vignettes/datasets.Rmd
datasets.Rmd
This data set is in R available as antimicrobials, after you load the AMR package.
antimicrobials
AMR
It was last updated on 9 July 2026 19:05:33 UTC. Find more info about -the contents, (scientific) source, and structure of this data set +It was last updated on 13 August 2026 09:12:12 UTC. Find more info +about the contents, (scientific) source, and structure of this data set here. Direct download links: diff --git a/articles/datasets.md b/articles/datasets.md index fa8514dbd..7bbd0d132 100644 --- a/articles/datasets.md +++ b/articles/datasets.md @@ -100,7 +100,7 @@ names: This data set is in R available as `antimicrobials`, after you load the `AMR` package. -It was last updated on 9 July 2026 19:05:33 UTC. Find more info about +It was last updated on 13 August 2026 09:12:12 UTC. Find more info about the contents, (scientific) source, and structure of this [data set here](https://amr-for-r.org/reference/antimicrobials.html). diff --git a/articles/index.html b/articles/index.html index 3165adaef..43c119ff9 100644 --- a/articles/index.html +++ b/articles/index.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9085 + 3.0.1.9086 diff --git a/authors.html b/authors.html index e792ba25c..aa372de14 100644 --- a/authors.html +++ b/authors.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9085 + 3.0.1.9086 diff --git a/deps/bootstrap-5.3.8/fonts/ee91700cdbf7ce16c054c2bb8946c736.woff2 b/deps/bootstrap-5.3.8/fonts/109cfdfecabbfbf5e2364aaceece5d12.woff2 similarity index 100% rename from deps/bootstrap-5.3.8/fonts/ee91700cdbf7ce16c054c2bb8946c736.woff2 rename to deps/bootstrap-5.3.8/fonts/109cfdfecabbfbf5e2364aaceece5d12.woff2 diff --git a/deps/bootstrap-5.3.8/fonts/c2f002b3a87d3f9bfeebb23d32cfd9f8.woff2 b/deps/bootstrap-5.3.8/fonts/5cd426f27cf61d86c207d97f8db6cf8a.woff2 similarity index 100% rename from deps/bootstrap-5.3.8/fonts/c2f002b3a87d3f9bfeebb23d32cfd9f8.woff2 rename to deps/bootstrap-5.3.8/fonts/5cd426f27cf61d86c207d97f8db6cf8a.woff2 diff --git a/deps/bootstrap-5.3.8/fonts/07d40e985ad7c747025dabb9f22142c4.woff2 b/deps/bootstrap-5.3.8/fonts/a8e2cb7ac3da2c4d38cd7c8c06ca5e46.woff2 similarity index 100% rename from deps/bootstrap-5.3.8/fonts/07d40e985ad7c747025dabb9f22142c4.woff2 rename to deps/bootstrap-5.3.8/fonts/a8e2cb7ac3da2c4d38cd7c8c06ca5e46.woff2 diff --git a/deps/bootstrap-5.3.8/fonts/1f5e011d6aae0d98fc0518e1a303e99a.woff2 b/deps/bootstrap-5.3.8/fonts/c0540813382b64c1dde636c1fa0b592a.woff2 similarity index 100% rename from deps/bootstrap-5.3.8/fonts/1f5e011d6aae0d98fc0518e1a303e99a.woff2 rename to deps/bootstrap-5.3.8/fonts/c0540813382b64c1dde636c1fa0b592a.woff2 diff --git a/deps/bootstrap-5.3.8/fonts/626330658504e338ee86aec8e957426b.woff2 b/deps/bootstrap-5.3.8/fonts/e0243c1a22ed284bb57c07b3ac886694.woff2 similarity index 100% rename from deps/bootstrap-5.3.8/fonts/626330658504e338ee86aec8e957426b.woff2 rename to deps/bootstrap-5.3.8/fonts/e0243c1a22ed284bb57c07b3ac886694.woff2 diff --git a/index.html b/index.html index 81be9b605..87da97e89 100644 --- a/index.html +++ b/index.html @@ -33,7 +33,7 @@ AMR (for R) - 3.0.1.9085 + 3.0.1.9086 diff --git a/news/index.html b/news/index.html index e9514b40b..ee623df5b 100644 --- a/news/index.html +++ b/news/index.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9085 + 3.0.1.9086 @@ -49,15 +49,15 @@
It was last updated on 13 August 2026 09:12:12 UTC. Find more info +about the contents, (scientific) source, and structure of this data set here.
Direct download links:
Planned as v3.1.0, end of June 2026.
domain
microorganisms
mo_kingdom()
"Pseudomonadati"
"Bacteria"
mo_domain()
kingdom
future
as.sir()
wisca()
future::plan(future::multisession)
parallel = TRUE
clinical_breakpoints
breakpoint_type = "ECOFF"
wisca_plot()
options(AMR_guideline = "EUCAST 2012")
interpretive_rules()
resistance()
susceptibility()
count_resistant()
count_susceptible()
top_n_microorganisms()
property_for_each
property = NULL
After installing this package, R knows ~97 000 distinct microbial species (updated mei 2026) and all ~620 antimicrobial and antiviral drugs by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI 2011-2026 and EUCAST 2011-2026 are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package 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 and the University Medical Center Groningen.
After installing this package, R knows ~97 000 distinct microbial species (updated May 2026) and all ~620 antimicrobial and antiviral drugs by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI 2011-2026 and EUCAST 2011-2026 are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package 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 and the University Medical Center Groningen.
The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Hindi, Indonesian, Italian, Japanese, Korean, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swahili, Swedish, Turkish, Ukrainian, Urdu, and Vietnamese. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.