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< h1 data-toc-skip > Data sets for download / own use< / h1 >
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< h4 data-toc-skip class = "date" > 09 May 2022< / h4 >
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< small class = "dont-index" > Source: < a href = "https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class = "external-link" > < code > vignettes/datasets.Rmd< / code > < / a > < / small >
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< div class = "hidden name" > < code > datasets.Rmd< / code > < / div >
< / div >
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< p > All reference data (about microorganisms, antibiotics, R/SI
interpretation, EUCAST rules, etc.) in this < code > AMR< / code > package are
reliable, up-to-date and freely available. We continually export our
data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also
supply tab separated files that are machine-readable and suitable for
input in any software program, such as laboratory information
systems.< / p >
< p > On this page, we explain how to download them and how the structure
of the data sets look like.< / p >
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< p class = "dataset-within-r" >
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If you are reading this page from within R, please
< a href = "https://msberends.github.io/AMR/articles/datasets.html" > visit
our website< / a > , which is automatically updated with every code change.
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< / p >
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< div class = "section level2" >
< h2 id = "microorganisms-currently-accepted-names" > Microorganisms (currently accepted names)< a class = "anchor" aria-label = "anchor" href = "#microorganisms-currently-accepted-names" > < / a >
< / h2 >
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< p > A data set with 70,760 rows and 16 columns, containing the following
column names:< br > < em > mo< / em > , < em > fullname< / em > , < em > kingdom< / em > , < em > phylum< / em > ,
< em > class< / em > , < em > order< / em > , < em > family< / em > , < em > genus< / em > ,
< em > species< / em > , < em > subspecies< / em > , < em > rank< / em > , < em > ref< / em > ,
< em > species_id< / em > , < em > source< / em > , < em > prevalence< / em > and
< em > snomed< / em > .< / p >
< p > This data set is in R available as < code > microorganisms< / code > , after
you load the < code > AMR< / code > package.< / p >
< p > It was last updated on 29 November 2021 11:38:23 UTC. Find more info
about the structure of this data set < a href = "https://msberends.github.io/AMR/reference/microorganisms.html" > here< / a > .< / p >
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< p > < strong > Direct download links:< / strong > < / p >
< ul >
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< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.rds" class = "external-link" > R
file< / a > (1.3 MB)< br >
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< / li >
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< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.xlsx" class = "external-link" > Excel
file< / a > (6.4 MB)< br >
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< / li >
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< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.txt" class = "external-link" > plain
text file< / a > (13.1 MB)< br >
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< / li >
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< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sas" class = "external-link" > SAS
file< / a > (30.7 MB)< br >
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< / li >
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< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sav" class = "external-link" > SPSS
file< / a > (16.3 MB)< br >
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< / li >
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< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.dta" class = "external-link" > Stata
file< / a > (27.5 MB)< / li >
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< / ul >
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< p > < strong > NOTE: The exported files for SAS, SPSS and Stata do not
contain SNOMED codes, as their file size would exceed 100 MB; the file
size limit of GitHub.< / strong > Advice? Use R instead.< / p >
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< div class = "section level3" >
< h3 id = "source" > Source< a class = "anchor" aria-label = "anchor" href = "#source" > < / a >
< / h3 >
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< p > Our full taxonomy of microorganisms is based on the authoritative and
comprehensive:< / p >
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< ul >
< li >
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< a href = "http://www.catalogueoflife.org" class = "external-link" > Catalogue of Life< / a >
(included version: 2019)< / li >
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< li >
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< a href = "https://lpsn.dsmz.de" class = "external-link" > List of Prokaryotic names with
Standing in Nomenclature< / a > (LPSN, last updated: 5 October 2021)< / li >
< li > US Edition of SNOMED CT from 1 September 2020, retrieved from the < a href = "https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009" class = "external-link" > Public
Health Information Network Vocabulary Access and Distribution System
(PHIN VADS)< / a > , OID 2.16.840.1.114222.4.11.1009, version 12< / li >
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< / ul >
< / div >
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< div class = "section level3" >
< h3 id = "example-content" > Example content< a class = "anchor" aria-label = "anchor" href = "#example-content" > < / a >
< / h3 >
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< p > Included (sub)species per taxonomic kingdom:< / p >
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< table class = "table" >
< thead > < tr class = "header" >
< th align = "center" > Kingdom< / th >
< th align = "center" > Number of (sub)species< / th >
< / tr > < / thead >
< tbody >
< tr class = "odd" >
< td align = "center" > (unknown kingdom)< / td >
< td align = "center" > 1< / td >
< / tr >
< tr class = "even" >
< td align = "center" > Animalia< / td >
< td align = "center" > 2,153< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > Archaea< / td >
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< td align = "center" > 694< / td >
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< / tr >
< tr class = "even" >
< td align = "center" > Bacteria< / td >
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< td align = "center" > 22,852< / td >
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< / tr >
< tr class = "odd" >
< td align = "center" > Chromista< / td >
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< td align = "center" > 32,167< / td >
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< / tr >
< tr class = "even" >
< td align = "center" > Fungi< / td >
< td align = "center" > 9,582< / td >
< / tr >
< / tbody >
< / table >
< p > Example rows when filtering on genus < em > Escherichia< / em > :< / p >
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< table style = "width:100%;" class = "table" >
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< colgroup >
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< col width = "5%" >
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< col width = "8%" >
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< col width = "3%" >
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< col width = "5%" >
< col width = "7%" >
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< col width = "6%" >
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< col width = "7%" >
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< col width = "4%" >
< col width = "4%" >
< col width = "4%" >
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< col width = "3%" >
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< col width = "9%" >
< col width = "4%" >
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< col width = "2%" >
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< col width = "4%" >
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< col width = "16%" >
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< / colgroup >
< thead > < tr class = "header" >
< th align = "center" > mo< / th >
< th align = "center" > fullname< / th >
< th align = "center" > kingdom< / th >
< th align = "center" > phylum< / th >
< th align = "center" > class< / th >
< th align = "center" > order< / th >
< th align = "center" > family< / th >
< th align = "center" > genus< / th >
< th align = "center" > species< / th >
< th align = "center" > subspecies< / th >
< th align = "center" > rank< / th >
< th align = "center" > ref< / th >
< th align = "center" > species_id< / th >
< th align = "center" > source< / th >
< th align = "center" > prevalence< / th >
< th align = "center" > snomed< / th >
< / tr > < / thead >
< tbody >
< tr class = "odd" >
< td align = "center" > B_ESCHR< / td >
< td align = "center" > Escherichia< / td >
< td align = "center" > Bacteria< / td >
< td align = "center" > Proteobacteria< / td >
< td align = "center" > Gammaproteobacteria< / td >
< td align = "center" > Enterobacterales< / td >
< td align = "center" > Enterobacteriaceae< / td >
< td align = "center" > Escherichia< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > genus< / td >
< td align = "center" > < / td >
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< td align = "center" > 515602< / td >
< td align = "center" > LPSN< / td >
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< td align = "center" > 1< / td >
< td align = "center" > 64735005< / td >
< / tr >
< tr class = "even" >
< td align = "center" > B_ESCHR_ALBR< / td >
< td align = "center" > Escherichia albertii< / td >
< td align = "center" > Bacteria< / td >
< td align = "center" > Proteobacteria< / td >
< td align = "center" > Gammaproteobacteria< / td >
< td align = "center" > Enterobacterales< / td >
< td align = "center" > Enterobacteriaceae< / td >
< td align = "center" > Escherichia< / td >
< td align = "center" > albertii< / td >
< td align = "center" > < / td >
< td align = "center" > species< / td >
< td align = "center" > Huys et al., 2003< / td >
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< td align = "center" > 776053< / td >
< td align = "center" > LPSN< / td >
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< td align = "center" > 1< / td >
< td align = "center" > 419388003< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > B_ESCHR_COLI< / td >
< td align = "center" > Escherichia coli< / td >
< td align = "center" > Bacteria< / td >
< td align = "center" > Proteobacteria< / td >
< td align = "center" > Gammaproteobacteria< / td >
< td align = "center" > Enterobacterales< / td >
< td align = "center" > Enterobacteriaceae< / td >
< td align = "center" > Escherichia< / td >
< td align = "center" > coli< / td >
< td align = "center" > < / td >
< td align = "center" > species< / td >
< td align = "center" > Castellani et al., 1919< / td >
2021-12-02 13:32:14 +01:00
< td align = "center" > 776057< / td >
< td align = "center" > LPSN< / td >
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< td align = "center" > 1< / td >
2021-03-11 21:42:30 +01:00
< td align = "center" > 1095001000112106, 715307006, 737528008, …< / td >
2020-08-16 21:38:42 +02:00
< / tr >
< tr class = "even" >
< td align = "center" > B_ESCHR_FRGS< / td >
< td align = "center" > Escherichia fergusonii< / td >
< td align = "center" > Bacteria< / td >
< td align = "center" > Proteobacteria< / td >
< td align = "center" > Gammaproteobacteria< / td >
< td align = "center" > Enterobacterales< / td >
< td align = "center" > Enterobacteriaceae< / td >
< td align = "center" > Escherichia< / td >
< td align = "center" > fergusonii< / td >
< td align = "center" > < / td >
< td align = "center" > species< / td >
< td align = "center" > Farmer et al., 1985< / td >
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< td align = "center" > 776059< / td >
< td align = "center" > LPSN< / td >
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< td align = "center" > 1< / td >
< td align = "center" > 72461005< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > B_ESCHR_HRMN< / td >
< td align = "center" > Escherichia hermannii< / td >
< td align = "center" > Bacteria< / td >
< td align = "center" > Proteobacteria< / td >
< td align = "center" > Gammaproteobacteria< / td >
< td align = "center" > Enterobacterales< / td >
< td align = "center" > Enterobacteriaceae< / td >
< td align = "center" > Escherichia< / td >
< td align = "center" > hermannii< / td >
< td align = "center" > < / td >
< td align = "center" > species< / td >
< td align = "center" > Brenner et al., 1983< / td >
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< td align = "center" > 776060< / td >
< td align = "center" > LPSN< / td >
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< td align = "center" > 1< / td >
< td align = "center" > 85786000< / td >
< / tr >
< tr class = "even" >
< td align = "center" > B_ESCHR_MRMT< / td >
< td align = "center" > Escherichia marmotae< / td >
< td align = "center" > Bacteria< / td >
< td align = "center" > Proteobacteria< / td >
< td align = "center" > Gammaproteobacteria< / td >
< td align = "center" > Enterobacterales< / td >
< td align = "center" > Enterobacteriaceae< / td >
< td align = "center" > Escherichia< / td >
< td align = "center" > marmotae< / td >
< td align = "center" > < / td >
< td align = "center" > species< / td >
< td align = "center" > Liu et al., 2015< / td >
< td align = "center" > 792928< / td >
2021-03-05 01:31:46 +01:00
< td align = "center" > LPSN< / td >
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< td align = "center" > 1< / td >
2021-03-11 21:42:30 +01:00
< td align = "center" > 14961000146107< / td >
2020-08-16 21:38:42 +02:00
< / tr >
< / tbody >
< / table >
< / div >
< / div >
2021-12-02 13:32:14 +01:00
< div class = "section level2" >
< h2 id = "microorganisms-previously-accepted-names" > Microorganisms (previously accepted names)< a class = "anchor" aria-label = "anchor" href = "#microorganisms-previously-accepted-names" > < / a >
< / h2 >
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< p > A data set with 14,338 rows and 4 columns, containing the following
column names:< br > < em > fullname< / em > , < em > fullname_new< / em > , < em > ref< / em > and
< em > prevalence< / em > .< / p >
< p > < strong > Note:< / strong > remember that the ‘ ’
scientific reference to the old taxonomic entries, i.e.
< em > ‘ ’ < / em > . For the scientific reference of the new names,
i.e. < em > ‘ ’ < / em > , see the
< code > microorganisms< / code > data set.< / p >
< p > This data set is in R available as < code > microorganisms.old< / code > ,
after you load the < code > AMR< / code > package.< / p >
< p > It was last updated on 6 October 2021 14:38:29 UTC. Find more info
about the structure of this data set < a href = "https://msberends.github.io/AMR/reference/microorganisms.old.html" > here< / a > .< / p >
2020-09-24 00:30:11 +02:00
< p > < strong > Direct download links:< / strong > < / p >
< ul >
2022-04-08 11:02:45 +02:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.rds" class = "external-link" > R
file< / a > (0.2 MB)< br >
2020-09-24 00:30:11 +02:00
< / li >
2022-04-08 11:02:45 +02:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.xlsx" class = "external-link" > Excel
file< / a > (0.5 MB)< br >
2020-09-24 00:30:11 +02:00
< / li >
2022-04-08 11:02:45 +02:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.txt" class = "external-link" > plain
text file< / a > (1 MB)< br >
2020-09-24 00:30:11 +02:00
< / li >
2022-04-08 11:02:45 +02:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.sas" class = "external-link" > SAS
file< / a > (2.1 MB)< br >
2020-09-24 00:30:11 +02:00
< / li >
2022-04-08 11:02:45 +02:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.sav" class = "external-link" > SPSS
file< / a > (1.3 MB)< br >
2020-09-24 00:30:11 +02:00
< / li >
2022-04-08 11:02:45 +02:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.dta" class = "external-link" > Stata
file< / a > (2 MB)< / li >
2020-09-24 00:30:11 +02:00
< / ul >
2021-12-02 13:32:14 +01:00
< div class = "section level3" >
< h3 id = "source-1" > Source< a class = "anchor" aria-label = "anchor" href = "#source-1" > < / a >
< / h3 >
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< p > This data set contains old, previously accepted taxonomic names. The
data sources are the same as the < code > microorganisms< / code > data
set:< / p >
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< ul >
< li >
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< a href = "http://www.catalogueoflife.org" class = "external-link" > Catalogue of Life< / a >
(included version: 2019)< / li >
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< li >
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< a href = "https://lpsn.dsmz.de" class = "external-link" > List of Prokaryotic names with
Standing in Nomenclature< / a > (LPSN, last updated: 5 October 2021)< / li >
2020-08-17 21:49:58 +02:00
< / ul >
< / div >
2021-12-02 13:32:14 +01:00
< div class = "section level3" >
< h3 id = "example-content-1" > Example content< a class = "anchor" aria-label = "anchor" href = "#example-content-1" > < / a >
< / h3 >
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< p > Example rows when filtering on < em > Escherichia< / em > :< / p >
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< table style = "width:100%;" class = "table" >
< colgroup >
< col width = "31%" >
< col width = "30%" >
< col width = "24%" >
< col width = "13%" >
< / colgroup >
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< thead > < tr class = "header" >
< th align = "center" > fullname< / th >
< th align = "center" > fullname_new< / th >
< th align = "center" > ref< / th >
< th align = "center" > prevalence< / th >
< / tr > < / thead >
< tbody >
< tr class = "odd" >
< td align = "center" > Escherichia adecarboxylata< / td >
< td align = "center" > Leclercia adecarboxylata< / td >
< td align = "center" > Leclerc, 1962< / td >
< td align = "center" > 1< / td >
< / tr >
< tr class = "even" >
< td align = "center" > Escherichia blattae< / td >
< td align = "center" > Shimwellia blattae< / td >
< td align = "center" > Burgess et al., 1973< / td >
< td align = "center" > 1< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > Escherichia vulneris< / td >
< td align = "center" > Pseudescherichia vulneris< / td >
< td align = "center" > Brenner et al., 1983< / td >
< td align = "center" > 1< / td >
< / tr >
< / tbody >
< / table >
< / div >
< / div >
2021-12-02 13:32:14 +01:00
< div class = "section level2" >
< h2 id = "antibiotic-agents" > Antibiotic agents< a class = "anchor" aria-label = "anchor" href = "#antibiotic-agents" > < / a >
< / h2 >
2022-04-08 11:02:45 +02:00
< p > A data set with 464 rows and 14 columns, containing the following
column names:< br > < em > ab< / em > , < em > cid< / em > , < em > name< / em > , < em > group< / em > , < em > atc< / em > ,
< em > atc_group1< / em > , < em > atc_group2< / em > , < em > abbreviations< / em > ,
< em > synonyms< / em > , < em > oral_ddd< / em > , < em > oral_units< / em > ,
< em > iv_ddd< / em > , < em > iv_units< / em > and < em > loinc< / em > .< / p >
< p > This data set is in R available as < code > antibiotics< / code > , after
you load the < code > AMR< / code > package.< / p >
< p > It was last updated on 14 December 2021 21:59:33 UTC. Find more info
about the structure of this data set < a href = "https://msberends.github.io/AMR/reference/antibiotics.html" > here< / a > .< / p >
2020-09-24 00:30:11 +02:00
< p > < strong > Direct download links:< / strong > < / p >
< ul >
2022-04-08 11:02:45 +02:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.rds" class = "external-link" > R
file< / a > (33 kB)< br >
2020-09-24 00:30:11 +02:00
< / li >
2022-04-08 11:02:45 +02:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.xlsx" class = "external-link" > Excel
file< / a > (65 kB)< br >
2020-09-24 00:30:11 +02:00
< / li >
2022-04-08 11:02:45 +02:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.txt" class = "external-link" > plain
text file< / a > (0.1 MB)< br >
2020-09-24 00:30:11 +02:00
< / li >
2022-04-08 11:02:45 +02:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sas" class = "external-link" > SAS
file< / a > (1.8 MB)< br >
2020-09-24 00:30:11 +02:00
< / li >
2022-04-08 11:02:45 +02:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sav" class = "external-link" > SPSS
file< / a > (0.3 MB)< br >
2020-09-24 00:30:11 +02:00
< / li >
2022-04-08 11:02:45 +02:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.dta" class = "external-link" > Stata
file< / a > (0.3 MB)< / li >
2020-09-24 00:30:11 +02:00
< / ul >
2021-12-02 13:32:14 +01:00
< div class = "section level3" >
< h3 id = "source-2" > Source< a class = "anchor" aria-label = "anchor" href = "#source-2" > < / a >
< / h3 >
2022-04-08 11:02:45 +02:00
< p > This data set contains all EARS-Net and ATC codes gathered from WHO
and WHONET, and all compound IDs from PubChem. It also contains all
brand names (synonyms) as found on PubChem and Defined Daily Doses
(DDDs) for oral and parenteral administration.< / p >
2020-08-16 21:38:42 +02:00
< ul >
< li >
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< a href = "https://www.whocc.no/atc_ddd_index/" class = "external-link" > ATC/DDD index from WHO
Collaborating Centre for Drug Statistics Methodology< / a > (note: this may
not be used for commercial purposes, but is freely available from the
WHO CC website for personal use)< / li >
< li > < a href = "https://pubchem.ncbi.nlm.nih.gov" class = "external-link" > PubChem by the US
National Library of Medicine< / a > < / li >
2021-12-02 13:32:14 +01:00
< li > < a href = "https://whonet.org" class = "external-link" > WHONET software 2019< / a > < / li >
2020-08-16 21:38:42 +02:00
< / ul >
< / div >
2021-12-02 13:32:14 +01:00
< div class = "section level3" >
< h3 id = "example-content-2" > Example content< a class = "anchor" aria-label = "anchor" href = "#example-content-2" > < / a >
< / h3 >
< table style = "width:100%;" class = "table" >
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< colgroup >
< col width = "1%" >
< col width = "2%" >
< col width = "8%" >
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< col width = "7%" >
2021-08-16 21:54:34 +02:00
< col width = "7%" >
2021-01-18 16:57:56 +01:00
< col width = "13%" >
2021-08-16 21:54:34 +02:00
< col width = "17%" >
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< col width = "6%" >
2021-08-16 21:54:34 +02:00
< col width = "13%" >
2020-08-16 21:38:42 +02:00
< col width = "2%" >
< col width = "3%" >
2021-08-16 21:54:34 +02:00
< col width = "2%" >
< col width = "2%" >
2021-01-18 16:57:56 +01:00
< col width = "9%" >
2020-08-16 21:38:42 +02:00
< / colgroup >
< thead > < tr class = "header" >
< th align = "center" > ab< / th >
< th align = "center" > cid< / th >
< th align = "center" > name< / th >
< th align = "center" > group< / th >
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< th align = "center" > atc< / th >
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< th align = "center" > atc_group1< / th >
< th align = "center" > atc_group2< / th >
< th align = "center" > abbreviations< / th >
< th align = "center" > synonyms< / th >
< th align = "center" > oral_ddd< / th >
< th align = "center" > oral_units< / th >
< th align = "center" > iv_ddd< / th >
< th align = "center" > iv_units< / th >
< th align = "center" > loinc< / th >
< / tr > < / thead >
< tbody >
< tr class = "odd" >
< td align = "center" > AMK< / td >
< td align = "center" > 37768< / td >
< td align = "center" > Amikacin< / td >
< td align = "center" > Aminoglycosides< / td >
2021-08-16 21:54:34 +02:00
< td align = "center" > D06AX12, J01GB06, S01AA21< / td >
2020-08-16 21:38:42 +02:00
< td align = "center" > Aminoglycoside antibacterials< / td >
< td align = "center" > Other aminoglycosides< / td >
< td align = "center" > ak, ami, amik, …< / td >
< td align = "center" > amicacin, amikacillin, amikacin, …< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > 1.0< / td >
< td align = "center" > g< / td >
< td align = "center" > 13546-7, 15098-7, 17798-0, …< / td >
< / tr >
< tr class = "even" >
< td align = "center" > AMX< / td >
< td align = "center" > 33613< / td >
< td align = "center" > Amoxicillin< / td >
< td align = "center" > Beta-lactams/penicillins< / td >
2021-08-16 21:54:34 +02:00
< td align = "center" > J01CA04< / td >
2020-08-16 21:38:42 +02:00
< td align = "center" > Beta-lactam antibacterials, penicillins< / td >
< td align = "center" > Penicillins with extended spectrum< / td >
< td align = "center" > ac, amox, amx< / td >
< td align = "center" > actimoxi, amoclen, amolin, …< / td >
2020-09-24 00:30:11 +02:00
< td align = "center" > 1.5< / td >
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< td align = "center" > g< / td >
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< td align = "center" > 3.0< / td >
2020-08-16 21:38:42 +02:00
< td align = "center" > g< / td >
< td align = "center" > 16365-9, 25274-2, 3344-9, …< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > AMC< / td >
< td align = "center" > 23665637< / td >
< td align = "center" > Amoxicillin/clavulanic acid< / td >
< td align = "center" > Beta-lactams/penicillins< / td >
2021-08-16 21:54:34 +02:00
< td align = "center" > J01CR02< / td >
2020-08-16 21:38:42 +02:00
< td align = "center" > Beta-lactam antibacterials, penicillins< / td >
2022-04-08 11:02:45 +02:00
< td align = "center" > Combinations of penicillins, incl.
inhibitors< / td >
2020-08-16 21:38:42 +02:00
< td align = "center" > a/c, amcl, aml, …< / td >
< td align = "center" > amocla, amoclan, amoclav, …< / td >
2020-09-24 00:30:11 +02:00
< td align = "center" > 1.5< / td >
2020-08-16 21:38:42 +02:00
< td align = "center" > g< / td >
< td align = "center" > 3.0< / td >
< td align = "center" > g< / td >
< td align = "center" > < / td >
< / tr >
< tr class = "even" >
< td align = "center" > AMP< / td >
< td align = "center" > 6249< / td >
< td align = "center" > Ampicillin< / td >
< td align = "center" > Beta-lactams/penicillins< / td >
2021-08-16 21:54:34 +02:00
< td align = "center" > J01CA01, S01AA19< / td >
2020-08-16 21:38:42 +02:00
< td align = "center" > Beta-lactam antibacterials, penicillins< / td >
< td align = "center" > Penicillins with extended spectrum< / td >
< td align = "center" > am, amp, ampi< / td >
< td align = "center" > acillin, adobacillin, amblosin, …< / td >
< td align = "center" > 2.0< / td >
< td align = "center" > g< / td >
2020-09-24 00:30:11 +02:00
< td align = "center" > 6.0< / td >
2020-08-16 21:38:42 +02:00
< td align = "center" > g< / td >
< td align = "center" > 21066-6, 3355-5, 33562-0, …< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > AZM< / td >
< td align = "center" > 447043< / td >
< td align = "center" > Azithromycin< / td >
< td align = "center" > Macrolides/lincosamides< / td >
2021-08-16 21:54:34 +02:00
< td align = "center" > J01FA10, S01AA26< / td >
2020-08-16 21:38:42 +02:00
< td align = "center" > Macrolides, lincosamides and streptogramins< / td >
< td align = "center" > Macrolides< / td >
< td align = "center" > az, azi, azit, …< / td >
< td align = "center" > aritromicina, azasite, azenil, …< / td >
< td align = "center" > 0.3< / td >
< td align = "center" > g< / td >
< td align = "center" > 0.5< / td >
< td align = "center" > g< / td >
< td align = "center" > 16420-2, 25233-8< / td >
< / tr >
< tr class = "even" >
2021-01-18 16:57:56 +01:00
< td align = "center" > PEN< / td >
< td align = "center" > 5904< / td >
< td align = "center" > Benzylpenicillin< / td >
< td align = "center" > Beta-lactams/penicillins< / td >
2021-08-16 21:54:34 +02:00
< td align = "center" > J01CE01, S01AA14< / td >
2021-01-18 16:57:56 +01:00
< td align = "center" > Combinations of antibacterials< / td >
< td align = "center" > Combinations of antibacterials< / td >
< td align = "center" > bepe, pen, peni, …< / td >
< td align = "center" > abbocillin, ayercillin, bencilpenicilina, …< / td >
2020-08-16 21:38:42 +02:00
< td align = "center" > < / td >
< td align = "center" > < / td >
2021-01-18 16:57:56 +01:00
< td align = "center" > 3.6< / td >
2020-08-16 21:38:42 +02:00
< td align = "center" > g< / td >
2021-01-18 16:57:56 +01:00
< td align = "center" > 3913-1< / td >
2020-08-16 21:38:42 +02:00
< / tr >
< / tbody >
< / table >
< / div >
< / div >
2021-12-02 13:32:14 +01:00
< div class = "section level2" >
< h2 id = "antiviral-agents" > Antiviral agents< a class = "anchor" aria-label = "anchor" href = "#antiviral-agents" > < / a >
< / h2 >
2022-04-08 11:02:45 +02:00
< p > A data set with 102 rows and 9 columns, containing the following
column names:< br > < em > atc< / em > , < em > cid< / em > , < em > name< / em > , < em > atc_group< / em > ,
< em > synonyms< / em > , < em > oral_ddd< / em > , < em > oral_units< / em > ,
< em > iv_ddd< / em > and < em > iv_units< / em > .< / p >
< p > This data set is in R available as < code > antivirals< / code > , after you
load the < code > AMR< / code > package.< / p >
< p > It was last updated on 29 August 2020 19:53:07 UTC. Find more info
about the structure of this data set < a href = "https://msberends.github.io/AMR/reference/antibiotics.html" > here< / a > .< / p >
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< p > < strong > Direct download links:< / strong > < / p >
< ul >
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< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.rds" class = "external-link" > R
file< / a > (5 kB)< br >
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< / li >
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< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.xlsx" class = "external-link" > Excel
file< / a > (14 kB)< br >
2020-09-24 00:30:11 +02:00
< / li >
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< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.txt" class = "external-link" > plain
text file< / a > (16 kB)< br >
2020-09-24 00:30:11 +02:00
< / li >
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< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sas" class = "external-link" > SAS
file< / a > (80 kB)< br >
2020-09-24 00:30:11 +02:00
< / li >
2022-04-08 11:02:45 +02:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sav" class = "external-link" > SPSS
file< / a > (68 kB)< br >
2020-09-24 00:30:11 +02:00
< / li >
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< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.dta" class = "external-link" > Stata
file< / a > (67 kB)< / li >
2020-09-24 00:30:11 +02:00
< / ul >
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< div class = "section level3" >
< h3 id = "source-3" > Source< a class = "anchor" aria-label = "anchor" href = "#source-3" > < / a >
< / h3 >
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< p > This data set contains all ATC codes gathered from WHO and all
compound IDs from PubChem. It also contains all brand names (synonyms)
as found on PubChem and Defined Daily Doses (DDDs) for oral and
parenteral administration.< / p >
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< ul >
< li >
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< a href = "https://www.whocc.no/atc_ddd_index/" class = "external-link" > ATC/DDD index from WHO
Collaborating Centre for Drug Statistics Methodology< / a > (note: this may
not be used for commercial purposes, but is freely available from the
WHO CC website for personal use)< / li >
< li > < a href = "https://pubchem.ncbi.nlm.nih.gov" class = "external-link" > PubChem by the US
National Library of Medicine< / a > < / li >
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< / ul >
< / div >
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< div class = "section level3" >
< h3 id = "example-content-3" > Example content< a class = "anchor" aria-label = "anchor" href = "#example-content-3" > < / a >
< / h3 >
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< table class = "table" >
< colgroup >
< col width = "4%" >
< col width = "5%" >
< col width = "9%" >
< col width = "32%" >
< col width = "30%" >
< col width = "4%" >
< col width = "5%" >
< col width = "3%" >
< col width = "4%" >
< / colgroup >
< thead > < tr class = "header" >
< th align = "center" > atc< / th >
< th align = "center" > cid< / th >
< th align = "center" > name< / th >
< th align = "center" > atc_group< / th >
< th align = "center" > synonyms< / th >
< th align = "center" > oral_ddd< / th >
< th align = "center" > oral_units< / th >
< th align = "center" > iv_ddd< / th >
< th align = "center" > iv_units< / th >
< / tr > < / thead >
< tbody >
< tr class = "odd" >
< td align = "center" > J05AF06< / td >
< td align = "center" > 441300< / td >
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< td align = "center" > Abacavir< / td >
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< td align = "center" > Nucleoside and nucleotide reverse transcriptase
inhibitors< / td >
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< td align = "center" > Abacavir, Abacavir sulfate, Ziagen< / td >
< td align = "center" > 0.6< / td >
< td align = "center" > g< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< / tr >
< tr class = "even" >
< td align = "center" > J05AB01< / td >
< td align = "center" > 135398513< / td >
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< td align = "center" > Aciclovir< / td >
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< td align = "center" > Nucleosides and nucleotides excl. reverse
transcriptase inhibitors< / td >
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< td align = "center" > Acicloftal, Aciclovier, Aciclovir, …< / td >
< td align = "center" > 4.0< / td >
< td align = "center" > g< / td >
< td align = "center" > 4< / td >
< td align = "center" > g< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > J05AF08< / td >
< td align = "center" > 60871< / td >
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< td align = "center" > Adefovir dipivoxil< / td >
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< td align = "center" > Nucleoside and nucleotide reverse transcriptase
inhibitors< / td >
< td align = "center" > Adefovir di ester, Adefovir dipivoxil, Adefovir
Dipivoxil, …< / td >
2020-08-16 21:38:42 +02:00
< td align = "center" > 10.0< / td >
< td align = "center" > mg< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< / tr >
< tr class = "even" >
< td align = "center" > J05AE05< / td >
< td align = "center" > 65016< / td >
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< td align = "center" > Amprenavir< / td >
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< td align = "center" > Protease inhibitors< / td >
< td align = "center" > Agenerase, Amprenavir, Amprenavirum, …< / td >
< td align = "center" > 1.2< / td >
< td align = "center" > g< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< / tr >
< tr class = "odd" >
< td align = "center" > J05AP06< / td >
< td align = "center" > 16076883< / td >
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< td align = "center" > Asunaprevir< / td >
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< td align = "center" > Antivirals for treatment of HCV infections< / td >
< td align = "center" > Asunaprevir, Sunvepra< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< / tr >
< tr class = "even" >
< td align = "center" > J05AE08< / td >
< td align = "center" > 148192< / td >
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< td align = "center" > Atazanavir< / td >
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< td align = "center" > Protease inhibitors< / td >
< td align = "center" > Atazanavir, Atazanavir Base, Latazanavir, …< / td >
< td align = "center" > 0.3< / td >
< td align = "center" > g< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< / tr >
< / tbody >
< / table >
< / div >
< / div >
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< div class = "section level2" >
< h2 id = "intrinsic-bacterial-resistance" > Intrinsic bacterial resistance< a class = "anchor" aria-label = "anchor" href = "#intrinsic-bacterial-resistance" > < / a >
< / h2 >
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< p > A data set with 134,956 rows and 2 columns, containing the following
column names:< br > < em > mo< / em > and < em > ab< / em > .< / p >
< p > This data set is in R available as < code > intrinsic_resistant< / code > ,
after you load the < code > AMR< / code > package.< / p >
< p > It was last updated on 14 December 2021 21:59:33 UTC. Find more info
about the structure of this data set < a href = "https://msberends.github.io/AMR/reference/intrinsic_resistant.html" > here< / a > .< / p >
2020-09-24 00:30:11 +02:00
< p > < strong > Direct download links:< / strong > < / p >
< ul >
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< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.rds" class = "external-link" > R
file< / a > (78 kB)< br >
2020-09-24 00:30:11 +02:00
< / li >
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< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.xlsx" class = "external-link" > Excel
file< / a > (0.9 MB)< br >
2020-09-24 00:30:11 +02:00
< / li >
2022-04-08 11:02:45 +02:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.txt" class = "external-link" > plain
text file< / a > (5.1 MB)< br >
2020-09-24 00:30:11 +02:00
< / li >
2022-04-08 11:02:45 +02:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sas" class = "external-link" > SAS
file< / a > (10.4 MB)< br >
2020-09-24 00:30:11 +02:00
< / li >
2022-04-08 11:02:45 +02:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sav" class = "external-link" > SPSS
file< / a > (7.4 MB)< br >
2020-09-24 00:30:11 +02:00
< / li >
2022-04-08 11:02:45 +02:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.dta" class = "external-link" > Stata
file< / a > (10.2 MB)< / li >
2020-09-24 00:30:11 +02:00
< / ul >
2021-12-02 13:32:14 +01:00
< div class = "section level3" >
< h3 id = "source-4" > Source< a class = "anchor" aria-label = "anchor" href = "#source-4" > < / a >
< / h3 >
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< p > This data set contains all defined intrinsic resistance by EUCAST of
2022-05-09 17:08:40 +02:00
all bug-drug combinations, and is based on < a href = "https://www.eucast.org/expert_rules_and_expected_phenotypes/" class = "external-link" > ‘
2022-04-08 11:02:45 +02:00
Expert Rules’ ‘ ’
v3.3< / a > (2021).< / p >
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< / div >
2021-12-02 13:32:14 +01:00
< div class = "section level3" >
< h3 id = "example-content-4" > Example content< a class = "anchor" aria-label = "anchor" href = "#example-content-4" > < / a >
< / h3 >
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< p > Example rows when filtering on < em > Enterobacter cloacae< / em > :< / p >
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< table class = "table" >
< thead > < tr class = "header" >
< th align = "center" > microorganism< / th >
< th align = "center" > antibiotic< / th >
< / tr > < / thead >
< tbody >
< tr class = "odd" >
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< td align = "center" > Enterobacter cloacae< / td >
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< td align = "center" > Acetylmidecamycin< / td >
< / tr >
< tr class = "even" >
< td align = "center" > Enterobacter cloacae< / td >
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< td align = "center" > Amoxicillin/clavulanic acid< / td >
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< / tr >
< tr class = "odd" >
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< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Ampicillin< / td >
< / tr >
< tr class = "even" >
< td align = "center" > Enterobacter cloacae< / td >
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< td align = "center" > Amoxicillin< / td >
2020-09-24 00:30:11 +02:00
< / tr >
< tr class = "odd" >
< td align = "center" > Enterobacter cloacae< / td >
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< td align = "center" > Acetylspiramycin< / td >
2020-09-24 00:30:11 +02:00
< / tr >
< tr class = "even" >
< td align = "center" > Enterobacter cloacae< / td >
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< td align = "center" > Avoparcin< / td >
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< / tr >
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< tr class = "odd" >
< td align = "center" > Enterobacter cloacae< / td >
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< td align = "center" > Azithromycin< / td >
2021-12-11 13:41:31 +01:00
< / tr >
< tr class = "even" >
< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Cadazolid< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > Enterobacter cloacae< / td >
2021-12-14 22:59:27 +01:00
< td align = "center" > Cephalothin< / td >
2020-08-16 21:38:42 +02:00
< / tr >
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< tr class = "even" >
< td align = "center" > Enterobacter cloacae< / td >
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< td align = "center" > Cefadroxil< / td >
2020-09-24 00:30:11 +02:00
< / tr >
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< tr class = "odd" >
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< td align = "center" > Enterobacter cloacae< / td >
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< td align = "center" > Clindamycin< / td >
2020-09-24 00:30:11 +02:00
< / tr >
< tr class = "even" >
< td align = "center" > Enterobacter cloacae< / td >
2020-08-29 21:41:46 +02:00
< td align = "center" > Clarithromycin< / td >
2020-08-16 21:38:42 +02:00
< / tr >
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< tr class = "odd" >
< td align = "center" > Enterobacter cloacae< / td >
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< td align = "center" > Cycloserine< / td >
2020-09-24 00:30:11 +02:00
< / tr >
< tr class = "even" >
< td align = "center" > Enterobacter cloacae< / td >
2021-12-14 22:59:27 +01:00
< td align = "center" > Cefazolin< / td >
2020-09-24 00:30:11 +02:00
< / tr >
< tr class = "odd" >
< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Dalbavancin< / td >
< / tr >
2020-08-16 21:38:42 +02:00
< tr class = "even" >
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< td align = "center" > Enterobacter cloacae< / td >
2020-09-24 00:30:11 +02:00
< td align = "center" > Dirithromycin< / td >
2020-08-29 21:41:46 +02:00
< / tr >
< tr class = "odd" >
< td align = "center" > Enterobacter cloacae< / td >
2020-08-16 21:38:42 +02:00
< td align = "center" > Erythromycin< / td >
< / tr >
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< tr class = "even" >
< td align = "center" > Enterobacter cloacae< / td >
2020-09-24 00:30:11 +02:00
< td align = "center" > Flurithromycin< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > Enterobacter cloacae< / td >
2021-12-14 22:59:27 +01:00
< td align = "center" > Cefoxitin< / td >
2020-08-29 21:41:46 +02:00
< / tr >
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< tr class = "even" >
< td align = "center" > Enterobacter cloacae< / td >
2021-12-14 22:59:27 +01:00
< td align = "center" > Fusidic acid< / td >
2021-12-11 13:41:31 +01:00
< / tr >
< tr class = "odd" >
< td align = "center" > Enterobacter cloacae< / td >
2021-12-14 22:59:27 +01:00
< td align = "center" > Gamithromycin< / td >
< / tr >
< tr class = "even" >
< td align = "center" > Enterobacter cloacae< / td >
2020-09-24 00:30:11 +02:00
< td align = "center" > Josamycin< / td >
< / tr >
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< tr class = "odd" >
< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Kitasamycin< / td >
< / tr >
2021-12-11 13:41:31 +01:00
< tr class = "even" >
< td align = "center" > Enterobacter cloacae< / td >
2021-12-14 22:59:27 +01:00
< td align = "center" > Cephalexin< / td >
2021-12-11 13:41:31 +01:00
< / tr >
2020-08-29 21:41:46 +02:00
< tr class = "odd" >
< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Lincomycin< / td >
< / tr >
< tr class = "even" >
< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Linezolid< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > Enterobacter cloacae< / td >
2021-12-14 22:59:27 +01:00
< td align = "center" > Miocamycin< / td >
2020-09-24 00:30:11 +02:00
< / tr >
< tr class = "even" >
< td align = "center" > Enterobacter cloacae< / td >
2021-12-14 22:59:27 +01:00
< td align = "center" > Meleumycin< / td >
2021-12-11 13:41:31 +01:00
< / tr >
< tr class = "odd" >
< td align = "center" > Enterobacter cloacae< / td >
2021-12-14 22:59:27 +01:00
< td align = "center" > Midecamycin< / td >
2020-09-24 00:30:11 +02:00
< / tr >
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< tr class = "even" >
< td align = "center" > Enterobacter cloacae< / td >
2021-12-14 22:59:27 +01:00
< td align = "center" > Norvancomycin< / td >
2021-12-11 13:41:31 +01:00
< / tr >
2020-09-24 00:30:11 +02:00
< tr class = "odd" >
< td align = "center" > Enterobacter cloacae< / td >
2021-12-14 22:59:27 +01:00
< td align = "center" > Oleandomycin< / td >
2020-09-24 00:30:11 +02:00
< / tr >
< tr class = "even" >
< td align = "center" > Enterobacter cloacae< / td >
2021-12-14 22:59:27 +01:00
< td align = "center" > Oritavancin< / td >
2020-09-24 00:30:11 +02:00
< / tr >
< tr class = "odd" >
< td align = "center" > Enterobacter cloacae< / td >
2021-12-14 22:59:27 +01:00
< td align = "center" > Benzylpenicillin< / td >
2020-09-24 00:30:11 +02:00
< / tr >
< tr class = "even" >
< td align = "center" > Enterobacter cloacae< / td >
2021-12-14 22:59:27 +01:00
< td align = "center" > Pristinamycin< / td >
2020-09-24 00:30:11 +02:00
< / tr >
< tr class = "odd" >
< td align = "center" > Enterobacter cloacae< / td >
2021-12-14 22:59:27 +01:00
< td align = "center" > Pirlimycin< / td >
2020-08-29 21:41:46 +02:00
< / tr >
< tr class = "even" >
< td align = "center" > Enterobacter cloacae< / td >
2021-12-14 22:59:27 +01:00
< td align = "center" > Primycin< / td >
2020-08-29 21:41:46 +02:00
< / tr >
< tr class = "odd" >
< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Quinupristin/dalfopristin< / td >
< / tr >
< tr class = "even" >
< td align = "center" > Enterobacter cloacae< / td >
2020-09-24 00:30:11 +02:00
< td align = "center" > Ramoplanin< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > Enterobacter cloacae< / td >
2020-08-29 21:41:46 +02:00
< td align = "center" > Rifampicin< / td >
< / tr >
2020-09-24 00:30:11 +02:00
< tr class = "even" >
< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Rokitamycin< / td >
< / tr >
2020-08-29 21:41:46 +02:00
< tr class = "odd" >
< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Roxithromycin< / td >
< / tr >
< tr class = "even" >
< td align = "center" > Enterobacter cloacae< / td >
2021-12-14 22:59:27 +01:00
< td align = "center" > Ampicillin/sulbactam< / td >
2020-09-24 00:30:11 +02:00
< / tr >
< tr class = "odd" >
< td align = "center" > Enterobacter cloacae< / td >
2021-12-14 22:59:27 +01:00
< td align = "center" > Solithromycin< / td >
2020-09-24 00:30:11 +02:00
< / tr >
< tr class = "even" >
< td align = "center" > Enterobacter cloacae< / td >
2021-12-14 22:59:27 +01:00
< td align = "center" > Spiramycin< / td >
2020-08-29 21:41:46 +02:00
< / tr >
< tr class = "odd" >
< td align = "center" > Enterobacter cloacae< / td >
2021-12-11 13:41:31 +01:00
< td align = "center" > Teicoplanin< / td >
2020-09-24 00:30:11 +02:00
< / tr >
< tr class = "even" >
< td align = "center" > Enterobacter cloacae< / td >
2021-12-14 22:59:27 +01:00
< td align = "center" > Thiacetazone< / td >
2020-09-24 00:30:11 +02:00
< / tr >
< tr class = "odd" >
< td align = "center" > Enterobacter cloacae< / td >
2021-12-14 22:59:27 +01:00
< td align = "center" > Tilmicosin< / td >
2020-09-24 00:30:11 +02:00
< / tr >
< tr class = "even" >
< td align = "center" > Enterobacter cloacae< / td >
2021-12-14 22:59:27 +01:00
< td align = "center" > Tildipirosin< / td >
2020-09-24 00:30:11 +02:00
< / tr >
< tr class = "odd" >
< td align = "center" > Enterobacter cloacae< / td >
2021-12-14 22:59:27 +01:00
< td align = "center" > Telithromycin< / td >
2021-12-11 13:41:31 +01:00
< / tr >
< tr class = "even" >
< td align = "center" > Enterobacter cloacae< / td >
2021-12-14 22:59:27 +01:00
< td align = "center" > Telavancin< / td >
2021-12-11 13:41:31 +01:00
< / tr >
< tr class = "odd" >
< td align = "center" > Enterobacter cloacae< / td >
2020-09-24 00:30:11 +02:00
< td align = "center" > Troleandomycin< / td >
< / tr >
< tr class = "even" >
< td align = "center" > Enterobacter cloacae< / td >
2021-12-11 13:41:31 +01:00
< td align = "center" > Tulathromycin< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Tylosin< / td >
< / tr >
< tr class = "even" >
< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Tylvalosin< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > Enterobacter cloacae< / td >
2021-12-14 22:59:27 +01:00
< td align = "center" > Tedizolid< / td >
< / tr >
< tr class = "even" >
< td align = "center" > Enterobacter cloacae< / td >
2020-08-29 21:41:46 +02:00
< td align = "center" > Vancomycin< / td >
< / tr >
2021-12-14 22:59:27 +01:00
< tr class = "odd" >
< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Nafithromycin< / td >
< / tr >
2020-08-16 21:38:42 +02:00
< / tbody >
< / table >
< / div >
< / div >
2021-12-02 13:32:14 +01:00
< div class = "section level2" >
< h2 id = "interpretation-from-mic-values-disk-diameters-to-rsi" > Interpretation from MIC values / disk diameters to R/SI< a class = "anchor" aria-label = "anchor" href = "#interpretation-from-mic-values-disk-diameters-to-rsi" > < / a >
< / h2 >
2022-04-08 11:02:45 +02:00
< p > A data set with 20,318 rows and 11 columns, containing the following
column names:< br > < em > guideline< / em > , < em > method< / em > , < em > site< / em > , < em > mo< / em > ,
< em > rank_index< / em > , < em > ab< / em > , < em > ref_tbl< / em > , < em > disk_dose< / em > ,
< em > breakpoint_S< / em > , < em > breakpoint_R< / em > and < em > uti< / em > .< / p >
< p > This data set is in R available as < code > rsi_translation< / code > ,
after you load the < code > AMR< / code > package.< / p >
< p > It was last updated on 14 December 2021 21:59:33 UTC. Find more info
about the structure of this data set < a href = "https://msberends.github.io/AMR/reference/rsi_translation.html" > here< / a > .< / p >
2020-09-24 00:30:11 +02:00
< p > < strong > Direct download links:< / strong > < / p >
< ul >
2022-04-08 11:02:45 +02:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.rds" class = "external-link" > R
file< / a > (39 kB)< br >
2020-09-24 00:30:11 +02:00
< / li >
2022-04-08 11:02:45 +02:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.xlsx" class = "external-link" > Excel
file< / a > (0.7 MB)< br >
2020-09-24 00:30:11 +02:00
< / li >
2022-04-08 11:02:45 +02:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.txt" class = "external-link" > plain
text file< / a > (1.7 MB)< br >
2020-09-24 00:30:11 +02:00
< / li >
2022-04-08 11:02:45 +02:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sas" class = "external-link" > SAS
file< / a > (3.6 MB)< br >
2020-09-24 00:30:11 +02:00
< / li >
2022-04-08 11:02:45 +02:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sav" class = "external-link" > SPSS
file< / a > (2.2 MB)< br >
2020-09-24 00:30:11 +02:00
< / li >
2022-04-08 11:02:45 +02:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.dta" class = "external-link" > Stata
file< / a > (3.4 MB)< / li >
2020-09-24 00:30:11 +02:00
< / ul >
2021-12-02 13:32:14 +01:00
< div class = "section level3" >
< h3 id = "source-5" > Source< a class = "anchor" aria-label = "anchor" href = "#source-5" > < / a >
< / h3 >
2022-04-08 11:02:45 +02:00
< p > This data set contains interpretation rules for MIC values and disk
diffusion diameters. Included guidelines are CLSI (2010-2021) and EUCAST
(2011-2021).< / p >
2020-08-16 21:38:42 +02:00
< / div >
2021-12-02 13:32:14 +01:00
< div class = "section level3" >
< h3 id = "example-content-5" > Example content< a class = "anchor" aria-label = "anchor" href = "#example-content-5" > < / a >
< / h3 >
2020-08-16 21:38:42 +02:00
< table class = "table" >
< colgroup >
2021-12-13 10:18:28 +01:00
< col width = "9%" >
2020-08-16 21:38:42 +02:00
< col width = "5%" >
< col width = "4%" >
2021-12-13 10:18:28 +01:00
< col width = "16%" >
< col width = "8%" >
< col width = "11%" >
2020-08-16 21:38:42 +02:00
< col width = "9%" >
2021-12-13 10:18:28 +01:00
< col width = "8%" >
< col width = "10%" >
< col width = "10%" >
< col width = "5%" >
2020-08-16 21:38:42 +02:00
< / colgroup >
< thead > < tr class = "header" >
< th align = "center" > guideline< / th >
< th align = "center" > method< / th >
< th align = "center" > site< / th >
< th align = "center" > mo< / th >
2021-12-13 10:18:28 +01:00
< th align = "center" > rank_index< / th >
2020-08-16 21:38:42 +02:00
< th align = "center" > ab< / th >
< th align = "center" > ref_tbl< / th >
< th align = "center" > disk_dose< / th >
< th align = "center" > breakpoint_S< / th >
< th align = "center" > breakpoint_R< / th >
< th align = "center" > uti< / th >
< / tr > < / thead >
< tbody >
< tr class = "odd" >
2021-01-18 16:57:56 +01:00
< td align = "center" > EUCAST 2021< / td >
2021-12-13 10:18:28 +01:00
< td align = "center" > MIC< / td >
2020-08-16 21:38:42 +02:00
< td align = "center" > < / td >
2021-12-13 10:18:28 +01:00
< td align = "center" > Aspergillus fumigatus< / td >
< td align = "center" > 2< / td >
< td align = "center" > Amphotericin B< / td >
< td align = "center" > Aspergillus< / td >
< td align = "center" > < / td >
< td align = "center" > 1< / td >
< td align = "center" > 4< / td >
2020-08-16 21:38:42 +02:00
< td align = "center" > FALSE< / td >
< / tr >
< tr class = "even" >
2021-01-18 16:57:56 +01:00
< td align = "center" > EUCAST 2021< / td >
2021-12-13 10:18:28 +01:00
< td align = "center" > MIC< / td >
< td align = "center" > < / td >
< td align = "center" > Aspergillus niger< / td >
< td align = "center" > 2< / td >
< td align = "center" > Amphotericin B< / td >
< td align = "center" > Aspergillus< / td >
< td align = "center" > < / td >
< td align = "center" > 1< / td >
< td align = "center" > 4< / td >
< td align = "center" > FALSE< / td >
2020-08-16 21:38:42 +02:00
< / tr >
< tr class = "odd" >
2021-01-18 16:57:56 +01:00
< td align = "center" > EUCAST 2021< / td >
2020-08-16 21:38:42 +02:00
< td align = "center" > MIC< / td >
< td align = "center" > < / td >
2021-12-13 10:18:28 +01:00
< td align = "center" > Candida< / td >
< td align = "center" > 3< / td >
< td align = "center" > Amphotericin B< / td >
< td align = "center" > Candida< / td >
2020-08-16 21:38:42 +02:00
< td align = "center" > < / td >
2021-12-13 10:18:28 +01:00
< td align = "center" > 1< / td >
< td align = "center" > 2< / td >
2020-08-16 21:38:42 +02:00
< td align = "center" > FALSE< / td >
< / tr >
< tr class = "even" >
2021-01-18 16:57:56 +01:00
< td align = "center" > EUCAST 2021< / td >
2020-08-16 21:38:42 +02:00
< td align = "center" > MIC< / td >
< td align = "center" > < / td >
2021-12-13 10:18:28 +01:00
< td align = "center" > Candida albicans< / td >
< td align = "center" > 2< / td >
< td align = "center" > Amphotericin B< / td >
< td align = "center" > Candida< / td >
< td align = "center" > < / td >
< td align = "center" > 1< / td >
< td align = "center" > 2< / td >
< td align = "center" > FALSE< / td >
2020-08-16 21:38:42 +02:00
< / tr >
< tr class = "odd" >
2021-01-18 16:57:56 +01:00
< td align = "center" > EUCAST 2021< / td >
2020-08-16 21:38:42 +02:00
< td align = "center" > MIC< / td >
< td align = "center" > < / td >
2021-12-13 10:18:28 +01:00
< td align = "center" > Candida krusei< / td >
< td align = "center" > 2< / td >
< td align = "center" > Amphotericin B< / td >
< td align = "center" > Candida< / td >
2020-08-16 21:38:42 +02:00
< td align = "center" > < / td >
2021-12-13 10:18:28 +01:00
< td align = "center" > 1< / td >
< td align = "center" > 2< / td >
2020-08-16 21:38:42 +02:00
< td align = "center" > FALSE< / td >
< / tr >
< tr class = "even" >
2021-01-18 16:57:56 +01:00
< td align = "center" > EUCAST 2021< / td >
2020-08-16 21:38:42 +02:00
< td align = "center" > MIC< / td >
< td align = "center" > < / td >
2021-12-13 10:18:28 +01:00
< td align = "center" > Candida parapsilosis< / td >
< td align = "center" > 2< / td >
< td align = "center" > Amphotericin B< / td >
< td align = "center" > Candida< / td >
2020-08-16 21:38:42 +02:00
< td align = "center" > < / td >
2021-12-13 10:18:28 +01:00
< td align = "center" > 1< / td >
< td align = "center" > 2< / td >
2020-08-16 21:38:42 +02:00
< td align = "center" > FALSE< / td >
< / tr >
< / tbody >
< / table >
< / div >
2021-01-18 16:57:56 +01:00
< / div >
2021-12-02 13:32:14 +01:00
< div class = "section level2" >
< h2 id = "dosage-guidelines-from-eucast" > Dosage guidelines from EUCAST< a class = "anchor" aria-label = "anchor" href = "#dosage-guidelines-from-eucast" > < / a >
< / h2 >
2022-04-08 11:02:45 +02:00
< p > A data set with 169 rows and 9 columns, containing the following
column names:< br > < em > ab< / em > , < em > name< / em > , < em > type< / em > , < em > dose< / em > ,
< em > dose_times< / em > , < em > administration< / em > , < em > notes< / em > ,
< em > original_txt< / em > and < em > eucast_version< / em > .< / p >
< p > This data set is in R available as < code > dosage< / code > , after you
load the < code > AMR< / code > package.< / p >
< p > It was last updated on 25 January 2021 20:58:20 UTC. Find more info
about the structure of this data set < a href = "https://msberends.github.io/AMR/reference/dosage.html" > here< / a > .< / p >
2021-01-18 16:57:56 +01:00
< p > < strong > Direct download links:< / strong > < / p >
< ul >
2022-04-08 11:02:45 +02:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.rds" class = "external-link" > R
file< / a > (3 kB)< br >
2021-01-18 16:57:56 +01:00
< / li >
2022-04-08 11:02:45 +02:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.xlsx" class = "external-link" > Excel
file< / a > (14 kB)< br >
2021-01-18 16:57:56 +01:00
< / li >
2022-04-08 11:02:45 +02:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.txt" class = "external-link" > plain
text file< / a > (15 kB)< br >
2021-01-18 16:57:56 +01:00
< / li >
2022-04-08 11:02:45 +02:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sas" class = "external-link" > SAS
file< / a > (52 kB)< br >
2021-01-18 16:57:56 +01:00
< / li >
2022-04-08 11:02:45 +02:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sav" class = "external-link" > SPSS
file< / a > (45 kB)< br >
2021-01-18 16:57:56 +01:00
< / li >
2022-04-08 11:02:45 +02:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.dta" class = "external-link" > Stata
file< / a > (44 kB)< / li >
2021-01-18 16:57:56 +01:00
< / ul >
2021-12-02 13:32:14 +01:00
< div class = "section level3" >
< h3 id = "source-6" > Source< a class = "anchor" aria-label = "anchor" href = "#source-6" > < / a >
< / h3 >
2022-04-08 11:02:45 +02:00
< p > EUCAST breakpoints used in this package are based on the dosages in
this data set.< / p >
< p > Currently included dosages in the data set are meant for: < a href = "https://www.eucast.org/clinical_breakpoints/" class = "external-link" > ‘
Breakpoint Tables’ < / a > (2021).< / p >
2021-01-18 16:57:56 +01:00
< / div >
2021-12-02 13:32:14 +01:00
< div class = "section level3" >
< h3 id = "example-content-6" > Example content< a class = "anchor" aria-label = "anchor" href = "#example-content-6" > < / a >
< / h3 >
2021-01-18 16:57:56 +01:00
< table class = "table" >
2022-04-08 11:02:45 +02:00
< colgroup >
< col width = "4%" >
< col width = "10%" >
< col width = "15%" >
< col width = "10%" >
< col width = "9%" >
< col width = "13%" >
< col width = "5%" >
< col width = "16%" >
< col width = "13%" >
< / colgroup >
2021-01-18 16:57:56 +01:00
< thead > < tr class = "header" >
< th align = "center" > ab< / th >
< th align = "center" > name< / th >
< th align = "center" > type< / th >
< th align = "center" > dose< / th >
< th align = "center" > dose_times< / th >
< th align = "center" > administration< / th >
< th align = "center" > notes< / th >
< th align = "center" > original_txt< / th >
< th align = "center" > eucast_version< / th >
< / tr > < / thead >
< tbody >
< tr class = "odd" >
< td align = "center" > AMK< / td >
< td align = "center" > Amikacin< / td >
< td align = "center" > standard_dosage< / td >
< td align = "center" > 25-30 mg/kg< / td >
< td align = "center" > 1< / td >
< td align = "center" > iv< / td >
< td align = "center" > < / td >
< td align = "center" > 25-30 mg/kg x 1 iv< / td >
< td align = "center" > 11< / td >
< / tr >
< tr class = "even" >
< td align = "center" > AMX< / td >
< td align = "center" > Amoxicillin< / td >
< td align = "center" > high_dosage< / td >
< td align = "center" > 2 g< / td >
< td align = "center" > 6< / td >
< td align = "center" > iv< / td >
< td align = "center" > < / td >
< td align = "center" > 2 g x 6 iv< / td >
< td align = "center" > 11< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > AMX< / td >
< td align = "center" > Amoxicillin< / td >
< td align = "center" > standard_dosage< / td >
< td align = "center" > 1 g< / td >
< td align = "center" > 3< / td >
< td align = "center" > iv< / td >
< td align = "center" > < / td >
< td align = "center" > 1 g x 3-4 iv< / td >
< td align = "center" > 11< / td >
< / tr >
< tr class = "even" >
< td align = "center" > AMX< / td >
< td align = "center" > Amoxicillin< / td >
< td align = "center" > high_dosage< / td >
< td align = "center" > 0.75-1 g< / td >
< td align = "center" > 3< / td >
< td align = "center" > oral< / td >
< td align = "center" > < / td >
< td align = "center" > 0.75-1 g x 3 oral< / td >
< td align = "center" > 11< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > AMX< / td >
< td align = "center" > Amoxicillin< / td >
< td align = "center" > standard_dosage< / td >
< td align = "center" > 0.5 g< / td >
< td align = "center" > 3< / td >
< td align = "center" > oral< / td >
< td align = "center" > < / td >
< td align = "center" > 0.5 g x 3 oral< / td >
< td align = "center" > 11< / td >
< / tr >
< tr class = "even" >
< td align = "center" > AMX< / td >
< td align = "center" > Amoxicillin< / td >
< td align = "center" > uncomplicated_uti< / td >
< td align = "center" > 0.5 g< / td >
< td align = "center" > 3< / td >
< td align = "center" > oral< / td >
< td align = "center" > < / td >
< td align = "center" > 0.5 g x 3 oral< / td >
< td align = "center" > 11< / td >
< / tr >
< / tbody >
< / table >
< / div >
2020-08-16 21:38:42 +02:00
< / div >
< / div >
< div class = "col-md-3 hidden-xs hidden-sm" id = "pkgdown-sidebar" >
< nav id = "toc" data-toggle = "toc" > < h2 data-toc-skip > Contents< / h2 >
< / nav >
< / div >
< / div >
< footer > < div class = "copyright" >
2021-12-02 13:32:14 +01:00
< p > < / p >
2022-05-09 17:08:40 +02:00
< p > Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.< / p >
2020-08-16 21:38:42 +02:00
< / div >
< div class = "pkgdown" >
2021-12-02 13:32:14 +01:00
< p > < / p >
2022-05-09 17:08:40 +02:00
< p > Site built with < a href = "https://pkgdown.r-lib.org/" class = "external-link" > pkgdown< / a > 2.0.3.< / p >
2020-08-16 21:38:42 +02:00
< / div >
< / footer >
< / div >
2021-12-02 13:32:14 +01:00
2020-08-16 21:38:42 +02:00
< / body >
< / html >
