-
-Used in 175 countries
Since its first public
-release in early 2018, this R package has been used in almost all
-countries in the world. Click the map to enlarge and to see the country
-names.
+ Used in 175 countries
Since its first public release in early 2018, this R package has been used in almost all countries in the world. Click the map to enlarge and to see the country names.
Data sets for download / own use
-08 April 2022
+09 May 2022
Source:vignettes/datasets.Rmd
datasets.RmdSource
This data set contains all defined intrinsic resistance by EUCAST of -all bug-drug combinations, and is based on ‘EUCAST +all bug-drug combinations, and is based on ‘EUCAST Expert Rules’ and ‘EUCAST Intrinsic Resistance and Unusual Phenotypes’ v3.3 (2021).
AMR (for R) 
-Update March 2022: All functions in this package are considered to be -stable. Updates to the AMR interpretation rules (such as by EUCAST and -CLSI), the microbial taxonomy, and the antibiotic dosages will all be -updated every 6 to 12 months.
+Update March 2022: All functions in this package are considered to be stable. Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months.
What is AMR (for R)?
-AMR is a free, open-source and independent R package (see Copyright) to simplify the analysis and prediction
-of Antimicrobial Resistance (AMR) and to work with microbial and
-antimicrobial data and properties, by using evidence-based methods.
-Our aim is to provide a standard for clean and
-reproducible AMR data analysis, that can therefore empower
-epidemiological analyses to continuously enable surveillance and
-treatment evaluation in any setting.
After installing this package, R knows ~71,000 distinct -microbial species and all ~570 antibiotic, antimycotic -and antiviral drugs by name and code (including ATC, -WHONET/EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about -valid R/SI and MIC values. It supports any data format, including -WHONET/EARS-Net data.
-The AMR package is available in
-
-Danish,
-
-Dutch,
-
-English,
-
-French,
-
-German,
-
-Italian,
-
-Portuguese,
-
-Russian,
-
-Spanish and
-
-Swedish. Antimicrobial drug (group) names and colloquial microorganism
-names are provided in these languages.
This package is fully independent -of any other R package and works on Windows, macOS and Linux with -all versions of R since R-3.0 (April 2013). It was designed to -work in any setting, including those with very limited -resources. It was created for both routine data analysis and -academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration -with non-profit organisations Certe -Medical Diagnostics and Advice Foundation and University Medical Center Groningen. This -R package formed the basis of two PhD theses (DOI -10.33612/diss.177417131 and DOI -10.33612/diss.192486375) but is actively and -durably maintained by two public healthcare organisations in the -Netherlands.
+AMR is a free, open-source and independent R package (see Copyright) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. Our aim is to provide a standard for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.
After installing this package, R knows ~71,000 distinct microbial species and all ~570 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, WHONET/EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.
+The AMR package is available in Danish, Dutch, English, French, German, Italian, Portuguese, Russian, Spanish and Swedish. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.
This package is fully independent of any other R package and works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice Foundation and University Medical Center Groningen. This R package formed the basis of two PhD theses (DOI 10.33612/diss.177417131 and DOI 10.33612/diss.192486375) but is actively and durably maintained by two public healthcare organisations in the Netherlands.
-With
With AMR (for R), there’s always a knowledgeable
-microbiologist by your side!
+With AMR (for R), there’s always a knowledgeable microbiologist by your side!
# AMR works great with dplyr, but it's not required or neccesary
@@ -276,12 +224,7 @@ microbiologist by your side!select(bacteria,
aminoglycosides(),
carbapenems())
-
AMR (for R), there’s always a knowledgeable microbiologist by your side!
# AMR works great with dplyr, but it's not required or neccesary
@@ -276,12 +224,7 @@ microbiologist by your side!select(bacteria,
aminoglycosides(),
carbapenems())With only having defined a row filter on Gram-negative bacteria with
-intrinsic resistance to cefotaxime (mo_is_gram_negative()
-and mo_is_intrinsic_resistant()) and a column selection on
-two antibiotic groups (aminoglycosides() and
-carbapenems()), the reference data about all microorganisms and all antibiotics in the
-AMR package make sure you get what you meant:
With only having defined a row filter on Gram-negative bacteria with intrinsic resistance to cefotaxime (mo_is_gram_negative() and mo_is_intrinsic_resistant()) and a column selection on two antibiotic groups (aminoglycosides() and carbapenems()), the reference data about all microorganisms and all antibiotics in the AMR package make sure you get what you meant:
| bacteria | @@ -395,14 +338,9 @@ two antibiotic groups (
|---|
