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< img src = "../logo.svg" class = "logo" alt = "" > < h1 > Add Custom Antimicrobials< / h1 >
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< small class = "dont-index" > Source: < a href = "https://github.com/msberends/AMR/blob/main/R/custom_antimicrobials.R" class = "external-link" > < code > R/custom_antimicrobials.R< / code > < / a > < / small >
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< div class = "d-none name" > < code > add_custom_antimicrobials.Rd< / code > < / div >
< / div >
< div class = "ref-description section level2" >
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< p > With < code > add_custom_antimicrobials()< / code > you can add your own custom antimicrobial drug names and codes.< / 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_antimicrobials< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > < span class = "op" > )< / span > < / span >
< span > < / span >
< span > < span class = "fu" > clear_custom_antimicrobials< / 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 >
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< dl > < dt id = "arg-x" > x< a class = "anchor" aria-label = "anchor" href = "#arg-x" > < / a > < / 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 = "antibiotics.html" > antibiotics< / a > data set, at least containing columns "ab" and "name"< / p > < / dd >
< / dl > < / div >
< div class = "section level2" >
< h2 id = "details" > Details< a class = "anchor" aria-label = "anchor" href = "#details" > < / a > < / h2 >
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< p > < strong > Important:< / strong > Due to how < span style = "R" > R< / span > works, the < code > add_custom_antimicrobials()< / code > function has to be run in every < span style = "R" > R< / span > session - added antimicrobials are not stored between sessions and are thus lost when < span style = "R" > R< / span > is exited.< / p >
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< p > There are two ways to circumvent this and automate the process of adding antimicrobials:< / p >
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< p > < strong > Method 1:< / strong > Using the package option < code > < a href = "AMR-options.html" > AMR_custom_ab< / 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 = "antibiotics.html" > antibiotics< / a > data set (containing at the very least columns "ab" and "name") 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_ab.rds"< / code > , or any remote location.< / p > < / li >
< li > < p > Set the file location to the package option < code > < a href = "AMR-options.html" > AMR_custom_ab< / a > < / code > : < code > options(AMR_custom_ab = "~/my_custom_ab.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 antimicrobial codes:< / span > < / span >
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< 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_ab < span class = "op" > =< / span > < span class = "st" > "~/my_custom_ab.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_antimicrobials()< / code > function.< / p > < / li >
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< / ol > < p > < strong > Method 2:< / strong > Loading the antimicrobial additions directly from your < code > .Rprofile< / code > file. Note that the definitions will be stored in a user-specific < span style = "R" > R< / span > file, which is a suboptimal workflow. 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_antimicrobials.html" > add_custom_antimicrobials< / 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 > ab < span class = "op" > =< / span > < span class = "st" > "TESTAB"< / span > ,< / span >
< span > name < span class = "op" > =< / span > < span class = "st" > "Test Antibiotic"< / span > ,< / span >
< span > group < span class = "op" > =< / span > < span class = "st" > "Test Group"< / span > < span class = "op" > )< / span > < / span >
< span > < span class = "op" > )< / span > < / span > < / code > < / pre > < p > < / p > < / div > < / li >
< / ol > < p > Use < code > clear_custom_antimicrobials()< / 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_microorganisms.html" > add_custom_microorganisms()< / a > < / code > to add custom microorganisms.< / 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 >
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< 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 > < / span >
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< span class = "r-in" > < span > < span class = "co" > # returns NA and throws a warning (which is suppressed here):< / span > < / span > < / span >
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< span class = "r-in" > < span > < span class = "fu" > < a href = "https://rdrr.io/r/base/warning.html" class = "external-link" > suppressWarnings< / a > < / span > < span class = "op" > (< / span > < / span > < / span >
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< span class = "r-in" > < span > < span class = "fu" > < a href = "as.ab.html" > as.ab< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "testab"< / span > < span class = "op" > )< / span > < / span > < / span >
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< 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 > Class 'ab'< / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] < NA> < / span >
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< 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.ab() and< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # all ab_*() functions< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > add_custom_antimicrobials< / 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 >
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< span class = "r-in" > < span > ab < span class = "op" > =< / span > < span class = "st" > "TESTAB"< / span > ,< / span > < / span >
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< span class = "r-in" > < span > name < span class = "op" > =< / span > < span class = "st" > "Test Antibiotic"< / span > ,< / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # you can add any property present in the< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # 'antibiotics' data set, such as 'group':< / span > < / span > < / span >
< span class = "r-in" > < span > group < span class = "op" > =< / span > < span class = "st" > "Test Group"< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "op" > )< / span > < / span > < / span >
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< 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-in" > < span > < / span > < / span >
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< span class = "r-in" > < span > < span class = "co" > # "testab" is now a new antibiotic:< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "as.ab.html" > as.ab< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "testab"< / span > < span class = "op" > )< / span > < / span > < / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > Class 'ab'< / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] TESTAB< / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "ab_property.html" > ab_name< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "testab"< / span > < span class = "op" > )< / span > < / span > < / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Test Antibiotic"< / span >
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< span class = "r-in" > < span > < span class = "fu" > < a href = "ab_property.html" > ab_group< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "testab"< / span > < span class = "op" > )< / span > < / span > < / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Test Group"< / span >
< span class = "r-in" > < span > < / span > < / span >
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< span class = "r-in" > < span > < span class = "fu" > < a href = "ab_property.html" > ab_info< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "testab"< / span > < span class = "op" > )< / span > < / span > < / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > $ab< / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "TESTAB"< / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $cid< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] NA< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $name< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Test Antibiotic"< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $group< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Test Group"< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $atc< / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] NA< / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $atc_group1< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] NA< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $atc_group2< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] NA< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $tradenames< / span >
2022-10-22 10:25:54 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] NA< / span >
2022-10-10 21:46:42 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $loinc< / span >
2022-10-22 10:25:54 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] NA< / span >
2022-10-10 21:46:42 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $ddd< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $ddd$oral< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $ddd$oral$amount< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] NA< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $ddd$oral$units< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] NA< / span >
< 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 > $ddd$iv< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $ddd$iv$amount< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] NA< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $ddd$iv$units< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] NA< / span >
< 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 > < / span >
2022-10-11 11:00:04 +02:00
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # Add Co-fluampicil, which is one of the many J01CR50 codes, see< / span > < / span > < / span >
2024-03-03 23:31:52 +01:00
< span class = "r-in" > < span > < span class = "co" > # https://atcddd.fhi.no/ddd/list_of_ddds_combined_products/< / span > < / span > < / span >
2022-10-11 11:00:04 +02:00
< span class = "r-in" > < span > < span class = "fu" > add_custom_antimicrobials< / span > < span class = "op" > (< / span > < / span > < / span >
2022-10-30 14:40:31 +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 > ab < span class = "op" > =< / span > < span class = "st" > "COFLU"< / span > ,< / span > < / span >
< span class = "r-in" > < span > name < span class = "op" > =< / span > < span class = "st" > "Co-fluampicil"< / span > ,< / span > < / span >
< span class = "r-in" > < span > atc < span class = "op" > =< / span > < span class = "st" > "J01CR50"< / span > ,< / span > < / span >
2022-12-27 16:14:41 +01:00
< span class = "r-in" > < span > group < span class = "op" > =< / span > < span class = "st" > "Beta-lactams/penicillins"< / span > < / span > < / span >
2022-10-30 14:40:31 +01:00
< span class = "r-in" > < span > < span class = "op" > )< / span > < / span > < / span >
2022-10-11 11:00:04 +02:00
< span class = "r-in" > < span > < span class = "op" > )< / span > < / span > < / span >
2022-11-24 20:37:19 +01:00
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > ℹ < / span >
2022-10-11 11:00:04 +02:00
< span class = "r-in" > < span > < span class = "fu" > < a href = "ab_property.html" > ab_atc< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "Co-fluampicil"< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "J01CR50"< / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "ab_property.html" > ab_name< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "J01CR50"< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Co-fluampicil"< / span >
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # even antibiotic selectors work< / span > < / span > < / span >
2022-10-30 14:40:31 +01:00
< span class = "r-in" > < span > < span class = "va" > x< / span > < span class = "op" > < -< / 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 >
2022-10-30 21:14:42 +01:00
< span class = "r-in" > < span > random_column < span class = "op" > =< / span > < span class = "st" > "some value"< / span > ,< / span > < / span >
2023-01-21 23:53:21 +01:00
< span class = "r-in" > < span > coflu < span class = "op" > =< / span > < span class = "fu" > < a href = "as.sir.html" > as.sir< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "S"< / span > < span class = "op" > )< / span > ,< / span > < / span >
< span class = "r-in" > < span > ampicillin < span class = "op" > =< / span > < span class = "fu" > < a href = "as.sir.html" > as.sir< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "R"< / span > < span class = "op" > )< / span > < / span > < / span >
2022-10-30 14:40:31 +01:00
< span class = "r-in" > < span > < span class = "op" > )< / span > < / span > < / span >
2022-10-11 11:00:04 +02:00
< span class = "r-in" > < span > < span class = "va" > x< / span > < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > random_column coflu ampicillin< / span >
2022-10-30 21:14:42 +01:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 1 some value S R< / span >
2022-10-11 11:00:04 +02:00
< span class = "r-in" > < span > < span class = "va" > x< / span > < span class = "op" > [< / span > , < span class = "fu" > < a href = "antibiotic_class_selectors.html" > betalactams< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > ]< / span > < / span > < / span >
2022-11-24 20:37:19 +01:00
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > ℹ < / span >
2022-10-11 11:00:04 +02:00
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > 'ampicillin'< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > coflu ampicillin< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 1 S R< / span >
2022-10-15 15:28:27 +02:00
< span class = "r-in" > < span > < span class = "co" > # }< / span > < / span > < / span >
2022-10-10 21:46:42 +02:00
< / code > < / pre > < / div >
2022-10-10 20:27:14 +02:00
< / div >
2024-07-16 15:00:55 +02:00
< / main > < aside class = "col-md-3" > < nav id = "toc" aria-label = "Table of contents" > < h2 > On this page< / h2 >
2022-10-10 20:27:14 +02:00
< / nav > < / aside > < / div >
< footer > < div class = "pkgdown-footer-left" >
2024-04-23 10:39:01 +02:00
< 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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2024-09-19 14:48:19 +02:00
< 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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< / body > < / html >
