first_isolate mutate(first = first_isolate(info = TRUE)) #> ℹ Determining first isolates using an episode length of 365 days #> ℹ Using column 'bacteria' as input for `col_mo`. +#> ℹ Column 'first' is SIR eligible (despite only having empty values), since +#> it seems to be cefozopran (ZOP) #> ℹ Using column 'date' as input for `col_date`. #> ℹ Using column 'patient_id' as input for `col_patient_id`. #> ℹ Basing inclusion on all antimicrobial results, using a points threshold diff --git a/articles/AMR.md b/articles/AMR.md index 5668880a0..e164c7a0d 100644 --- a/articles/AMR.md +++ b/articles/AMR.md @@ -3,7 +3,7 @@ **Note:** values on this page will change with every website update since they are based on randomly created values and the page was written in [R Markdown](https://rmarkdown.rstudio.com/). However, the -methodology remains unchanged. This page was generated on 08 January +methodology remains unchanged. This page was generated on 16 January 2026. ## Introduction @@ -52,9 +52,9 @@ structure of your data generally look like this: | date | patient_id | mo | AMX | CIP | |:----------:|:----------:|:----------------:|:---:|:---:| -| 2026-01-08 | abcd | Escherichia coli | S | S | -| 2026-01-08 | abcd | Escherichia coli | S | R | -| 2026-01-08 | efgh | Escherichia coli | R | S | +| 2026-01-16 | abcd | Escherichia coli | S | S | +| 2026-01-16 | abcd | Escherichia coli | S | R | +| 2026-01-16 | efgh | Escherichia coli | R | S | ### Needed R packages @@ -318,6 +318,8 @@ our_data <- our_data %>% mutate(first = first_isolate(info = TRUE)) #> ℹ Determining first isolates using an episode length of 365 days #> ℹ Using column 'bacteria' as input for `col_mo`. +#> ℹ Column 'first' is SIR eligible (despite only having empty values), since +#> it seems to be cefozopran (ZOP) #> ℹ Using column 'date' as input for `col_date`. #> ℹ Using column 'patient_id' as input for `col_patient_id`. #> ℹ Basing inclusion on all antimicrobial results, using a points threshold diff --git a/articles/AMR_for_Python.html b/articles/AMR_for_Python.html index f70b90464..15b750ebd 100644 --- a/articles/AMR_for_Python.html +++ b/articles/AMR_for_Python.html @@ -30,7 +30,7 @@ AMR (for R) - 3.0.1.9017 + 3.0.1.9018 diff --git a/articles/AMR_with_tidymodels.html b/articles/AMR_with_tidymodels.html index 09399451c..340970e54 100644 --- a/articles/AMR_with_tidymodels.html +++ b/articles/AMR_with_tidymodels.html @@ -30,7 +30,7 @@ AMR (for R) - 3.0.1.9017 + 3.0.1.9018 diff --git a/articles/EUCAST.html b/articles/EUCAST.html index d5a6d6140..a2e9dac31 100644 --- a/articles/EUCAST.html +++ b/articles/EUCAST.html @@ -30,7 +30,7 @@ AMR (for R) - 3.0.1.9017 + 3.0.1.9018 diff --git a/articles/PCA.html b/articles/PCA.html index 39c5d8f01..6535be334 100644 --- a/articles/PCA.html +++ b/articles/PCA.html @@ -30,7 +30,7 @@ AMR (for R) - 3.0.1.9017 + 3.0.1.9018 diff --git a/articles/WHONET.html b/articles/WHONET.html index ce9db5e84..1e84b6728 100644 --- a/articles/WHONET.html +++ b/articles/WHONET.html @@ -30,7 +30,7 @@ AMR (for R) - 3.0.1.9017 + 3.0.1.9018 diff --git a/articles/WISCA.html b/articles/WISCA.html index 5449ef804..981756bff 100644 --- a/articles/WISCA.html +++ b/articles/WISCA.html @@ -30,7 +30,7 @@ AMR (for R) - 3.0.1.9017 + 3.0.1.9018 diff --git a/articles/datasets.html b/articles/datasets.html index 7c6970643..e1e107eb8 100644 --- a/articles/datasets.html +++ b/articles/datasets.html @@ -30,7 +30,7 @@ AMR (for R) - 3.0.1.9017 + 3.0.1.9018 @@ -80,7 +80,7 @@ Download data sets for download / own use - 08 January 2026 + 16 January 2026 Source: vignettes/datasets.Rmd datasets.Rmd @@ -424,7 +424,7 @@ column names:ab, cid, name, group, a iv_ddd, iv_units, and loinc. This data set is in R available as antimicrobials, after you load the AMR package. -It was last updated on 6 January 2026 22:08:50 UTC. Find more info +It was last updated on 16 January 2026 09:57:03 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 e882d19cb..6d584cd4a 100644 --- a/articles/datasets.md +++ b/articles/datasets.md @@ -100,8 +100,8 @@ names: This data set is in R available as `antimicrobials`, after you load the `AMR` package. -It was last updated on 6 January 2026 22:08:50 UTC. Find more info about -the contents, (scientific) source, and structure of this [data set +It was last updated on 16 January 2026 09:57:03 UTC. Find more info +about the contents, (scientific) source, and structure of this [data set here](https://amr-for-r.org/reference/antimicrobials.html). **Direct download links:** diff --git a/articles/index.html b/articles/index.html index e58416c7f..30f094229 100644 --- a/articles/index.html +++ b/articles/index.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9017 + 3.0.1.9018 diff --git a/authors.html b/authors.html index bccfaac1f..96e707223 100644 --- a/authors.html +++ b/authors.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9017 + 3.0.1.9018 diff --git a/index.html b/index.html index 8e3e9a63e..0aee80457 100644 --- a/index.html +++ b/index.html @@ -33,7 +33,7 @@ AMR (for R) - 3.0.1.9017 + 3.0.1.9018 diff --git a/news/index.html b/news/index.html index a565dc453..51357b679 100644 --- a/news/index.html +++ b/news/index.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9017 + 3.0.1.9018 @@ -49,9 +49,9 @@ -AMR 3.0.1.9017 +AMR 3.0.1.9018 -New +New Integration with the tidymodels framework to allow seamless use of SIR, MIC and disk data in modelling pipelines via recipes step_mic_log2() to transform <mic> columns with log2, and step_sir_numeric() to convert <sir> columns to numeric @@ -71,13 +71,20 @@ AMR selectors phosphonics() and spiropyrimidinetriones() -ab_group() gained an argument all_groups to return all groups the antimicrobial drug is in (#246) +antimicrobials$group is now a list instead of a character, to contain any group the drug is in (#246) -Changed +Fixes Fixed a bug in antibiogram() for when no antimicrobials are set -Added taniborbactam (TAN) and cefepime/taniborbactam (FTA) to the antimicrobials data set Fixed a bug in as.sir() where for numeric input the arguments S, i, and R would not be considered (#244) +Fixed some foreign translations of antimicrobial drugs +Fixed a bug for printing column names to the console when using mutate_at(vars(...), as.mic) (#249) + + +Updates + +ab_group() gained an argument all_groups to return all groups the antimicrobial drug is in (#246) +Added taniborbactam (TAN) and cefepime/taniborbactam (FTA) to the antimicrobials data set Added explaining message to as.sir() when interpreting numeric values (e.g., 1 for S, 2 for I, 3 for R) (#244) Updated handling of capped MIC values (<, <=, >, >=) in as.sir() in the argument capped_mic_handling: (#243) Introduced four clearly defined options: "none", "conservative" (default), "standard", and "lenient" @@ -86,9 +93,6 @@ This results in more reliable behaviour compared to previous versions for capped MIC values Removed the "inverse" option, which has now become redundant -Fixed some foreign translations of antimicrobial drugs - -antimicrobials$group is now a list instead of a character, to contain any group the drug is in (#246) ab_group() now returns values consist with the AMR selectors (#246) diff --git a/news/index.md b/news/index.md index 2076bec76..0c78aabd6 100644 --- a/news/index.md +++ b/news/index.md @@ -1,6 +1,6 @@ # Changelog -## AMR 3.0.1.9017 +## AMR 3.0.1.9018 #### New @@ -22,20 +22,30 @@ [`phosphonics()`](https://amr-for-r.org/reference/antimicrobial_selectors.md) and [`spiropyrimidinetriones()`](https://amr-for-r.org/reference/antimicrobial_selectors.md) -- [`ab_group()`](https://amr-for-r.org/reference/ab_property.md) gained - an argument `all_groups` to return all groups the antimicrobial drug - is in ([\#246](https://github.com/msberends/AMR/issues/246)) +- `antimicrobials$group` is now a `list` instead of a `character`, to + contain any group the drug is in + ([\#246](https://github.com/msberends/AMR/issues/246)) -#### Changed +#### Fixes - Fixed a bug in [`antibiogram()`](https://amr-for-r.org/reference/antibiogram.md) for when no antimicrobials are set -- Added taniborbactam (`TAN`) and cefepime/taniborbactam (`FTA`) to the - `antimicrobials` data set - Fixed a bug in [`as.sir()`](https://amr-for-r.org/reference/as.sir.md) where for numeric input the arguments `S`, `i`, and `R` would not be considered ([\#244](https://github.com/msberends/AMR/issues/244)) +- Fixed some foreign translations of antimicrobial drugs +- Fixed a bug for printing column names to the console when using + `mutate_at(vars(...), as.mic)` + ([\#249](https://github.com/msberends/AMR/issues/249)) + +#### Updates + +- [`ab_group()`](https://amr-for-r.org/reference/ab_property.md) gained + an argument `all_groups` to return all groups the antimicrobial drug + is in ([\#246](https://github.com/msberends/AMR/issues/246)) +- Added taniborbactam (`TAN`) and cefepime/taniborbactam (`FTA`) to the + `antimicrobials` data set - Added explaining message to [`as.sir()`](https://amr-for-r.org/reference/as.sir.md) when interpreting numeric values (e.g., 1 for S, 2 for I, 3 for R) @@ -52,10 +62,6 @@ - This results in more reliable behaviour compared to previous versions for capped MIC values - Removed the `"inverse"` option, which has now become redundant -- Fixed some foreign translations of antimicrobial drugs -- `antimicrobials$group` is now a `list` instead of a `character`, to - contain any group the drug is in - ([\#246](https://github.com/msberends/AMR/issues/246)) - [`ab_group()`](https://amr-for-r.org/reference/ab_property.md) now returns values consist with the AMR selectors ([\#246](https://github.com/msberends/AMR/issues/246)) diff --git a/pkgdown.yml b/pkgdown.yml index b2bd1881a..9ac9ea3ea 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -10,7 +10,7 @@ articles: PCA: PCA.html WHONET: WHONET.html WISCA: WISCA.html -last_built: 2026-01-08T13:07Z +last_built: 2026-01-16T10:03Z urls: reference: https://amr-for-r.org/reference article: https://amr-for-r.org/articles diff --git a/reference/AMR-deprecated.html b/reference/AMR-deprecated.html index e49ea5816..85a5c3d89 100644 --- a/reference/AMR-deprecated.html +++ b/reference/AMR-deprecated.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9017 + 3.0.1.9018 diff --git a/reference/AMR-options.html b/reference/AMR-options.html index 0f7a9ca70..9c580b1ab 100644 --- a/reference/AMR-options.html +++ b/reference/AMR-options.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9017 + 3.0.1.9018 diff --git a/reference/AMR.html b/reference/AMR.html index cb3e6acd0..83216ea9f 100644 --- a/reference/AMR.html +++ b/reference/AMR.html @@ -21,7 +21,7 @@ The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish AMR (for R) - 3.0.1.9017 + 3.0.1.9018 diff --git a/reference/WHOCC.html b/reference/WHOCC.html index 107f39e0c..ddd8d68da 100644 --- a/reference/WHOCC.html +++ b/reference/WHOCC.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9017 + 3.0.1.9018 diff --git a/reference/WHONET.html b/reference/WHONET.html index cc790bc16..ec837b491 100644 --- a/reference/WHONET.html +++ b/reference/WHONET.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9017 + 3.0.1.9018 diff --git a/reference/ab_from_text.html b/reference/ab_from_text.html index 045c32b16..5c237113a 100644 --- a/reference/ab_from_text.html +++ b/reference/ab_from_text.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9017 + 3.0.1.9018 diff --git a/reference/ab_property.html b/reference/ab_property.html index bff8a2f1c..70ab7fc16 100644 --- a/reference/ab_property.html +++ b/reference/ab_property.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9017 + 3.0.1.9018 @@ -155,7 +155,7 @@ World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: https://atcddd.fhi.no/atc_ddd_index/ -European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm +European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: https://health.ec.europa.eu/documents/community-register/html/reg_hum_atc.htm Download Our Reference Data diff --git a/reference/ab_property.md b/reference/ab_property.md index f489eef93..408bef47d 100644 --- a/reference/ab_property.md +++ b/reference/ab_property.md @@ -155,7 +155,7 @@ World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: - + ## Download Our Reference Data diff --git a/reference/add_custom_antimicrobials.html b/reference/add_custom_antimicrobials.html index fa2006fb1..0302c6cec 100644 --- a/reference/add_custom_antimicrobials.html +++ b/reference/add_custom_antimicrobials.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9017 + 3.0.1.9018 diff --git a/reference/add_custom_microorganisms.html b/reference/add_custom_microorganisms.html index 241f6f7f0..ea0f74559 100644 --- a/reference/add_custom_microorganisms.html +++ b/reference/add_custom_microorganisms.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9017 + 3.0.1.9018 diff --git a/reference/age.html b/reference/age.html index db6e2b649..034d1aef8 100644 --- a/reference/age.html +++ b/reference/age.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9017 + 3.0.1.9018 @@ -112,16 +112,16 @@ df #> birth_date age age_exact age_at_y2k -#> 1 1980-02-27 45 45.86301 19 -#> 2 1953-07-26 72 72.45479 46 -#> 3 1949-09-02 76 76.35068 50 -#> 4 1986-08-03 39 39.43288 13 -#> 5 1932-11-19 93 93.13699 67 -#> 6 1949-03-30 76 76.77808 50 -#> 7 1996-06-23 29 29.54521 3 -#> 8 1963-09-16 62 62.31233 36 -#> 9 1952-05-16 73 73.64932 47 -#> 10 1952-11-14 73 73.15068 47 +#> 1 1980-02-27 45 45.88493 19 +#> 2 1953-07-26 72 72.47671 46 +#> 3 1949-09-02 76 76.37260 50 +#> 4 1986-08-03 39 39.45479 13 +#> 5 1932-11-19 93 93.15890 67 +#> 6 1949-03-30 76 76.80000 50 +#> 7 1996-06-23 29 29.56712 3 +#> 8 1963-09-16 62 62.33425 36 +#> 9 1952-05-16 73 73.67123 47 +#> 10 1952-11-14 73 73.17260 47
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 6 January 2026 22:08:50 UTC. Find more info +
It was last updated on 16 January 2026 09:57:03 UTC. Find more info about the contents, (scientific) source, and structure of this data set here.
Direct download links:
recipes
step_mic_log2()
<mic>
step_sir_numeric()
<sir>
phosphonics()
spiropyrimidinetriones()
ab_group()
all_groups
antimicrobials$group
list
character
antibiogram()
TAN
FTA
as.sir()
S
i
R
mutate_at(vars(...), as.mic)
<
<=
>
>=
capped_mic_handling
"none"
"conservative"
"standard"
"lenient"
"inverse"
World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: https://atcddd.fhi.no/atc_ddd_index/
European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm
European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: https://health.ec.europa.eu/documents/community-register/html/reg_hum_atc.htm