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< img src = "../logo.svg" class = "logo" alt = "" > < h1 > Add Custom Microorganisms< / h1 >
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< small class = "dont-index" > Source: < a href = "https://github.com/msberends/AMR/blob/HEAD/R/custom_microorganisms.R" class = "external-link" > < code > R/custom_microorganisms.R< / code > < / a > < / small >
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< p > With < code > add_custom_microorganisms()< / code > you can add your own custom microorganisms, such the non-taxonomic outcome of laboratory analysis.< / 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" > add_custom_microorganisms< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > < span class = "op" > )< / span > < / span >
< span > < / span >
< span > < span class = "fu" > clear_custom_microorganisms< / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < / span > < / code > < / pre > < / div >
< / div >
< div class = "section level2" >
< h2 id = "arguments" > Arguments< a class = "anchor" aria-label = "anchor" href = "#arguments" > < / a > < / h2 >
< dl > < dt > x< / dt >
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< dd > < p > a < a href = "https://rdrr.io/r/base/data.frame.html" class = "external-link" > data.frame< / a > resembling the < a href = "microorganisms.html" > microorganisms< / a > data set, at least containing column "genus" (case-insensitive)< / 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 will fill in missing taxonomy for you, if specific taxonomic columns are missing, see < em > Examples< / em > .< / p >
< p > < strong > Important:< / strong > Due to how < span style = "R" > R< / span > works, the < code > add_custom_microorganisms()< / code > function has to be run in every < span style = "R" > R< / span > session - added microorganisms are not stored between sessions and are thus lost when < span style = "R" > R< / span > is exited.< / p >
< p > There are two ways to automate this process:< / p >
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< p > < strong > Method 1:< / strong > Using the option < code > < a href = "AMR-options.html" > AMR_custom_mo< / a > < / code > , which is the preferred method. To use this method:< / p > < ol > < li > < p > Create a data set in the structure of the < a href = "microorganisms.html" > microorganisms< / a > data set (containing at the very least column "genus") and save it with < code > < a href = "https://rdrr.io/r/base/readRDS.html" class = "external-link" > saveRDS()< / a > < / code > to a location of choice, e.g. < code > "~/my_custom_mo.rds"< / code > , or any remote location.< / p > < / li >
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< li > < p > Set the file location to the option < code > < a href = "AMR-options.html" > AMR_custom_mo< / a > < / code > : < code > options(AMR_custom_mo = "~/my_custom_mo.rds")< / code > . This can even be a remote file location, such as an https URL. Since options are not saved between < span style = "R" > R< / span > sessions, it is best to save this option to the < code > .Rprofile< / code > file so that it will be loaded on start-up of < span style = "R" > R< / span > . To do this, open the < code > .Rprofile< / code > file using e.g. < code > utils::file.edit("~/.Rprofile")< / code > , add this text and save the file:< / p >
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< p > < / p > < div class = "sourceCode r" > < pre > < code > < span > < span class = "co" > # Add custom microorganism codes:< / span > < / span >
< span > < span class = "fu" > < a href = "https://rdrr.io/r/base/options.html" class = "external-link" > options< / a > < / span > < span class = "op" > (< / span > AMR_custom_mo < span class = "op" > =< / span > < span class = "st" > "~/my_custom_mo.rds"< / span > < span class = "op" > )< / span > < / span > < / code > < / pre > < p > < / p > < / div >
< p > Upon package load, this file will be loaded and run through the < code > add_custom_microorganisms()< / code > function.< / p > < / li >
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< / ol > < p > < strong > Method 2:< / strong > Loading the microorganism directly from your < code > .Rprofile< / code > file. An important downside is that this requires the < code > AMR< / code > package to be installed or else this method will fail. To use this method:< / p > < ol > < li > < p > Edit the < code > .Rprofile< / code > file using e.g. < code > utils::file.edit("~/.Rprofile")< / code > .< / p > < / li >
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< li > < p > Add a text like below and save the file:< / p >
< p > < / p > < div class = "sourceCode r" > < pre > < code > < span > < span class = "co" > # Add custom antibiotic drug codes:< / span > < / span >
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< span > < span class = "fu" > AMR< / span > < span class = "fu" > ::< / span > < span class = "fu" > < a href = "../reference/add_custom_microorganisms.html" > add_custom_microorganisms< / a > < / span > < span class = "op" > (< / span > < / span >
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< span > < span class = "fu" > < a href = "https://rdrr.io/r/base/data.frame.html" class = "external-link" > data.frame< / a > < / span > < span class = "op" > (< / span > genus < span class = "op" > =< / span > < span class = "st" > "Enterobacter"< / span > ,< / span >
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< span > species < span class = "op" > =< / span > < span class = "st" > "asburiae/cloacae"< / span > < span class = "op" > )< / span > < / span >
< span > < span class = "op" > )< / span > < / span > < / code > < / pre > < p > < / p > < / div > < / li >
< / ol > < p > Use < code > clear_custom_microorganisms()< / code > to clear the previously added antimicrobials.< / p >
< / div >
< div class = "section level2" >
< h2 id = "see-also" > See also< a class = "anchor" aria-label = "anchor" href = "#see-also" > < / a > < / h2 >
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< div class = "dont-index" > < p > < code > < a href = "add_custom_antimicrobials.html" > add_custom_antimicrobials()< / a > < / code > to add custom antimicrobials.< / p > < / 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" > # \donttest{< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # a combination of species is not formal taxonomy, so< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # this will result in only "Enterobacter asburiae":< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "mo_property.html" > mo_name< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "Enterobacter asburiae/cloacae"< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Enterobacter asburiae"< / span >
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # now add a custom entry - it will be considered by as.mo() and< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # all mo_*() functions< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > add_custom_microorganisms< / span > < span class = "op" > (< / span > < / span > < / span >
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< span class = "r-in" > < span > < span class = "fu" > < a href = "https://rdrr.io/r/base/data.frame.html" class = "external-link" > data.frame< / a > < / span > < span class = "op" > (< / span > < / span > < / span >
< span class = "r-in" > < span > genus < span class = "op" > =< / span > < span class = "st" > "Enterobacter"< / span > ,< / span > < / span >
< span class = "r-in" > < span > species < span class = "op" > =< / span > < span class = "st" > "asburiae/cloacae"< / span > < / span > < / span >
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< span class = "r-in" > < 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 >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > set.< / span >
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< span class = "r-in" > < span > < / span > < / span >
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< span class = "r-in" > < span > < span class = "co" > # E. asburiae/cloacae is now a new microorganism:< / span > < / span > < / span >
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< span class = "r-in" > < span > < span class = "fu" > < a href = "mo_property.html" > mo_name< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "Enterobacter asburiae/cloacae"< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Enterobacter asburiae/cloacae"< / span >
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< span class = "r-in" > < span > < / span > < / span >
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< span class = "r-in" > < span > < span class = "co" > # its code:< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "as.mo.html" > as.mo< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "Enterobacter asburiae/cloacae"< / span > < span class = "op" > )< / span > < / span > < / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > Class 'mo'< / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] CUSTOM1_ENTRBC_A_C< / span >
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< span class = "r-in" > < span > < / span > < / span >
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< span class = "r-in" > < span > < span class = "co" > # all internal algorithms will work as well:< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "mo_property.html" > mo_name< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "Ent asburia cloacae"< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Enterobacter asburiae/cloacae"< / span >
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # and even the taxonomy was added based on the genus!< / span > < / span > < / span >
2022-12-28 14:27:31 +01:00
< span class = "r-in" > < span > < span class = "fu" > < a href = "mo_property.html" > mo_family< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "E. asburiae/cloacae"< / span > < span class = "op" > )< / span > < / span > < / span >
2022-12-27 16:14:41 +01:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Enterobacteriaceae"< / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "mo_property.html" > mo_gramstain< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "Enterobacter asburiae/cloacae"< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Gram-negative"< / span >
< span class = "r-in" > < span > < / span > < / span >
2022-12-28 14:27:31 +01:00
< span class = "r-in" > < span > < span class = "fu" > < a href = "mo_property.html" > mo_info< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "Enterobacter asburiae/cloacae"< / span > < span class = "op" > )< / span > < / span > < / span >
2023-01-19 13:03:56 +01:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $mo< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "CUSTOM1_ENTRBC_A_C"< / span >
2023-01-14 17:20:52 +01:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
2022-12-27 16:14:41 +01:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $kingdom< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Bacteria"< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $phylum< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Pseudomonadota"< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $class< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Gammaproteobacteria"< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $order< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Enterobacterales"< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $family< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Enterobacteriaceae"< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $genus< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Enterobacter"< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $species< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "asburiae/cloacae"< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $subspecies< / span >
2022-12-28 14:27:31 +01:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] ""< / span >
2022-12-27 16:14:41 +01:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $status< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "accepted"< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $synonyms< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > NULL< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $gramstain< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Gram-negative"< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $url< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] ""< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $ref< / span >
2023-01-14 17:20:52 +01:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Self-added, 2023"< / span >
2022-12-27 16:14:41 +01:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $snomed< / span >
2023-02-08 17:01:47 +01:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] NA< / span >
2022-12-27 16:14:41 +01:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
2023-01-14 17:20:52 +01:00
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # the function tries to be forgiving:< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > add_custom_microorganisms< / span > < span class = "op" > (< / span > < / span > < / span >
2023-01-23 15:07:54 +01:00
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://rdrr.io/r/base/data.frame.html" class = "external-link" > data.frame< / a > < / span > < span class = "op" > (< / span > < / span > < / span >
< span class = "r-in" > < span > GENUS < span class = "op" > =< / span > < span class = "st" > "BACTEROIDES / PARABACTEROIDES SLASHLINE"< / span > ,< / span > < / span >
< span class = "r-in" > < span > SPECIES < span class = "op" > =< / span > < span class = "st" > "SPECIES"< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "op" > )< / span > < / span > < / span >
2023-01-14 20:00:10 +01:00
< span class = "r-in" > < span > < span class = "op" > )< / span > < / span > < / span >
2023-01-19 13:03:56 +01:00
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > ℹ < / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > set.< / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "mo_property.html" > mo_name< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "BACTEROIDES / PARABACTEROIDES"< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Bacteroides/Parabacteroides"< / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "mo_property.html" > mo_rank< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "BACTEROIDES / PARABACTEROIDES"< / span > < span class = "op" > )< / span > < / span > < / span >
2023-01-14 20:00:10 +01:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "genus"< / span >
2023-01-19 13:03:56 +01:00
< span class = "r-in" > < span > < / span > < / span >
2023-01-14 20:00:10 +01:00
< span class = "r-in" > < span > < span class = "co" > # taxonomy still works, although a slashline genus was given as input:< / span > < / span > < / span >
2023-01-19 13:03:56 +01:00
< span class = "r-in" > < span > < span class = "fu" > < a href = "mo_property.html" > mo_family< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "Bacteroides/Parabacteroides"< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Bacteroidaceae"< / span >
< span class = "r-in" > < span > < / span > < / span >
2023-01-14 17:20:52 +01:00
< span class = "r-in" > < span > < / span > < / span >
2023-01-14 20:00:10 +01:00
< span class = "r-in" > < span > < span class = "co" > # for groups and complexes, set them as species or subspecies:< / span > < / span > < / span >
2023-01-14 17:20:52 +01:00
< span class = "r-in" > < span > < span class = "fu" > add_custom_microorganisms< / span > < span class = "op" > (< / span > < / span > < / span >
2023-01-23 15:07:54 +01:00
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://rdrr.io/r/base/data.frame.html" class = "external-link" > data.frame< / a > < / span > < span class = "op" > (< / span > < / span > < / span >
< span class = "r-in" > < span > genus < span class = "op" > =< / span > < span class = "st" > "Citrobacter"< / span > ,< / span > < / span >
< span class = "r-in" > < span > species < 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" > "freundii"< / span > , < span class = "st" > "braakii complex"< / span > < span class = "op" > )< / span > ,< / span > < / span >
< span class = "r-in" > < span > subspecies < 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" > "complex"< / span > , < span class = "st" > ""< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "op" > )< / span > < / span > < / span >
2023-01-14 20:00:10 +01:00
< span class = "r-in" > < span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > ℹ < / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > internal microorganisms data set.< / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "mo_property.html" > mo_name< / 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 = "st" > "C. freundii complex"< / span > , < span class = "st" > "C. braakii complex"< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Citrobacter freundii complex" "Citrobacter braakii complex" < / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "mo_property.html" > mo_species< / 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 = "st" > "C. freundii complex"< / span > , < span class = "st" > "C. braakii complex"< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "freundii complex" "braakii complex" < / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "mo_property.html" > mo_gramstain< / 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 = "st" > "C. freundii complex"< / span > , < span class = "st" > "C. braakii complex"< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Gram-negative" "Gram-negative"< / span >
2022-12-27 16:14:41 +01:00
< span class = "r-in" > < span > < span class = "co" > # }< / span > < / span > < / span >
< / code > < / pre > < / div >
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< / main > < aside class = "col-md-3" > < nav id = "toc" > < h2 > On this page< / h2 >
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< 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 >
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