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< img src = "../logo.svg" class = "logo" alt = "" > < h1 > Data sets for download / own use< / h1 >
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< h4 data-toc-skip class = "date" > 12 March 2023< / 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 >
< div class = "d-none name" > < code > datasets.Rmd< / code > < / div >
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< p > All reference data (about microorganisms, antibiotics, SIR
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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, MS Excel, Apache Feather, Apache
Parquet, SPSS, SAS, and Stata. We also provide tab-separated text 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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< div class = "section level2" >
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< h2 id = "microorganisms-full-microbial-taxonomy" >
< code > microorganisms< / code > : Full Microbial Taxonomy< a class = "anchor" aria-label = "anchor" href = "#microorganisms-full-microbial-taxonomy" > < / a >
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< / h2 >
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< p > A data set with 52 142 rows and 22 columns, containing the following
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column names:< br > < em > mo< / em > , < em > fullname< / em > , < em > status< / 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 > source< / em > , < em > lpsn< / em > , < em > lpsn_parent< / em > ,
< em > lpsn_renamed_to< / em > , < em > gbif< / em > , < em > gbif_parent< / em > ,
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< em > gbif_renamed_to< / em > , < em > prevalence< / em > , and < em > snomed< / em > .< / p >
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< p > This data set is in R available as < code > microorganisms< / code > , after
you load the < code > AMR< / code > package.< / p >
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< p > It was last updated on 26 February 2023 20:26:58 UTC. Find more info
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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" > original
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R Data Structure (RDS) file< / a > (1.2 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" > tab-separated
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text file< / a > (11.3 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" > Microsoft
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Excel workbook< / a > (5 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.feather" class = "external-link" > Apache
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Feather file< / a > (5.4 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.parquet" class = "external-link" > Apache
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Parquet file< / a > (2.6 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
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data file< / a > (50.9 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" > IBM
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SPSS Statistics data file< / a > (16.9 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
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DTA file< / a > (47.1 MB)< / li >
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< / ul >
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< p > < strong > NOTE: The exported files for SAS, SPSS and Stata contain only
the first 50 SNOMED codes per record, as their file size would otherwise
exceed 100 MB; the file size limit of GitHub.< / strong > Advice? Use R
instead.< / p >
< p > The tab-separated text file and Microsoft Excel workbook both contain
all SNOMED codes as comma separated values.< / 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 > This data set contains the full microbial taxonomy of five kingdoms
from the List of Prokaryotic names with Standing in Nomenclature (LPSN)
and the Global Biodiversity Information Facility (GBIF):< / p >
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< ul >
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< li > Parte, AC < em > et al.< / em > (2020). < strong > List of Prokaryotic names
with Standing in Nomenclature (LPSN) moves to the DSMZ.< / strong >
International Journal of Systematic and Evolutionary Microbiology, 70,
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5607-5612; . Accessed from < a href = "https://lpsn.dsmz.de" class = "external-link uri" > https://lpsn.dsmz.de< / a > on 11 December, 2022.< / li >
< li > GBIF Secretariat (2022). GBIF Backbone Taxonomy. Checklist dataset .
Accessed from < a href = "https://www.gbif.org" class = "external-link uri" > https://www.gbif.org< / a > on 11 December, 2022.< / li >
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< li > Public Health Information Network Vocabulary Access and Distribution
System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value
Set Name ‘ ’ < a href = "https://phinvads.cdc.gov" class = "external-link uri" > https://phinvads.cdc.gov< / a >
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< / li >
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< / ul >
< / div >
< div class = "section level3" >
< h3 id = "example-content" > Example content< a class = "anchor" aria-label = "anchor" href = "#example-content" > < / a >
< / h3 >
< p > Included (sub)species per taxonomic kingdom:< / p >
< 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 >
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< td align = "center" > 1< / td >
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< / tr >
< tr class = "even" >
< td align = "center" > Animalia< / td >
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< td align = "center" > 1 379< / td >
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< / tr >
< tr class = "odd" >
< td align = "center" > Archaea< / td >
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< td align = "center" > 1 314< / td >
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< / tr >
< tr class = "even" >
< td align = "center" > Bacteria< / td >
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< td align = "center" > 36 476< / td >
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< / tr >
< tr class = "odd" >
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< td align = "center" > Fungi< / td >
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< td align = "center" > 7 901< / td >
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< / tr >
< tr class = "even" >
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< td align = "center" > Protozoa< / td >
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< td align = "center" > 5 071< / td >
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< / tr >
< / tbody >
< / table >
< p > Example rows when filtering on genus < em > Escherichia< / em > :< / p >
< table style = "width:100%;" class = "table" >
< colgroup >
< col width = "3%" >
< col width = "7%" >
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< col width = "2%" >
< col width = "2%" >
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< col width = "4%" >
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< col width = "5%" >
< col width = "5%" >
< col width = "5%" >
< col width = "3%" >
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< col width = "4%" >
< col width = "3%" >
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< col width = "2%" >
< col width = "7%" >
< col width = "2%" >
< col width = "2%" >
< col width = "3%" >
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< col width = "4%" >
< col width = "2%" >
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< col width = "3%" >
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< col width = "4%" >
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< col width = "3%" >
< col width = "12%" >
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< / colgroup >
< thead > < tr class = "header" >
< th align = "center" > mo< / th >
< th align = "center" > fullname< / th >
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< th align = "center" > status< / th >
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< 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" > source< / th >
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< th align = "center" > lpsn< / th >
< th align = "center" > lpsn_parent< / th >
< th align = "center" > lpsn_renamed_to< / th >
< th align = "center" > gbif< / th >
< th align = "center" > gbif_parent< / th >
< th align = "center" > gbif_renamed_to< / th >
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< 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 >
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< td align = "center" > accepted< / td >
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< td align = "center" > Bacteria< / td >
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< td align = "center" > Pseudomonadota< / td >
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< 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 >
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< td align = "center" > Castellani et al., 1919< / td >
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< td align = "center" > LPSN< / td >
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< td align = "center" > 515602< / td >
< td align = "center" > 482< / td >
< td align = "center" > < / td >
< td align = "center" > 3221780< / td >
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< td align = "center" > 11158430< / td >
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< td align = "center" > < / td >
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< td align = "center" > 1.0< / td >
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< td align = "center" > 407310004, 407251000, 407281008, …< / td >
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< / tr >
< tr class = "even" >
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< td align = "center" > B_ESCHR_ADCR< / td >
< td align = "center" > Escherichia adecarboxylata< / td >
< td align = "center" > synonym< / td >
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< td align = "center" > Bacteria< / td >
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< td align = "center" > Pseudomonadota< / td >
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< td align = "center" > Gammaproteobacteria< / td >
< td align = "center" > Enterobacterales< / td >
< td align = "center" > Enterobacteriaceae< / td >
< td align = "center" > Escherichia< / td >
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< td align = "center" > adecarboxylata< / td >
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< td align = "center" > < / td >
< td align = "center" > species< / td >
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< td align = "center" > Leclerc, 1962< / td >
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< td align = "center" > LPSN< / td >
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< td align = "center" > 776052< / td >
< td align = "center" > 515602< / td >
< td align = "center" > 777447< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
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< td align = "center" > 1.0< / td >
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< td align = "center" > < / td >
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< / tr >
< tr class = "odd" >
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< td align = "center" > B_ESCHR_ALBR< / td >
< td align = "center" > Escherichia albertii< / td >
< td align = "center" > accepted< / td >
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< td align = "center" > Bacteria< / td >
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< td align = "center" > Pseudomonadota< / td >
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< td align = "center" > Gammaproteobacteria< / td >
< td align = "center" > Enterobacterales< / td >
< td align = "center" > Enterobacteriaceae< / td >
< td align = "center" > Escherichia< / td >
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< td align = "center" > albertii< / td >
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< td align = "center" > < / td >
< td align = "center" > species< / td >
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< td align = "center" > Huys et al., 2003< / td >
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< td align = "center" > LPSN< / td >
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< td align = "center" > 776053< / td >
< td align = "center" > 515602< / td >
< td align = "center" > < / td >
< td align = "center" > 5427575< / td >
< td align = "center" > 3221780< / td >
< td align = "center" > < / td >
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< td align = "center" > 1.0< / td >
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< td align = "center" > 419388003< / td >
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< / tr >
< tr class = "even" >
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< td align = "center" > B_ESCHR_BLTT< / td >
< td align = "center" > Escherichia blattae< / td >
< td align = "center" > synonym< / td >
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< td align = "center" > Bacteria< / td >
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< td align = "center" > Pseudomonadota< / td >
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< td align = "center" > Gammaproteobacteria< / td >
< td align = "center" > Enterobacterales< / td >
< td align = "center" > Enterobacteriaceae< / td >
< td align = "center" > Escherichia< / td >
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< td align = "center" > blattae< / td >
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< td align = "center" > < / td >
< td align = "center" > species< / td >
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< td align = "center" > Burgess et al., 1973< / td >
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< td align = "center" > LPSN< / td >
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< td align = "center" > 776056< / td >
< td align = "center" > 515602< / td >
< td align = "center" > 788468< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
2022-12-20 16:22:22 +01:00
< td align = "center" > 1.5< / td >
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< td align = "center" > < / td >
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< / tr >
< tr class = "odd" >
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< td align = "center" > B_ESCHR_COLI< / td >
< td align = "center" > Escherichia coli< / td >
< td align = "center" > accepted< / td >
2022-08-21 16:59:35 +02:00
< td align = "center" > Bacteria< / td >
2022-10-05 12:32:07 +02:00
< td align = "center" > Pseudomonadota< / td >
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< td align = "center" > Gammaproteobacteria< / td >
< td align = "center" > Enterobacterales< / td >
< td align = "center" > Enterobacteriaceae< / td >
< td align = "center" > Escherichia< / td >
2022-10-05 12:32:07 +02:00
< td align = "center" > coli< / td >
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< td align = "center" > < / td >
< td align = "center" > species< / td >
2022-10-05 12:32:07 +02:00
< td align = "center" > Castellani et al., 1919< / td >
2022-08-21 16:59:35 +02:00
< td align = "center" > LPSN< / td >
2022-10-05 12:32:07 +02:00
< td align = "center" > 776057< / td >
< td align = "center" > 515602< / td >
< td align = "center" > < / td >
2022-12-12 00:23:03 +01:00
< td align = "center" > 11286021< / td >
2022-10-05 12:32:07 +02:00
< td align = "center" > 3221780< / td >
< td align = "center" > < / td >
2022-12-19 15:40:05 +01:00
< td align = "center" > 1.0< / td >
2022-10-05 12:32:07 +02:00
< td align = "center" > 1095001000112106, 715307006, 737528008, …< / td >
2022-08-21 16:59:35 +02:00
< / tr >
< tr class = "even" >
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< td align = "center" > B_ESCHR_DYSN< / td >
< td align = "center" > Escherichia dysenteriae< / td >
< td align = "center" > accepted< / td >
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< td align = "center" > Bacteria< / td >
2022-10-05 12:32:07 +02:00
< td align = "center" > Pseudomonadota< / td >
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< td align = "center" > Gammaproteobacteria< / td >
< td align = "center" > Enterobacterales< / td >
< td align = "center" > Enterobacteriaceae< / td >
< td align = "center" > Escherichia< / td >
2022-10-05 12:32:07 +02:00
< td align = "center" > dysenteriae< / td >
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< td align = "center" > < / td >
< td align = "center" > species< / td >
2022-10-05 12:32:07 +02:00
< td align = "center" > < / td >
< td align = "center" > GBIF< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > 10862979< / td >
< td align = "center" > 3221780< / td >
< td align = "center" > < / td >
2022-12-20 16:22:22 +01:00
< td align = "center" > 1.5< / td >
2022-10-05 12:32:07 +02:00
< td align = "center" > < / td >
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< / tr >
< / tbody >
< / table >
< / div >
< / div >
< div class = "section level2" >
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< h2 id = "antibiotics-antibiotic-antifungal-drugs" >
< code > antibiotics< / code > : Antibiotic (+Antifungal) Drugs< a class = "anchor" aria-label = "anchor" href = "#antibiotics-antibiotic-antifungal-drugs" > < / a >
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< / h2 >
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< p > A data set with 483 rows and 14 columns, containing the following
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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 > ,
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< em > iv_ddd< / em > , < em > iv_units< / em > , and < em > loinc< / em > .< / p >
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< p > This data set is in R available as < code > antibiotics< / code > , after
you load the < code > AMR< / code > package.< / p >
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< p > It was last updated on 22 February 2023 13:38:57 UTC. Find more info
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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/antibiotics.rds" class = "external-link" > original
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R Data Structure (RDS) file< / a > (39 kB)< br >
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< / li >
2022-10-29 14:24:08 +02:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.txt" class = "external-link" > tab-separated
2022-10-29 19:07:26 +02:00
text file< / a > (0.1 MB)< br >
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< / li >
2022-10-29 14:24:08 +02:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.xlsx" class = "external-link" > Microsoft
2022-10-30 14:40:31 +01:00
Excel workbook< / a > (66 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/antibiotics.feather" class = "external-link" > Apache
2022-10-30 14:40:31 +01:00
Feather file< / a > (0.1 MB)< br >
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< / li >
2022-10-29 14:24:08 +02:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.parquet" class = "external-link" > Apache
2022-10-30 14:40:31 +01:00
Parquet file< / a > (97 kB)< br >
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< / li >
2022-10-29 14:24:08 +02:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sas" class = "external-link" > SAS
2022-10-30 14:40:31 +01:00
data file< / a > (1.9 MB)< br >
2022-08-26 23:31:20 +02:00
< / li >
2022-10-29 14:24:08 +02:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sav" class = "external-link" > IBM
SPSS Statistics data file< / a > (0.3 MB)< br >
2022-08-26 23:31:20 +02:00
< / li >
2022-10-29 14:24:08 +02:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.dta" class = "external-link" > Stata
2022-10-30 14:40:31 +01:00
DTA file< / a > (0.4 MB)< / li >
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< / ul >
2022-10-29 19:07:26 +02:00
< p > The tab-separated text file and Microsoft Excel workbook, and SAS,
SPSS and Stata files all contain the ATC codes, common abbreviations,
trade names and LOINC codes as comma separated values.< / p >
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< div class = "section level3" >
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< h3 id = "source-1" > Source< a class = "anchor" aria-label = "anchor" href = "#source-1" > < / a >
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< / h3 >
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< 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 >
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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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< li > < a href = "https://whonet.org" class = "external-link" > WHONET software 2019< / a > < / li >
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< li > < a href = "https://loinc.org" class = "external-link" > LOINC (Logical Observation Identifiers
Names and Codes)< / a > < / li >
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< / ul >
< / div >
< div class = "section level3" >
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< h3 id = "example-content-1" > Example content< a class = "anchor" aria-label = "anchor" href = "#example-content-1" > < / a >
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< / h3 >
< table style = "width:100%;" class = "table" >
< colgroup >
< col width = "1%" >
< col width = "2%" >
< col width = "8%" >
< col width = "7%" >
< col width = "7%" >
< col width = "13%" >
< col width = "17%" >
< col width = "6%" >
< col width = "13%" >
< col width = "2%" >
< col width = "3%" >
< col width = "2%" >
< col width = "2%" >
< col width = "9%" >
< / 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 >
< th align = "center" > atc< / th >
< 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 >
< td align = "center" > D06AX12, J01GB06, S01AA21< / td >
< 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 >
< td align = "center" > J01CA04< / td >
< 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 >
< td align = "center" > 1.5< / td >
< td align = "center" > g< / td >
< td align = "center" > 3.0< / td >
< 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 >
< td align = "center" > J01CR02< / td >
< td align = "center" > Beta-lactam antibacterials, penicillins< / td >
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< td align = "center" > Combinations of penicillins, incl.
inhibitors< / td >
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< td align = "center" > a/c, amcl, aml, …< / td >
< td align = "center" > amocla, amoclan, amoclav, …< / td >
< td align = "center" > 1.5< / td >
< 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 >
< td align = "center" > J01CA01, S01AA19< / td >
< 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 >
< td align = "center" > 6.0< / td >
< 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 >
< td align = "center" > J01FA10, S01AA26< / td >
< td align = "center" > Macrolides, lincosamides and streptogramins< / td >
< td align = "center" > Macrolides< / td >
< td align = "center" > az, azi, azit, …< / td >
2022-10-30 14:40:31 +01:00
< td align = "center" > aritromicina, aruzilina, azasite, …< / td >
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< 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" >
< td align = "center" > PEN< / td >
< td align = "center" > 5904< / td >
< td align = "center" > Benzylpenicillin< / td >
< td align = "center" > Beta-lactams/penicillins< / td >
< td align = "center" > J01CE01, S01AA14< / td >
< 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 >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > 3.6< / td >
< td align = "center" > g< / td >
2022-10-30 14:40:31 +01:00
< td align = "center" > < / td >
2022-08-21 16:59:35 +02:00
< / tr >
< / tbody >
< / table >
< / div >
< / div >
< div class = "section level2" >
2022-11-13 08:54:32 +01:00
< h2 id = "antivirals-antiviral-drugs" >
< code > antivirals< / code > : Antiviral Drugs< a class = "anchor" aria-label = "anchor" href = "#antivirals-antiviral-drugs" > < / a >
2022-08-21 16:59:35 +02:00
< / h2 >
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< p > A data set with 120 rows and 11 columns, containing the following
column names:< br > < em > av< / em > , < em > name< / em > , < em > atc< / em > , < em > cid< / em > ,
< em > atc_group< / em > , < em > synonyms< / em > , < em > oral_ddd< / em > ,
2023-02-22 14:47:35 +01:00
< em > oral_units< / em > , < em > iv_ddd< / em > , < em > iv_units< / em > , and
2022-11-13 08:54:32 +01:00
< em > loinc< / em > .< / p >
2022-10-29 14:24:08 +02:00
< p > This data set is in R available as < code > antivirals< / code > , after you
load the < code > AMR< / code > package.< / p >
2022-11-13 08:54:32 +01:00
< p > It was last updated on 13 November 2022 07:46:10 UTC. Find more info
2022-10-29 14:24:08 +02:00
about the structure of this data set < a href = "https://msberends.github.io/AMR/reference/antibiotics.html" > here< / a > .< / p >
2022-08-21 16:59:35 +02:00
< p > < strong > Direct download links:< / strong > < / p >
< ul >
2022-10-29 14:24:08 +02:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.rds" class = "external-link" > original
2022-11-13 08:54:32 +01:00
R Data Structure (RDS) file< / a > (5 kB)< br >
2022-08-26 23:31:20 +02:00
< / li >
2022-10-29 14:24:08 +02:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.txt" class = "external-link" > tab-separated
2022-11-13 08:54:32 +01:00
text file< / a > (16 kB)< br >
2022-08-21 16:59:35 +02:00
< / li >
2022-10-29 14:24:08 +02:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.xlsx" class = "external-link" > Microsoft
2022-11-13 08:54:32 +01:00
Excel workbook< / a > (16 kB)< br >
2022-08-21 16:59:35 +02:00
< / li >
2022-10-29 14:24:08 +02:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.feather" class = "external-link" > Apache
2022-11-13 08:54:32 +01:00
Feather file< / a > (15 kB)< br >
2022-08-21 16:59:35 +02:00
< / li >
2022-10-29 14:24:08 +02:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.parquet" class = "external-link" > Apache
2022-11-13 08:54:32 +01:00
Parquet file< / a > (13 kB)< br >
2022-08-21 16:59:35 +02:00
< / li >
2022-10-29 14:24:08 +02:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sas" class = "external-link" > SAS
2022-11-13 08:54:32 +01:00
data file< / a > (84 kB)< br >
2022-08-21 16:59:35 +02:00
< / li >
2022-10-29 14:24:08 +02:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sav" class = "external-link" > IBM
2022-11-13 08:54:32 +01:00
SPSS Statistics data file< / a > (30 kB)< br >
2022-08-26 23:31:20 +02:00
< / li >
2022-10-29 14:24:08 +02:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.dta" class = "external-link" > Stata
2022-11-13 08:54:32 +01:00
DTA file< / a > (73 kB)< / li >
2022-08-21 16:59:35 +02:00
< / ul >
2022-10-29 19:07:26 +02:00
< p > The tab-separated text file and Microsoft Excel workbook, and SAS,
2022-11-13 08:54:32 +01:00
SPSS and Stata files all contain the trade names and LOINC codes as
comma separated values.< / p >
2022-08-21 16:59:35 +02:00
< div class = "section level3" >
2022-10-05 12:32:07 +02:00
< h3 id = "source-2" > Source< a class = "anchor" aria-label = "anchor" href = "#source-2" > < / a >
2022-08-21 16:59:35 +02:00
< / h3 >
2022-10-29 14:24:08 +02:00
< 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 >
2022-08-21 16:59:35 +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 >
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< li > < a href = "https://loinc.org" class = "external-link" > LOINC (Logical Observation Identifiers
Names and Codes)< / a > < / li >
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< / ul >
< / div >
< div class = "section level3" >
2022-10-05 12:32:07 +02:00
< h3 id = "example-content-2" > Example content< a class = "anchor" aria-label = "anchor" href = "#example-content-2" > < / a >
2022-08-21 16:59:35 +02:00
< / h3 >
< table class = "table" >
< colgroup >
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< col width = "2%" >
< col width = "8%" >
< col width = "3%" >
< col width = "4%" >
< col width = "28%" >
< col width = "23%" >
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< col width = "4%" >
< col width = "4%" >
< col width = "3%" >
< col width = "4%" >
2022-11-13 08:54:32 +01:00
< col width = "13%" >
2022-08-21 16:59:35 +02:00
< / colgroup >
< thead > < tr class = "header" >
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< th align = "center" > av< / th >
< th align = "center" > name< / th >
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< th align = "center" > atc< / th >
< th align = "center" > cid< / 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 >
2022-11-13 08:54:32 +01:00
< th align = "center" > loinc< / th >
2022-08-21 16:59:35 +02:00
< / tr > < / thead >
< tbody >
< tr class = "odd" >
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< td align = "center" > ABA< / td >
< td align = "center" > Abacavir< / td >
2022-08-21 16:59:35 +02:00
< td align = "center" > J05AF06< / td >
< td align = "center" > 441300< / td >
2022-10-29 14:24:08 +02:00
< td align = "center" > Nucleoside and nucleotide reverse transcriptase
inhibitors< / td >
2022-11-13 08:54:32 +01:00
< td align = "center" > abacavir sulfate, avacavir, ziagen< / td >
2022-08-21 16:59:35 +02:00
< td align = "center" > 0.6< / td >
< td align = "center" > g< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
2022-11-13 08:54:32 +01:00
< td align = "center" > 29113-8, 78772-1, 78773-9, …< / td >
2022-08-21 16:59:35 +02:00
< / tr >
< tr class = "even" >
2022-11-13 08:54:32 +01:00
< td align = "center" > ACI< / td >
< td align = "center" > Aciclovir< / td >
2022-08-21 16:59:35 +02:00
< td align = "center" > J05AB01< / td >
< td align = "center" > 135398513< / td >
2022-10-29 14:24:08 +02:00
< td align = "center" > Nucleosides and nucleotides excl. reverse
transcriptase inhibitors< / td >
2022-11-13 08:54:32 +01:00
< td align = "center" > acicloftal, aciclovier, aciclovirum, …< / td >
2022-08-21 16:59:35 +02:00
< td align = "center" > 4.0< / td >
< td align = "center" > g< / td >
< td align = "center" > 4< / td >
< td align = "center" > g< / td >
2022-11-13 08:54:32 +01:00
< td align = "center" > < / td >
2022-08-21 16:59:35 +02:00
< / tr >
< tr class = "odd" >
2022-11-13 08:54:32 +01:00
< td align = "center" > ADD< / td >
< td align = "center" > Adefovir dipivoxil< / td >
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< td align = "center" > J05AF08< / td >
< td align = "center" > 60871< / td >
2022-10-29 14:24:08 +02:00
< td align = "center" > Nucleoside and nucleotide reverse transcriptase
inhibitors< / td >
2022-11-13 08:54:32 +01:00
< td align = "center" > adefovir di, adefovir di ester, adefovir dipivoxyl,
…< / td >
2022-08-21 16:59:35 +02:00
< td align = "center" > 10.0< / td >
< td align = "center" > mg< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
2022-11-13 08:54:32 +01:00
< td align = "center" > < / td >
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< / tr >
< tr class = "even" >
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< td align = "center" > AME< / td >
< td align = "center" > Amenamevir< / td >
< td align = "center" > J05AX26< / td >
< td align = "center" > 11397521< / td >
< td align = "center" > Other antivirals< / td >
< td align = "center" > amenalief< / td >
< td align = "center" > 0.4< / td >
< td align = "center" > g< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< / tr >
< tr class = "odd" >
< td align = "center" > AMP< / td >
< td align = "center" > Amprenavir< / td >
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< td align = "center" > J05AE05< / td >
< td align = "center" > 65016< / td >
< td align = "center" > Protease inhibitors< / td >
2022-11-13 08:54:32 +01:00
< td align = "center" > agenerase, carbamate, prozei< / td >
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< td align = "center" > 1.2< / td >
< td align = "center" > g< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
2022-11-13 08:54:32 +01:00
< td align = "center" > 29114-6, 31028-4, 78791-1< / td >
2022-08-21 16:59:35 +02:00
< / tr >
2022-11-13 08:54:32 +01:00
< tr class = "even" >
< td align = "center" > ASU< / td >
< td align = "center" > Asunaprevir< / td >
2022-08-21 16:59:35 +02:00
< td align = "center" > J05AP06< / td >
< td align = "center" > 16076883< / td >
< td align = "center" > Antivirals for treatment of HCV infections< / td >
2022-11-13 08:54:32 +01:00
< td align = "center" > sunvepra, sunvepratrade< / td >
< td align = "center" > 0.2< / td >
2022-08-21 16:59:35 +02:00
< td align = "center" > g< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
2022-11-13 08:54:32 +01:00
< td align = "center" > < / td >
2022-08-21 16:59:35 +02:00
< / tr >
< / tbody >
< / table >
< / div >
< / div >
< div class = "section level2" >
2023-01-21 23:53:21 +01:00
< h2 id = "clinical_breakpoints-interpretation-from-mic-values-disk-diameters-to-sir" >
< code > clinical_breakpoints< / code > : Interpretation from MIC values
& disk diameters to SIR< a class = "anchor" aria-label = "anchor" href = "#clinical_breakpoints-interpretation-from-mic-values-disk-diameters-to-sir" > < / a >
2022-08-21 16:59:35 +02:00
< / h2 >
2023-02-10 16:26:36 +01:00
< p > A data set with 18 308 rows and 11 columns, containing the following
2022-10-29 14:24:08 +02:00
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 > ,
2023-02-22 14:47:35 +01:00
< em > breakpoint_S< / em > , < em > breakpoint_R< / em > , and < em > uti< / em > .< / p >
2023-01-21 23:53:21 +01:00
< p > This data set is in R available as < code > clinical_breakpoints< / code > ,
2022-10-29 14:24:08 +02:00
after you load the < code > AMR< / code > package.< / p >
2023-01-21 23:53:21 +01:00
< p > It was last updated on 21 January 2023 22:47:20 UTC. Find more info
about the structure of this data set < a href = "https://msberends.github.io/AMR/reference/clinical_breakpoints.html" > here< / a > .< / p >
2022-08-21 16:59:35 +02:00
< p > < strong > Direct download links:< / strong > < / p >
< ul >
2023-01-21 23:53:21 +01:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.rds" class = "external-link" > original
2022-10-29 14:24:08 +02:00
R Data Structure (RDS) file< / a > (42 kB)< br >
2022-08-26 23:31:20 +02:00
< / li >
2023-01-21 23:53:21 +01:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.txt" class = "external-link" > tab-separated
2022-10-29 14:24:08 +02:00
text file< / a > (1.9 MB)< br >
2022-08-21 16:59:35 +02:00
< / li >
2023-01-21 23:53:21 +01:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.xlsx" class = "external-link" > Microsoft
2022-10-29 14:24:08 +02:00
Excel workbook< / a > (0.8 MB)< br >
2022-08-21 16:59:35 +02:00
< / li >
2023-01-21 23:53:21 +01:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.feather" class = "external-link" > Apache
2022-10-29 14:24:08 +02:00
Feather file< / a > (0.7 MB)< br >
2022-08-21 16:59:35 +02:00
< / li >
2023-01-21 23:53:21 +01:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.parquet" class = "external-link" > Apache
2022-10-29 14:24:08 +02:00
Parquet file< / a > (87 kB)< br >
2022-08-21 16:59:35 +02:00
< / li >
2023-01-21 23:53:21 +01:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.sas" class = "external-link" > SAS
2022-10-29 14:24:08 +02:00
data file< / a > (3.6 MB)< br >
2022-08-21 16:59:35 +02:00
< / li >
2023-01-21 23:53:21 +01:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.sav" class = "external-link" > IBM
2022-10-29 14:24:08 +02:00
SPSS Statistics data file< / a > (2.3 MB)< br >
2022-08-26 23:31:20 +02:00
< / li >
2023-01-21 23:53:21 +01:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.dta" class = "external-link" > Stata
2022-10-29 14:24:08 +02:00
DTA file< / a > (3.4 MB)< / li >
2022-08-21 16:59:35 +02:00
< / ul >
< div class = "section level3" >
2022-10-05 12:32:07 +02:00
< h3 id = "source-3" > Source< a class = "anchor" aria-label = "anchor" href = "#source-3" > < / a >
2022-08-21 16:59:35 +02:00
< / h3 >
2022-10-29 14:24:08 +02:00
< p > This data set contains interpretation rules for MIC values and disk
diffusion diameters. Included guidelines are CLSI (2013-2022) and EUCAST
(2013-2022).< / p >
2022-08-21 16:59:35 +02:00
< / div >
< div class = "section level3" >
2022-10-05 12:32:07 +02:00
< h3 id = "example-content-3" > Example content< a class = "anchor" aria-label = "anchor" href = "#example-content-3" > < / a >
2022-08-21 16:59:35 +02:00
< / h3 >
< table style = "width:100%;" class = "table" >
< colgroup >
< col width = "8%" >
< col width = "5%" >
< col width = "3%" >
< col width = "8%" >
< col width = "14%" >
< col width = "7%" >
< col width = "3%" >
< col width = "10%" >
< col width = "8%" >
< col width = "7%" >
< col width = "8%" >
< col width = "8%" >
< col width = "4%" >
< / 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 >
< th align = "center" > mo_name< / th >
< th align = "center" > rank_index< / th >
< th align = "center" > ab< / th >
< th align = "center" > ab_name< / 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" >
< td align = "center" > EUCAST 2022< / td >
< td align = "center" > MIC< / td >
< td align = "center" > < / td >
< td align = "center" > F_ASPRG_MGTS< / td >
< td align = "center" > Aspergillus fumigatus< / td >
< td align = "center" > 2< / td >
< td align = "center" > AMB< / td >
< td align = "center" > Amphotericin B< / td >
< td align = "center" > Aspergillus< / td >
< td align = "center" > < / td >
< td align = "center" > 1< / td >
< td align = "center" > 1< / td >
< td align = "center" > FALSE< / td >
< / tr >
< tr class = "even" >
< td align = "center" > EUCAST 2022< / td >
< td align = "center" > MIC< / td >
< td align = "center" > < / td >
< td align = "center" > F_ASPRG_NIGR< / td >
< td align = "center" > Aspergillus niger< / td >
< td align = "center" > 2< / td >
< td align = "center" > AMB< / td >
< td align = "center" > Amphotericin B< / td >
< td align = "center" > Aspergillus< / td >
< td align = "center" > < / td >
< td align = "center" > 1< / td >
< td align = "center" > 1< / td >
< td align = "center" > FALSE< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > EUCAST 2022< / td >
< td align = "center" > MIC< / td >
< td align = "center" > < / td >
2022-10-22 22:10:04 +02:00
< td align = "center" > F_CANDD_ALBC< / td >
< td align = "center" > Candida albicans< / td >
< td align = "center" > 2< / td >
2022-08-21 16:59:35 +02:00
< td align = "center" > AMB< / td >
< td align = "center" > Amphotericin B< / td >
< td align = "center" > Candida< / td >
< td align = "center" > < / td >
< td align = "center" > 1< / td >
< td align = "center" > 1< / td >
< td align = "center" > FALSE< / td >
< / tr >
< tr class = "even" >
< td align = "center" > EUCAST 2022< / td >
< td align = "center" > MIC< / td >
< td align = "center" > < / td >
2022-10-22 22:10:04 +02:00
< td align = "center" > F_CANDD_DBLN< / td >
< td align = "center" > Candida dubliniensis< / td >
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< td align = "center" > 2< / td >
< td align = "center" > AMB< / td >
< td align = "center" > Amphotericin B< / td >
< td align = "center" > Candida< / td >
< td align = "center" > < / td >
< td align = "center" > 1< / td >
< td align = "center" > 1< / td >
< td align = "center" > FALSE< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > EUCAST 2022< / td >
< td align = "center" > MIC< / td >
< td align = "center" > < / td >
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< td align = "center" > F_CANDD_GLBR< / td >
< td align = "center" > Candida glabrata< / td >
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< td align = "center" > 2< / td >
< td align = "center" > AMB< / td >
< td align = "center" > Amphotericin B< / td >
< td align = "center" > Candida< / td >
< td align = "center" > < / td >
< td align = "center" > 1< / td >
< td align = "center" > 1< / td >
< td align = "center" > FALSE< / td >
< / tr >
< tr class = "even" >
< td align = "center" > EUCAST 2022< / td >
< td align = "center" > MIC< / td >
< td align = "center" > < / td >
< td align = "center" > F_CANDD_KRUS< / td >
< td align = "center" > Candida krusei< / td >
< td align = "center" > 2< / td >
< td align = "center" > AMB< / td >
< td align = "center" > Amphotericin B< / td >
< td align = "center" > Candida< / td >
< td align = "center" > < / td >
< td align = "center" > 1< / td >
< td align = "center" > 1< / td >
< td align = "center" > FALSE< / td >
< / tr >
< / tbody >
< / table >
< / div >
< / div >
< div class = "section level2" >
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< h2 id = "intrinsic_resistant-intrinsic-bacterial-resistance" >
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< code > intrinsic_resistant< / code > : Intrinsic Bacterial
Resistance< a class = "anchor" aria-label = "anchor" href = "#intrinsic_resistant-intrinsic-bacterial-resistance" > < / a >
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< / h2 >
2023-02-10 16:26:36 +01:00
< p > A data set with 134 634 rows and 2 columns, containing the following
2022-10-29 14:24:08 +02:00
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 >
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< p > It was last updated on 16 December 2022 15:10:43 UTC. Find more info
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about the structure of this data set < a href = "https://msberends.github.io/AMR/reference/intrinsic_resistant.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/intrinsic_resistant.rds" class = "external-link" > original
2022-12-16 16:17:49 +01:00
R Data Structure (RDS) file< / a > (78 kB)< br >
2022-08-26 23:31:20 +02:00
< / li >
2022-10-29 14:24:08 +02:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.txt" class = "external-link" > tab-separated
2022-12-16 16:17:49 +01:00
text file< / a > (5.1 MB)< br >
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< / li >
2022-10-29 14:24:08 +02:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.xlsx" class = "external-link" > Microsoft
2022-12-16 16:17:49 +01:00
Excel workbook< / a > (1.3 MB)< br >
2022-08-21 16:59:35 +02:00
< / li >
2022-10-29 14:24:08 +02:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.feather" class = "external-link" > Apache
2022-12-16 16:17:49 +01:00
Feather file< / a > (1.2 MB)< br >
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< / li >
2022-10-29 14:24:08 +02:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.parquet" class = "external-link" > Apache
2022-12-16 16:17:49 +01:00
Parquet file< / a > (0.2 MB)< br >
2022-08-21 16:59:35 +02:00
< / li >
2022-10-29 14:24:08 +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
2022-12-16 16:17:49 +01:00
data file< / a > (9.8 MB)< br >
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< / li >
2022-10-29 14:24:08 +02:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sav" class = "external-link" > IBM
2022-12-16 16:17:49 +01:00
SPSS Statistics data file< / a > (7.4 MB)< br >
2022-08-26 23:31:20 +02:00
< / li >
2022-10-29 14:24:08 +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
2022-12-16 16:17:49 +01:00
DTA file< / a > (9.5 MB)< / li >
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< / ul >
< div class = "section level3" >
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< h3 id = "source-4" > Source< a class = "anchor" aria-label = "anchor" href = "#source-4" > < / a >
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< / h3 >
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< p > This data set contains all defined intrinsic resistance by EUCAST of
all bug-drug combinations, and is based on < a href = "https://www.eucast.org/expert_rules_and_expected_phenotypes/" class = "external-link" > ‘
Expert Rules’ ‘ ’
v3.3< / a > (2021).< / p >
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< / div >
< div class = "section level3" >
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< h3 id = "example-content-4" > Example content< a class = "anchor" aria-label = "anchor" href = "#example-content-4" > < / a >
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< / h3 >
< p > Example rows when filtering on < em > Enterobacter cloacae< / em > :< / p >
< table class = "table" >
< thead > < tr class = "header" >
< th align = "center" > microorganism< / th >
< th align = "center" > antibiotic< / th >
< / tr > < / thead >
< tbody >
< tr class = "odd" >
< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Acetylmidecamycin< / td >
< / tr >
< tr class = "even" >
< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Acetylspiramycin< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Amoxicillin< / td >
< / tr >
< tr class = "even" >
< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Amoxicillin/clavulanic acid< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Ampicillin< / td >
< / tr >
< tr class = "even" >
< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Ampicillin/sulbactam< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Avoparcin< / td >
< / tr >
< tr class = "even" >
< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Azithromycin< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Benzylpenicillin< / td >
< / 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 >
< td align = "center" > Cefadroxil< / td >
< / tr >
< tr class = "even" >
< td align = "center" > Enterobacter cloacae< / td >
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< td align = "center" > Cefalexin< / td >
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< / tr >
< tr class = "odd" >
< td align = "center" > Enterobacter cloacae< / td >
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< td align = "center" > Cefalotin< / td >
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< / tr >
< tr class = "even" >
< td align = "center" > Enterobacter cloacae< / td >
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< td align = "center" > Cefazolin< / td >
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< / tr >
< tr class = "odd" >
< td align = "center" > Enterobacter cloacae< / td >
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< td align = "center" > Cefoxitin< / td >
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< / tr >
< tr class = "even" >
< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Clarithromycin< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Clindamycin< / td >
< / tr >
< tr class = "even" >
< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Cycloserine< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Dalbavancin< / td >
< / tr >
< tr class = "even" >
< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Dirithromycin< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Erythromycin< / td >
< / tr >
< tr class = "even" >
< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Flurithromycin< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Fusidic acid< / td >
< / tr >
< tr class = "even" >
< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Gamithromycin< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Josamycin< / td >
< / tr >
< tr class = "even" >
< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Kitasamycin< / td >
< / tr >
< 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 >
< td align = "center" > Meleumycin< / td >
< / tr >
< tr class = "even" >
< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Midecamycin< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Miocamycin< / td >
< / tr >
< tr class = "even" >
< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Nafithromycin< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Norvancomycin< / td >
< / tr >
< tr class = "even" >
< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Oleandomycin< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Oritavancin< / td >
< / tr >
< tr class = "even" >
< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Pirlimycin< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Primycin< / td >
< / tr >
< tr class = "even" >
< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Pristinamycin< / td >
< / 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 >
< td align = "center" > Ramoplanin< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Rifampicin< / td >
< / tr >
< tr class = "even" >
< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Rokitamycin< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Roxithromycin< / td >
< / tr >
< tr class = "even" >
< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Solithromycin< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Spiramycin< / td >
< / tr >
< tr class = "even" >
< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Tedizolid< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Teicoplanin< / td >
< / tr >
< tr class = "even" >
< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Telavancin< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Telithromycin< / td >
< / tr >
< tr class = "even" >
< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Thiacetazone< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Tildipirosin< / td >
< / tr >
< tr class = "even" >
< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Tilmicosin< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > Enterobacter cloacae< / td >
< td align = "center" > Troleandomycin< / td >
< / tr >
< tr class = "even" >
< td align = "center" > Enterobacter cloacae< / td >
< 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 >
< td align = "center" > Vancomycin< / td >
< / tr >
< / tbody >
< / table >
< / div >
< / div >
< div class = "section level2" >
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< h2 id = "dosage-dosage-guidelines-from-eucast" >
< code > dosage< / code > : Dosage Guidelines from EUCAST< a class = "anchor" aria-label = "anchor" href = "#dosage-dosage-guidelines-from-eucast" > < / a >
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< / h2 >
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< p > A data set with 336 rows and 9 columns, containing the following
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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 > ,
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< em > original_txt< / em > , and < em > eucast_version< / em > .< / p >
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< p > This data set is in R available as < code > dosage< / code > , after you
load the < code > AMR< / code > package.< / p >
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< p > It was last updated on 14 November 2022 14:20:39 UTC. Find more info
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about the structure of this data set < a href = "https://msberends.github.io/AMR/reference/dosage.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/dosage.rds" class = "external-link" > original
R Data Structure (RDS) file< / a > (3 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/dosage.txt" class = "external-link" > tab-separated
2022-11-14 15:27:45 +01:00
text file< / a > (29 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/dosage.xlsx" class = "external-link" > Microsoft
2022-11-14 15:27:45 +01:00
Excel workbook< / a > (19 kB)< br >
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< / li >
2022-10-29 14:24:08 +02:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.feather" class = "external-link" > Apache
2022-11-14 15:27:45 +01:00
Feather file< / a > (16 kB)< br >
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< / li >
2022-10-29 14:24:08 +02:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.parquet" class = "external-link" > Apache
2022-11-14 15:27:45 +01:00
Parquet file< / a > (8 kB)< br >
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< / li >
2022-10-29 14:24:08 +02:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sas" class = "external-link" > SAS
2022-11-14 15:27:45 +01:00
data file< / a > (92 kB)< br >
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< / li >
2022-10-29 14:24:08 +02:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sav" class = "external-link" > IBM
2022-11-14 15:27:45 +01:00
SPSS Statistics data file< / a > (43 kB)< br >
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< / li >
2022-10-29 14:24:08 +02:00
< li > Download as < a href = "https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.dta" class = "external-link" > Stata
2022-11-14 15:27:45 +01:00
DTA file< / a > (82 kB)< / li >
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< / ul >
< div class = "section level3" >
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< h3 id = "source-5" > Source< a class = "anchor" aria-label = "anchor" href = "#source-5" > < / a >
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< / h3 >
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< 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" > ‘
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Breakpoint Tables’ < / a > (2021) and < a href = "https://www.eucast.org/clinical_breakpoints/" class = "external-link" > ‘
Breakpoint Tables’ < / a > (2022).< / p >
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< / div >
< div class = "section level3" >
2022-10-05 12:32:07 +02:00
< h3 id = "example-content-5" > Example content< a class = "anchor" aria-label = "anchor" href = "#example-content-5" > < / a >
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< / h3 >
< table class = "table" >
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< 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 >
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< 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 >
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< td align = "center" > 12< / td >
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< / 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 >
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< td align = "center" > 12< / td >
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< / 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 >
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< td align = "center" > 12< / td >
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< / 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 >
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< td align = "center" > 12< / td >
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< / 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 >
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< td align = "center" > 12< / td >
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< / 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 >
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< td align = "center" > 12< / td >
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< / tr >
< / tbody >
< / table >
< / div >
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< / div >
< div class = "section level2" >
< h2 id = "example_isolates-example-data-for-practice" >
< code > example_isolates< / code > : Example Data for Practice< a class = "anchor" aria-label = "anchor" href = "#example_isolates-example-data-for-practice" > < / a >
< / h2 >
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< p > A data set with 2 000 rows and 46 columns, containing the following
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column names:< br > < em > date< / em > , < em > patient< / em > , < em > age< / em > , < em > gender< / em > ,
< em > ward< / em > , < em > mo< / em > , < em > PEN< / em > , < em > OXA< / em > , < em > FLC< / em > ,
< em > AMX< / em > , < em > AMC< / em > , < em > AMP< / em > , < em > TZP< / em > , < em > CZO< / em > ,
< em > FEP< / em > , < em > CXM< / em > , < em > FOX< / em > , < em > CTX< / em > , < em > CAZ< / em > ,
< em > CRO< / em > , < em > GEN< / em > , < em > TOB< / em > , < em > AMK< / em > , < em > KAN< / em > ,
< em > TMP< / em > , < em > SXT< / em > , < em > NIT< / em > , < em > FOS< / em > , < em > LNZ< / em > ,
< em > CIP< / em > , < em > MFX< / em > , < em > VAN< / em > , < em > TEC< / em > , < em > TCY< / em > ,
< em > TGC< / em > , < em > DOX< / em > , < em > ERY< / em > , < em > CLI< / em > , < em > AZM< / em > ,
< em > IPM< / em > , < em > MEM< / em > , < em > MTR< / em > , < em > CHL< / em > , < em > COL< / em > ,
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< em > MUP< / em > , and < em > RIF< / em > .< / p >
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< p > This data set is in R available as < code > example_isolates< / code > ,
after you load the < code > AMR< / code > package.< / p >
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< p > It was last updated on 21 January 2023 22:47:20 UTC. Find more info
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about the structure of this data set < a href = "https://msberends.github.io/AMR/reference/example_isolates.html" > here< / a > .< / p >
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< div class = "section level3" >
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< h3 id = "source-6" > Source< a class = "anchor" aria-label = "anchor" href = "#source-6" > < / a >
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< / h3 >
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< p > This data set contains randomised fictitious data, but reflects
reality and can be used to practise AMR data analysis.< / p >
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< / div >
< div class = "section level3" >
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< h3 id = "example-content-6" > Example content< a class = "anchor" aria-label = "anchor" href = "#example-content-6" > < / a >
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< / h3 >
< table class = "table" >
< colgroup >
< col width = "4%" >
< col width = "3%" >
< col width = "1%" >
< col width = "3%" >
< col width = "3%" >
< col width = "5%" >
< col width = "1%" >
< col width = "1%" >
< col width = "1%" >
< col width = "1%" >
< col width = "1%" >
< col width = "1%" >
< col width = "1%" >
< col width = "1%" >
< col width = "1%" >
< col width = "1%" >
< col width = "1%" >
< col width = "1%" >
< col width = "1%" >
< col width = "1%" >
< col width = "1%" >
< col width = "1%" >
< col width = "1%" >
< col width = "1%" >
< col width = "1%" >
< col width = "1%" >
< col width = "1%" >
< col width = "1%" >
< col width = "1%" >
< col width = "1%" >
< col width = "1%" >
< col width = "1%" >
< col width = "1%" >
< col width = "1%" >
< col width = "1%" >
< col width = "1%" >
< col width = "1%" >
< col width = "1%" >
< col width = "1%" >
< col width = "1%" >
< col width = "1%" >
< col width = "1%" >
< col width = "1%" >
< col width = "1%" >
< col width = "1%" >
< col width = "1%" >
< / colgroup >
< thead > < tr class = "header" >
< th align = "center" > date< / th >
< th align = "center" > patient< / th >
< th align = "center" > age< / th >
< th align = "center" > gender< / th >
< th align = "center" > ward< / th >
< th align = "center" > mo< / th >
< th align = "center" > PEN< / th >
< th align = "center" > OXA< / th >
< th align = "center" > FLC< / th >
< th align = "center" > AMX< / th >
< th align = "center" > AMC< / th >
< th align = "center" > AMP< / th >
< th align = "center" > TZP< / th >
< th align = "center" > CZO< / th >
< th align = "center" > FEP< / th >
< th align = "center" > CXM< / th >
< th align = "center" > FOX< / th >
< th align = "center" > CTX< / th >
< th align = "center" > CAZ< / th >
< th align = "center" > CRO< / th >
< th align = "center" > GEN< / th >
< th align = "center" > TOB< / th >
< th align = "center" > AMK< / th >
< th align = "center" > KAN< / th >
< th align = "center" > TMP< / th >
< th align = "center" > SXT< / th >
< th align = "center" > NIT< / th >
< th align = "center" > FOS< / th >
< th align = "center" > LNZ< / th >
< th align = "center" > CIP< / th >
< th align = "center" > MFX< / th >
< th align = "center" > VAN< / th >
< th align = "center" > TEC< / th >
< th align = "center" > TCY< / th >
< th align = "center" > TGC< / th >
< th align = "center" > DOX< / th >
< th align = "center" > ERY< / th >
< th align = "center" > CLI< / th >
< th align = "center" > AZM< / th >
< th align = "center" > IPM< / th >
< th align = "center" > MEM< / th >
< th align = "center" > MTR< / th >
< th align = "center" > CHL< / th >
< th align = "center" > COL< / th >
< th align = "center" > MUP< / th >
< th align = "center" > RIF< / th >
< / tr > < / thead >
< tbody >
< tr class = "odd" >
< td align = "center" > 2002-01-02< / td >
< td align = "center" > A77334< / td >
< td align = "center" > 65< / td >
< td align = "center" > F< / td >
< td align = "center" > Clinical< / td >
< td align = "center" > B_ESCHR_COLI< / td >
< td align = "center" > R< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > I< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > I< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > R< / td >
< td align = "center" > R< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > R< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > R< / td >
< td align = "center" > R< / td >
< td align = "center" > R< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > R< / td >
< td align = "center" > R< / td >
< td align = "center" > R< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > R< / td >
< / tr >
< tr class = "even" >
< td align = "center" > 2002-01-03< / td >
< td align = "center" > A77334< / td >
< td align = "center" > 65< / td >
< td align = "center" > F< / td >
< td align = "center" > Clinical< / td >
< td align = "center" > B_ESCHR_COLI< / td >
< td align = "center" > R< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > I< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > I< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > R< / td >
< td align = "center" > R< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > R< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > R< / td >
< td align = "center" > R< / td >
< td align = "center" > R< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > R< / td >
< td align = "center" > R< / td >
< td align = "center" > R< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > R< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > 2002-01-07< / td >
< td align = "center" > 067927< / td >
< td align = "center" > 45< / td >
< td align = "center" > F< / td >
< td align = "center" > ICU< / td >
< td align = "center" > B_STPHY_EPDR< / td >
< td align = "center" > R< / td >
< td align = "center" > < / td >
< td align = "center" > R< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > R< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > R< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > S< / td >
< td align = "center" > < / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > R< / td >
< td align = "center" > < / td >
< td align = "center" > R< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > R< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< / tr >
< tr class = "even" >
< td align = "center" > 2002-01-07< / td >
< td align = "center" > 067927< / td >
< td align = "center" > 45< / td >
< td align = "center" > F< / td >
< td align = "center" > ICU< / td >
< td align = "center" > B_STPHY_EPDR< / td >
< td align = "center" > R< / td >
< td align = "center" > < / td >
< td align = "center" > R< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > R< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > R< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > S< / td >
< td align = "center" > < / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > R< / td >
< td align = "center" > < / td >
< td align = "center" > R< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > R< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< / tr >
< tr class = "odd" >
< td align = "center" > 2002-01-13< / td >
< td align = "center" > 067927< / td >
< td align = "center" > 45< / td >
< td align = "center" > F< / td >
< td align = "center" > ICU< / td >
< td align = "center" > B_STPHY_EPDR< / td >
< td align = "center" > R< / td >
< td align = "center" > < / td >
< td align = "center" > R< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > R< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > R< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > R< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > S< / td >
< td align = "center" > < / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > R< / td >
< td align = "center" > < / td >
< td align = "center" > R< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > R< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< / tr >
< tr class = "even" >
< td align = "center" > 2002-01-13< / td >
< td align = "center" > 067927< / td >
< td align = "center" > 45< / td >
< td align = "center" > F< / td >
< td align = "center" > ICU< / td >
< td align = "center" > B_STPHY_EPDR< / td >
< td align = "center" > R< / td >
< td align = "center" > < / td >
< td align = "center" > R< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > R< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > R< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > R< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > S< / td >
< td align = "center" > < / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > R< / td >
< td align = "center" > R< / td >
< td align = "center" > R< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< td align = "center" > R< / td >
< td align = "center" > < / td >
< td align = "center" > < / td >
< / tr >
< / tbody >
< / table >
< / div >
< / div >
< div class = "section level2" >
< h2 id = "example_isolates_unclean-example-data-for-practice" >
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< code > example_isolates_unclean< / code > : Example Data for
Practice< a class = "anchor" aria-label = "anchor" href = "#example_isolates_unclean-example-data-for-practice" > < / a >
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< / h2 >
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< p > A data set with 3 000 rows and 8 columns, containing the following
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column names:< br > < em > patient_id< / em > , < em > hospital< / em > , < em > date< / em > ,
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< em > bacteria< / em > , < em > AMX< / em > , < em > AMC< / em > , < em > CIP< / em > , and
2022-10-29 14:24:08 +02:00
< em > GEN< / em > .< / p >
< p > This data set is in R available as
< code > example_isolates_unclean< / code > , after you load the
< code > AMR< / code > package.< / p >
2022-11-12 12:17:17 +01:00
< p > It was last updated on 27 August 2022 18:49:37 UTC. Find more info
2022-10-29 14:24:08 +02:00
about the structure of this data set < a href = "https://msberends.github.io/AMR/reference/example_isolates_unclean.html" > here< / a > .< / p >
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< div class = "section level3" >
2022-10-05 12:32:07 +02:00
< h3 id = "source-7" > Source< a class = "anchor" aria-label = "anchor" href = "#source-7" > < / a >
2022-08-28 22:45:38 +02:00
< / h3 >
2022-10-29 14:24:08 +02:00
< p > This data set contains randomised fictitious data, but reflects
reality and can be used to practise AMR data analysis.< / p >
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< / div >
< div class = "section level3" >
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< h3 id = "example-content-7" > Example content< a class = "anchor" aria-label = "anchor" href = "#example-content-7" > < / a >
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< / h3 >
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< table style = "width:100%;" class = "table" >
< colgroup >
< col width = "17%" >
< col width = "14%" >
< col width = "17%" >
< col width = "21%" >
< col width = "7%" >
< col width = "7%" >
< col width = "7%" >
< col width = "7%" >
< / colgroup >
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< thead > < tr class = "header" >
< th align = "center" > patient_id< / th >
< th align = "center" > hospital< / th >
< th align = "center" > date< / th >
< th align = "center" > bacteria< / th >
< th align = "center" > AMX< / th >
< th align = "center" > AMC< / th >
< th align = "center" > CIP< / th >
< th align = "center" > GEN< / th >
< / tr > < / thead >
< tbody >
< tr class = "odd" >
< td align = "center" > J3< / td >
< td align = "center" > A< / td >
< td align = "center" > 2012-11-21< / td >
< td align = "center" > E. coli< / td >
< td align = "center" > R< / td >
< td align = "center" > I< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< / tr >
< tr class = "even" >
< td align = "center" > R7< / td >
< td align = "center" > A< / td >
< td align = "center" > 2018-04-03< / td >
< td align = "center" > K. pneumoniae< / td >
< td align = "center" > R< / td >
< td align = "center" > I< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > P3< / td >
< td align = "center" > A< / td >
< td align = "center" > 2014-09-19< / td >
< td align = "center" > E. coli< / td >
< td align = "center" > R< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< / tr >
< tr class = "even" >
< td align = "center" > P10< / td >
< td align = "center" > A< / td >
< td align = "center" > 2015-12-10< / td >
< td align = "center" > E. coli< / td >
< td align = "center" > S< / td >
< td align = "center" > I< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > B7< / td >
< td align = "center" > A< / td >
< td align = "center" > 2015-03-02< / td >
< td align = "center" > E. coli< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< / tr >
< tr class = "even" >
< td align = "center" > W3< / td >
< td align = "center" > A< / td >
< td align = "center" > 2018-03-31< / td >
< td align = "center" > S. aureus< / td >
< td align = "center" > R< / td >
< td align = "center" > S< / td >
< td align = "center" > R< / td >
< td align = "center" > S< / td >
< / tr >
< / tbody >
< / table >
< / div >
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< / div >
< / main > < aside class = "col-md-3" > < nav id = "toc" > < h2 > On this page< / h2 >
< / nav > < / aside >
< / div >
< footer > < div class = "pkgdown-footer-left" >
< p > < / p >
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< p > < code > AMR< / code > (for R). Free and open-source, licenced under the < a target = "_blank" href = "https://github.com/msberends/AMR/blob/main/LICENSE" class = "external-link" > GNU General Public License version 2.0 (GPL-2)< / a > .< br > Developed at the < a target = "_blank" href = "https://www.rug.nl" class = "external-link" > University of Groningen< / a > and < a target = "_blank" href = "https://www.umcg.nl" class = "external-link" > University Medical Center Groningen< / a > in The Netherlands.< / p >
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< / div >
< div class = "pkgdown-footer-right" >
< p > < / p >
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< p > < a target = "_blank" href = "https://www.rug.nl" class = "external-link" > < img src = "https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_rug.svg" style = "max-width: 150px;" > < / a > < a target = "_blank" href = "https://www.umcg.nl" class = "external-link" > < img src = "https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_umcg.svg" style = "max-width: 150px;" > < / a > < / p >
2022-08-21 16:59:35 +02:00
< / div >
< / footer >
< / div >
< / body >
< / html >
