here< / a > .< / p >
< p > The latest and unpublished development version can be installed from GitHub in two ways:< / p >
< ol style = "list-style-type: decimal" >
< li >
< p > Manually, using:< / p >
2023-03-11 17:02:25 +01:00
< div class = "sourceCode" id = "cb12" > < pre class = "downlit sourceCode r" >
2022-08-21 16:59:35 +02:00
< code class = "sourceCode R" > < span > < span class = "fu" > < a href = "https://rdrr.io/r/utils/install.packages.html" class = "external-link" > install.packages< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "remotes"< / span > < span class = "op" > )< / span > < span class = "co" > # if you haven't already< / span > < / span >
2024-06-15 15:40:21 +02:00
< span > < span class = "fu" > remotes< / span > < span class = "fu" > ::< / span > < span class = "fu" > < a href = "https://remotes.r-lib.org/reference/install_github.html" class = "external-link" > install_github< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "msberends/AMR"< / span > < span class = "op" > )< / span > < / span > < / code > < / pre > < / div >
2022-08-21 16:59:35 +02:00
< / li >
< li >
< p > Automatically, using the < a href = "https://ropensci.org/r-universe/" class = "external-link" > rOpenSci R-universe platform< / a > , by adding < a href = "https://msberends.r-universe.dev" class = "external-link" > our R-universe address< / a > to your list of repositories (‘ ’ < / p >
2023-03-11 17:02:25 +01:00
< div class = "sourceCode" id = "cb13" > < pre class = "downlit sourceCode r" >
2022-08-21 16:59:35 +02:00
< code class = "sourceCode R" > < span > < span class = "fu" > < a href = "https://rdrr.io/r/base/options.html" class = "external-link" > options< / a > < / span > < span class = "op" > (< / span > repos < 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 = "https://rdrr.io/r/base/options.html" class = "external-link" > getOption< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "repos"< / span > < span class = "op" > )< / span > ,< / span >
< span > msberends < span class = "op" > =< / span > < span class = "st" > "https://msberends.r-universe.dev"< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < / span > < / code > < / pre > < / div >
< p > After this, you can install and update this < code > AMR< / code > package like any official release (e.g., using < code > install.packages("AMR")< / code > or in RStudio via < em > Tools< / em > > < em > Check for Package Updates…< / em > ).< / p >
< / li >
< / ol >
< / div >
< / div >
< div class = "section level3" >
< h3 id = "get-started" > Get started< a class = "anchor" aria-label = "anchor" href = "#get-started" > < / a >
< / h3 >
< p > To find out how to conduct AMR data analysis, please < a href = "./articles/AMR.html" > continue reading here to get started< / a > or click a link in the < a href = "https://msberends.github.io/AMR/articles/" > ‘ ’ < / a > .< / p >
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< h3 id = "partners" > Partners< a class = "anchor" aria-label = "anchor" href = "#partners" > < / a >
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< p > The development of this package is part of, related to, or made possible by the following non-profit organisations and initiatives:< / p >
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< div align = "center" >
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< p > < a href = "https://www.rug.nl" title = "University of Groningen" class = "external-link" > < img src = "./logo_rug.svg" style = "max-width: 200px;" > < / a > < a href = "https://www.umcg.nl" title = "University Medical Center Groningen" class = "external-link" > < img src = "./logo_umcg.svg" style = "max-width: 200px;" > < / a > < a href = "https://www.certe.nl" title = "Certe Medical Diagnostics and Advice Foundation" class = "external-link" > < img src = "./logo_certe.svg" style = "max-width: 200px;" > < / a > < a href = "https://www.deutschland-nederland.eu" title = "EurHealth-1-Health" class = "external-link" > < img src = "./logo_eh1h.png" style = "max-width: 200px;" > < / a > < a href = "https://www.deutschland-nederland.eu" title = "INTERREG" class = "external-link" > < img src = "./logo_interreg.png" style = "max-width: 200px;" > < / a > < / p >
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< div class = "section level3" >
< h3 id = "copyright" > Copyright< a class = "anchor" aria-label = "anchor" href = "#copyright" > < / a >
< / h3 >
< p > This R package is free, open-source software and licensed under the < a href = "./LICENSE-text.html" > GNU General Public License v2.0 (GPL-2)< / a > . In a nutshell, this means that this package:< / p >
< ul >
< li > < p > May be used for commercial purposes< / p > < / li >
< li > < p > May be used for private purposes< / p > < / li >
< li > < p > May < strong > not< / strong > be used for patent purposes< / p > < / li >
< li >
< p > May be modified, although:< / p >
< ul >
< li > Modifications < strong > must< / strong > be released under the same license when distributing the package< / li >
< li > Changes made to the code < strong > must< / strong > be documented< / li >
< / ul >
< / li >
< li >
< p > May be distributed, although:< / p >
< ul >
< li > Source code < strong > must< / strong > be made available when the package is distributed< / li >
< li > A copy of the license and copyright notice < strong > must< / strong > be included with the package.< / li >
< / ul >
< / li >
< li > < p > Comes with a LIMITATION of liability< / p > < / li >
< li > < p > Comes with NO warranty< / p > < / li >
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< / main > < aside class = "col-md-3" > < div class = "table-of-contents" >
< h2 data-toc-skip > Table of contents< / h2 >
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< li > < nav id = "toc" > < / nav > < / li >
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< div class = "links" >
< h2 data-toc-skip > Links< / h2 >
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< li > < a href = "https://cloud.r-project.org/package=AMR" class = "external-link" > View on CRAN< / a > < / li >
< li > < a href = "https://github.com/msberends/AMR/" class = "external-link" > Browse source code< / a > < / li >
< li > < a href = "https://github.com/msberends/AMR/issues" class = "external-link" > Report a bug< / a > < / li >
< / ul >
< / div >
< div class = "developers" >
< h2 data-toc-skip > Developers< / h2 >
< ul class = "list-unstyled" >
< li > Matthijs S. Berends < br > < small class = "roles" > Author, maintainer < / small > < a href = "https://orcid.org/0000-0001-7620-1800" target = "orcid.widget" aria-label = "ORCID" class = "external-link" > < span class = "fab fa-orcid orcid" aria-hidden = "true" > < / span > < / a > < / li >
< li > Dennis Souverein < br > < small class = "roles" > Author, contributor < / small > < a href = "https://orcid.org/0000-0003-0455-0336" target = "orcid.widget" aria-label = "ORCID" class = "external-link" > < span class = "fab fa-orcid orcid" aria-hidden = "true" > < / span > < / a > < / li >
< li > Erwin E. A. Hassing < br > < small class = "roles" > Author, contributor < / small > < / li >
< li > < a href = "authors.html" > More about authors...< / a > < / li >
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< / aside >
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< footer > < div class = "pkgdown-footer-left" >
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< 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 >
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< div class = "pkgdown-footer-right" >
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< p > < a target = "_blank" href = "https://www.rug.nl" class = "external-link" > < img src = "https://github.com/msberends/AMR/raw/main/pkgdown/assets/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/assets/logo_umcg.svg" style = "max-width: 150px;" > < / a > < / p >
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