From the shell:
# CRAN check from parent directory R CMD check AMR
#> Groups (n=4, named as 'order'): diff --git a/articles/PCA.md b/articles/PCA.md index 879ba066a..79cec35ca 100644 --- a/articles/PCA.md +++ b/articles/PCA.md @@ -123,7 +123,7 @@ summary(pca_result) #> [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales" #> Importance of components: #> PC1 PC2 PC3 PC4 PC5 PC6 PC7 -#> Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 1.232e-16 +#> Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 9.577e-17 #> Proportion of Variance 0.5799 0.3531 0.0471 0.01435 0.00541 0.00012 0.000e+00 #> Cumulative Proportion 0.5799 0.9330 0.9801 0.99446 0.99988 1.00000 1.000e+00 ``` diff --git a/articles/WHONET.html b/articles/WHONET.html index 29566860c..deb9deb19 100644 --- a/articles/WHONET.html +++ b/articles/WHONET.html @@ -30,7 +30,7 @@ AMR (for R) - 3.0.1.9055 + 3.0.1.9057 diff --git a/articles/WISCA.html b/articles/WISCA.html index 4947bee0c..1e3795b8b 100644 --- a/articles/WISCA.html +++ b/articles/WISCA.html @@ -30,7 +30,7 @@ AMR (for R) - 3.0.1.9055 + 3.0.1.9057 diff --git a/articles/datasets.html b/articles/datasets.html index 2037a11a2..b7bca639e 100644 --- a/articles/datasets.html +++ b/articles/datasets.html @@ -30,7 +30,7 @@ AMR (for R) - 3.0.1.9055 + 3.0.1.9057 @@ -80,7 +80,7 @@ Download data sets for download / own use - 30 April 2026 + 02 May 2026 Source: vignettes/datasets.Rmd datasets.Rmd @@ -424,8 +424,8 @@ 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 4 April 2026 09:51:50 UTC. Find more info -about the contents, (scientific) source, and structure of this data set +It was last updated on 2 May 2026 12:56:26 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 421f2d14a..cc92f970d 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 4 April 2026 09:51:50 UTC. Find more info about -the contents, (scientific) source, and structure of this [data set +It was last updated on 2 May 2026 12:56:26 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 eca3e2c8a..d59d3119f 100644 --- a/articles/index.html +++ b/articles/index.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9055 + 3.0.1.9057 diff --git a/authors.html b/authors.html index 49363e23f..afa4c3955 100644 --- a/authors.html +++ b/authors.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9055 + 3.0.1.9057 diff --git a/index.html b/index.html index 5343c6f28..2a5335a91 100644 --- a/index.html +++ b/index.html @@ -33,7 +33,7 @@ AMR (for R) - 3.0.1.9055 + 3.0.1.9057 diff --git a/llms.txt b/llms.txt index 2d147432c..1018552d7 100644 --- a/llms.txt +++ b/llms.txt @@ -606,7 +606,7 @@ from clinical text records, using [`clear_custom_antimicrobials()`](https://amr-for-r.org/reference/add_custom_antimicrobials.md) : Add Custom Antimicrobials -## Preparing data: antimicrobial results +## Interpreting data: antimicrobial results With [`as.mic()`](https://amr-for-r.org/reference/as.mic.md) and [`as.disk()`](https://amr-for-r.org/reference/as.disk.md) you can @@ -615,10 +615,10 @@ transform your raw input to valid MIC or disk diffusion values. Use data to let it only contain “R”, “I” and “S”, or to interpret MIC or disk diffusion values as SIR based on the lastest EUCAST and CLSI guidelines. Afterwards, you can extend antibiotic interpretations by -applying [EUCAST -rules](https://www.eucast.org/expert_rules_and_intrinsic_resistance/) +applying interpretive rules, for example [from +EUCAST](https://www.eucast.org/expert_rules_and_intrinsic_resistance/) with -[`eucast_rules()`](https://amr-for-r.org/reference/interpretive_rules.md). +[`interpretive_rules()`](https://amr-for-r.org/reference/interpretive_rules.md). - [`as.sir()`](https://amr-for-r.org/reference/as.sir.md) [`NA_sir_`](https://amr-for-r.org/reference/as.sir.md) @@ -643,8 +643,8 @@ with [`clsi_rules()`](https://amr-for-r.org/reference/interpretive_rules.md) [`eucast_dosage()`](https://amr-for-r.org/reference/interpretive_rules.md) : Apply Interpretive Rules -- [`custom_eucast_rules()`](https://amr-for-r.org/reference/custom_eucast_rules.md) - : Define Custom EUCAST Rules +- [`custom_interpretive_rules()`](https://amr-for-r.org/reference/custom_interpretive_rules.md) + : Define Custom Interpretive Rules ## Analysing data @@ -955,8 +955,8 @@ and other utilities. Especially the ‘like’ function can be useful: ## Other: statistical tests -Some statistical tests or methods are not part of base R and were added -to this package for convenience. +Some statistical tests or methods usable for AMR analyses are not part +of base R and were added to this package for convenience. - [`g.test()`](https://amr-for-r.org/reference/g.test.md) : @@ -973,7 +973,8 @@ to this package for convenience. These objects are deprecated, meaning that they will still work but show a warning that they will be removed in a future version. -- [`ab_class()`](https://amr-for-r.org/reference/AMR-deprecated.md) +- [`custom_eucast_rules()`](https://amr-for-r.org/reference/AMR-deprecated.md) + [`ab_class()`](https://amr-for-r.org/reference/AMR-deprecated.md) [`ab_selector()`](https://amr-for-r.org/reference/AMR-deprecated.md) : Deprecated Functions, Arguments, or Datasets diff --git a/news/index.html b/news/index.html index 0314470f0..6e08e40e5 100644 --- a/news/index.html +++ b/news/index.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9055 + 3.0.1.9057 @@ -49,96 +49,50 @@ -AMR 3.0.1.9055 -This will become release v3.1.0, intended for launch end of May. +AMR 3.0.1.9057 +Planned as v3.1.0, May 2026. -New -Support for clinical breakpoints of 2026 of both CLSI and EUCAST, by adding all of their over 5,700 new clinical breakpoints to the clinical_breakpoints data set for usage in as.sir(). EUCAST 2026 is now the new default guideline for all MIC and disk diffusion interpretations. -Support for the future package and its framework, as the previous implementation of parallel computing was slow - -Breaking change: as.sir() with parallel = TRUE now requires a non-sequential future::plan() to be active before the call — e.g., future::plan(future::multisession) — and throws an informative error if none is set. -New all-core usage setup: when the number of AB columns is smaller than the number of available cores, rows are now split into batches so all cores stay active (row-batch mode). Previously, a 6-column dataset on a 16-core machine would only use 6 cores; now all 16 are used, with each worker processing a smaller row slice (lower per-worker memory pressure and processing time) +New +EUCAST 2026 and CLSI 2026 breakpoints: over 5,700 new breakpoints added to the clinical_breakpoints data set; EUCAST 2026 is now the default for all MIC and disk diffusion interpretations +Wildtype/Non-wildtype (WT/NWT) output when using ECOFF-based interpretation, by setting breakpoint_type = "ECOFF" in as.sir(); WT/NWT results are fully supported in all resistance/susceptibility functions and plots (#254) +Faster parallel computing via the future package; breaking change: a non-sequential plan (e.g. future::plan(future::multisession)) must be active before using parallel = TRUE; antibiogram() and wisca() now also support parallel = TRUE (#281) -antibiogram() and wisca() gained a parallel argument using the same future/future.apply pattern: for WISCA, Monte Carlo simulations are split into (group, chunk) job pairs distributed across workers; for grouped antibiograms, each group is processed by a separate worker (#281) - -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 -New tidyselect helpers: - -all_sir(), all_sir_predictors() +tidymodels integration for using SIR, MIC and disk data in modelling pipelines: step_mic_log2(), step_sir_numeric(), and new column selectors all_sir(), all_mic(), all_disk() - -all_mic(), all_mic_predictors() +New esbl_isolates data set for practising AMR modelling +New antimicrobial selectors: ionophores(), peptides(), phosphonics(), spiropyrimidinetriones() - -all_disk(), all_disk_predictors() - - - -Data set esbl_isolates to practise with AMR modelling -AMR selectors ionophores(), peptides(), phosphonics() and spiropyrimidinetriones() - -Support for Wildtype (WT) / Non-wildtype (NWT) in as.sir(), all plotting functions, and all susceptibility/resistance functions. - -as.sir() gained an argument as_wt_nwt, which defaults to TRUE only when breakpoint_type = "ECOFF" (#254) -This transforms the output from S/R to WT/NWT -Functions such as susceptibility() count WT as S and NWT as R - -Function interpretive_rules(), which allows future implementation of CLSI interpretive rules (#235) - -eucast_rules() has become a wrapper around that function -Gained argument add_if_missing (default: TRUE). When set to FALSE, rules are only applied to cells that already contain an SIR value; NA cells are left untouched. This is useful with overwrite = TRUE to update reported results without imputing values for drugs that were not tested (#259) - -Function amr_course(), which allows for automated download and unpacking of a GitHub repository for e.g. webinar use -Two new NA objects, NA_ab_ and NA_mo_, analogous to base R’s NA_character_ and NA_integer_, for use in pipelines that require typed missing values +New interpretive_rules(), a unified function for EUCAST and CLSI interpretive rules; eucast_rules() is now a wrapper around it (#235, #259) +New amr_course() to download and unpack course or webinar materials from GitHub in one call +Typed missing value constants NA_ab_ and NA_mo_, for use in pipelines that need missing values of a specific class -Fixes -Fixed a bug in as.sir() where values that were purely numeric (e.g., "1") and matched the broad SIR-matching regex would be incorrectly stripped of all content by the Unicode letter filter -Fixed a bug in as.mic() where MIC values in scientific notation (e.g., "1e-3") were incorrectly handled because the letter e was removed along with other Unicode letters; scientific notation e is now preserved -Fixed a bug in as.ab() where certain AB codes containing “PH” or “TH” (such as ETH, MTH, PHE, PHN, STH, THA, THI1) would incorrectly return NA when combined in a vector with any untranslatable value (#245) -Fixed a bug in antibiogram() for when no antimicrobials are set -Fixed a bug in as.sir() where for numeric input the arguments S, I, and R would not be considered (#244) -Fixed a bug in plotting MIC values when keep_operators = "all" - -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) -Fixed a bug to disregard NI for susceptibility proportion functions -Fixed Italian translation of CoNS to Stafilococco coagulasi-negativo and CoPS to Stafilococco coagulasi-positivo (#256) -Fixed SIR and MIC coercion of combined values, e.g. as.sir("<= 0.002; S") or as.mic("S; 0.002") (#252) -Fixed translation of foreign languages in sir_df() (#272) -Fixed BRMO classification by including bacterial complexes (#275) -Fixed as.sir() for data frames silently deleting columns whose AB class was already <sir> when called a second time (re-running on already-converted data) (#278) -Fixed as.sir() for data frames incorrectly treating metadata columns (e.g. patient, ward) as antibiotic columns when their names coincidentally matched an antibiotic code; column content is now validated against AMR data patterns before inclusion -Fixed as.sir() ignoring info = FALSE for columns with no breakpoints (e.g. cefoxitin against E. coli) +Fixes + +as.sir() on data frames: already-converted SIR columns no longer dropped on re-run (#278); metadata columns (e.g. patient, ward) no longer misidentified as antibiotic columns; info = FALSE now suppresses all messages, including for columns without breakpoints + +as.mic(): values in scientific notation (e.g. 1e-3) now handled correctly + +as.ab(): codes containing “PH” or “TH” (e.g. ETH, PHE) no longer return NA when mixed with unrecognised input (#245) +Combined MIC/SIR input values (e.g. "<= 0.002; S" or "S; 0.002") now parsed correctly (#252) +BRMO classification now includes bacterial complexes (#275) +Translation fixes for Italian CoNS/CoPS names (#256), Dutch antimicrobials, and sir_df() foreign-language output (#272) -Updates +Updates -as.sir() with reference_data: custom guideline names now correctly classify values as R using EUCAST convention (> breakpoint_R for MIC, < breakpoint_R for disk); custom breakpoints with host = NA now serve as a host-agnostic fallback when no host-specific row matches (#239) -Extensive cli integration for better message handling and clickable links in messages and warnings (#191, #265) +custom_eucast_rules() renamed to custom_interpretive_rules(); old name deprecated but still works (#268) -mdro() now infers resistance for a missing base drug column from an available corresponding drug+inhibitor combination showing resistance (e.g., piperacillin is absent but required, while piperacillin/tazobactam available and resistant). Can be set with the new argument infer_from_combinations, which defaults to TRUE (#209). Note that this can yield a higher MDRO detection (which is a good thing as it has become more reliable). +mdro() can now infer resistance from a drug+inhibitor combination when the base drug column is absent (e.g. piperacillin inferred from piperacillin/tazobactam); controlled via new infer_from_combinations argument (default TRUE) (#209) -susceptibility() and resistance() gained the argument guideline, which defaults to EUCAST, for interpreting the ‘I’ category correctly. -Added to the antimicrobials data set: cefepime/taniborbactam (FTA), ceftibuten/avibactam (CTA), clorobiocin (CLB), kasugamycin (KAS), ostreogrycin (OST), taniborbactam (TAN), thiostrepton (THS), xeruborbactam (XER), and zorbamycin (ZOR) +susceptibility() / resistance(): new guideline argument (default EUCAST) to ensure the ‘I’ category is interpreted correctly per guideline +Capped MIC handling in as.sir() reworked into four clearly defined options: "none", "conservative" (new default), "standard", "lenient" (#243) -as.mic() and rescale_mic() gained the argument round_to_next_log2, which can be set to TRUE to round all values up to the nearest next log2 level (#255) +as.mic() / rescale_mic(): new round_to_next_log2 argument to round values up to the nearest log2 dilution level (#255) -antimicrobials$group is now a list instead of a character, to contain any group the drug is in (#246) - -ab_group() gained an argument all_groups to return all groups the antimicrobial drug is in (#246) -Added explaining message to as.sir() when interpreting numeric values (e.g., 1 for S, 2 for I, 3 for R) (#244) -Updated handling of capped MIC values (<, <=, >, >=) in as.sir() in the argument capped_mic_handling: (#243) -Introduced four clearly defined options: "none", "conservative" (default), "standard", and "lenient" - -Interpretation of capped MIC values now consistently returns "NI" (non-interpretable) when the true MIC could be at either side of a breakpoint, depending on the selected handling mode -This results in more reliable behaviour compared to previous versions for capped MIC values -Removed the "inverse" option, which has now become redundant - - -ab_group() now returns values consist with the AMR selectors (#246) +antimicrobials$group now a list, so drugs belonging to multiple groups are fully represented; use ab_group(all_groups = TRUE) to retrieve all groups for a drug (#246) +New antimicrobials added: cefepime/taniborbactam (FTA), ceftibuten/avibactam (CTA), clorobiocin (CLB), kasugamycin (KAS), ostreogrycin (OST), taniborbactam (TAN), thiostrepton (THS), xeruborbactam (XER), zorbamycin (ZOR) +Improved console messages with clickable links throughout, powered by cli (#191, #265) @@ -300,7 +254,7 @@ Disks of 0 to 5 mm are now allowed, the newly allowed range for disk diffusion (as.disk()) is now between 0 and 50 mm Updated italicise_taxonomy() to support HTML output -custom_eucast_rules() now supports multiple antimicrobials and antimicrobial groups to be affected by a single rule +custom_eucast_rules() now supports multiple antimicrobials and antimicrobial groups to be affected by a single rule mo_info() now contains an extra element rank and group_members (with the contents of the new mo_group_members() function) Updated all ATC codes from WHOCC diff --git a/news/index.md b/news/index.md index dcaefc859..a787e0995 100644 --- a/news/index.md +++ b/news/index.md @@ -1,201 +1,116 @@ # Changelog -## AMR 3.0.1.9055 +## AMR 3.0.1.9057 -This will become release v3.1.0, intended for launch end of May. +Planned as v3.1.0, May 2026. #### New -- Support for clinical breakpoints of 2026 of both CLSI and EUCAST, by - adding all of their over 5,700 new clinical breakpoints to the - `clinical_breakpoints` data set for usage in - [`as.sir()`](https://amr-for-r.org/reference/as.sir.md). EUCAST 2026 - is now the new default guideline for all MIC and disk diffusion - interpretations. -- Support for the [`future`](https://future.futureverse.org) package and - its framework, as the previous implementation of parallel computing - was slow - - **Breaking change**: - [`as.sir()`](https://amr-for-r.org/reference/as.sir.md) with - `parallel = TRUE` now requires a non-sequential - [`future::plan()`](https://future.futureverse.org/reference/plan.html) - to be active before the call — e.g., - `future::plan(future::multisession)` — and throws an informative - error if none is set. - - New all-core usage setup: when the number of AB columns is smaller - than the number of available cores, rows are now split into batches - so all cores stay active (row-batch mode). Previously, a 6-column - dataset on a 16-core machine would only use 6 cores; now all 16 are - used, with each worker processing a smaller row slice (lower - per-worker memory pressure and processing time) - - [`antibiogram()`](https://amr-for-r.org/reference/antibiogram.md) - and [`wisca()`](https://amr-for-r.org/reference/antibiogram.md) - gained a `parallel` argument using the same `future`/`future.apply` - pattern: for WISCA, Monte Carlo simulations are split into - `(group, chunk)` job pairs distributed across workers; for grouped - antibiograms, each group is processed by a separate worker - ([\#281](https://github.com/msberends/AMR/issues/281)) -- Integration with the *tidymodels* framework to allow seamless use of - SIR, MIC and disk data in modelling pipelines via `recipes` - - [`step_mic_log2()`](https://amr-for-r.org/reference/amr-tidymodels.md) - to transform `` columns with log2, and - [`step_sir_numeric()`](https://amr-for-r.org/reference/amr-tidymodels.md) - to convert `` columns to numeric - - New `tidyselect` helpers: - - [`all_sir()`](https://amr-for-r.org/reference/amr-tidymodels.md), - [`all_sir_predictors()`](https://amr-for-r.org/reference/amr-tidymodels.md) - - [`all_mic()`](https://amr-for-r.org/reference/amr-tidymodels.md), - [`all_mic_predictors()`](https://amr-for-r.org/reference/amr-tidymodels.md) - - [`all_disk()`](https://amr-for-r.org/reference/amr-tidymodels.md), - [`all_disk_predictors()`](https://amr-for-r.org/reference/amr-tidymodels.md) -- Data set `esbl_isolates` to practise with AMR modelling -- AMR selectors +- EUCAST 2026 and CLSI 2026 breakpoints: over 5,700 new breakpoints + added to the `clinical_breakpoints` data set; EUCAST 2026 is now the + default for all MIC and disk diffusion interpretations +- Wildtype/Non-wildtype (WT/NWT) output when using ECOFF-based + interpretation, by setting `breakpoint_type = "ECOFF"` in + [`as.sir()`](https://amr-for-r.org/reference/as.sir.md); WT/NWT + results are fully supported in all resistance/susceptibility functions + and plots ([\#254](https://github.com/msberends/AMR/issues/254)) +- Faster parallel computing via the `future` package; **breaking + change**: a non-sequential plan + (e.g. `future::plan(future::multisession)`) must be active before + using `parallel = TRUE`; + [`antibiogram()`](https://amr-for-r.org/reference/antibiogram.md) and + [`wisca()`](https://amr-for-r.org/reference/antibiogram.md) now also + support `parallel = TRUE` + ([\#281](https://github.com/msberends/AMR/issues/281)) +- *tidymodels* integration for using SIR, MIC and disk data in modelling + pipelines: + [`step_mic_log2()`](https://amr-for-r.org/reference/amr-tidymodels.md), + [`step_sir_numeric()`](https://amr-for-r.org/reference/amr-tidymodels.md), + and new column selectors + [`all_sir()`](https://amr-for-r.org/reference/amr-tidymodels.md), + [`all_mic()`](https://amr-for-r.org/reference/amr-tidymodels.md), + [`all_disk()`](https://amr-for-r.org/reference/amr-tidymodels.md) +- New `esbl_isolates` data set for practising AMR modelling +- New antimicrobial selectors: [`ionophores()`](https://amr-for-r.org/reference/antimicrobial_selectors.md), [`peptides()`](https://amr-for-r.org/reference/antimicrobial_selectors.md), - [`phosphonics()`](https://amr-for-r.org/reference/antimicrobial_selectors.md) - and + [`phosphonics()`](https://amr-for-r.org/reference/antimicrobial_selectors.md), [`spiropyrimidinetriones()`](https://amr-for-r.org/reference/antimicrobial_selectors.md) -- Support for Wildtype (WT) / Non-wildtype (NWT) in - [`as.sir()`](https://amr-for-r.org/reference/as.sir.md), all plotting - functions, and all susceptibility/resistance functions. - - [`as.sir()`](https://amr-for-r.org/reference/as.sir.md) gained an - argument `as_wt_nwt`, which defaults to `TRUE` only when - `breakpoint_type = "ECOFF"` - ([\#254](https://github.com/msberends/AMR/issues/254)) - - This transforms the output from S/R to WT/NWT - - Functions such as - [`susceptibility()`](https://amr-for-r.org/reference/proportion.md) - count WT as S and NWT as R -- Function +- New [`interpretive_rules()`](https://amr-for-r.org/reference/interpretive_rules.md), - which allows future implementation of CLSI interpretive rules - ([\#235](https://github.com/msberends/AMR/issues/235)) - - [`eucast_rules()`](https://amr-for-r.org/reference/interpretive_rules.md) - has become a wrapper around that function - - Gained argument `add_if_missing` (default: `TRUE`). When set to - `FALSE`, rules are only applied to cells that already contain an SIR - value; `NA` cells are left untouched. This is useful with - `overwrite = TRUE` to update reported results without imputing - values for drugs that were not tested - ([\#259](https://github.com/msberends/AMR/issues/259)) -- Function - [`amr_course()`](https://amr-for-r.org/reference/amr_course.md), which - allows for automated download and unpacking of a GitHub repository for - e.g. webinar use -- Two new `NA` objects, `NA_ab_` and `NA_mo_`, analogous to base R’s - `NA_character_` and `NA_integer_`, for use in pipelines that require - typed missing values + a unified function for EUCAST and CLSI interpretive rules; + [`eucast_rules()`](https://amr-for-r.org/reference/interpretive_rules.md) + is now a wrapper around it + ([\#235](https://github.com/msberends/AMR/issues/235), + [\#259](https://github.com/msberends/AMR/issues/259)) +- New [`amr_course()`](https://amr-for-r.org/reference/amr_course.md) to + download and unpack course or webinar materials from GitHub in one + call +- Typed missing value constants `NA_ab_` and `NA_mo_`, for use in + pipelines that need missing values of a specific class #### Fixes -- Fixed a bug in [`as.sir()`](https://amr-for-r.org/reference/as.sir.md) - where values that were purely numeric (e.g., `"1"`) and matched the - broad SIR-matching regex would be incorrectly stripped of all content - by the Unicode letter filter -- Fixed a bug in [`as.mic()`](https://amr-for-r.org/reference/as.mic.md) - where MIC values in scientific notation (e.g., `"1e-3"`) were - incorrectly handled because the letter `e` was removed along with - other Unicode letters; scientific notation `e` is now preserved -- Fixed a bug in [`as.ab()`](https://amr-for-r.org/reference/as.ab.md) - where certain AB codes containing “PH” or “TH” (such as `ETH`, `MTH`, - `PHE`, `PHN`, `STH`, `THA`, `THI1`) would incorrectly return `NA` when - combined in a vector with any untranslatable value +- [`as.sir()`](https://amr-for-r.org/reference/as.sir.md) on data + frames: already-converted SIR columns no longer dropped on re-run + ([\#278](https://github.com/msberends/AMR/issues/278)); metadata + columns (e.g. `patient`, `ward`) no longer misidentified as antibiotic + columns; `info = FALSE` now suppresses all messages, including for + columns without breakpoints +- [`as.mic()`](https://amr-for-r.org/reference/as.mic.md): values in + scientific notation (e.g. `1e-3`) now handled correctly +- [`as.ab()`](https://amr-for-r.org/reference/as.ab.md): codes + containing “PH” or “TH” (e.g. `ETH`, `PHE`) no longer return `NA` when + mixed with unrecognised input ([\#245](https://github.com/msberends/AMR/issues/245)) -- Fixed a bug in - [`antibiogram()`](https://amr-for-r.org/reference/antibiogram.md) for - when no antimicrobials are 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 a bug in plotting MIC values when `keep_operators = "all"` -- 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)) -- Fixed a bug to disregard `NI` for susceptibility proportion functions -- Fixed Italian translation of CoNS to Stafilococco coagulasi-negativo - and CoPS to Stafilococco coagulasi-positivo - ([\#256](https://github.com/msberends/AMR/issues/256)) -- Fixed SIR and MIC coercion of combined values, - e.g. `as.sir("<= 0.002; S")` or `as.mic("S; 0.002")` +- Combined MIC/SIR input values (e.g. `"<= 0.002; S"` or `"S; 0.002"`) + now parsed correctly ([\#252](https://github.com/msberends/AMR/issues/252)) -- Fixed translation of foreign languages in - [`sir_df()`](https://amr-for-r.org/reference/proportion.md) - ([\#272](https://github.com/msberends/AMR/issues/272)) -- Fixed BRMO classification by including bacterial complexes +- BRMO classification now includes bacterial complexes ([\#275](https://github.com/msberends/AMR/issues/275)) -- Fixed [`as.sir()`](https://amr-for-r.org/reference/as.sir.md) for data - frames silently deleting columns whose AB class was already `` - when called a second time (re-running on already-converted data) - ([\#278](https://github.com/msberends/AMR/issues/278)) -- Fixed [`as.sir()`](https://amr-for-r.org/reference/as.sir.md) for data - frames incorrectly treating metadata columns (e.g. `patient`, `ward`) - as antibiotic columns when their names coincidentally matched an - antibiotic code; column content is now validated against AMR data - patterns before inclusion -- Fixed [`as.sir()`](https://amr-for-r.org/reference/as.sir.md) ignoring - `info = FALSE` for columns with no breakpoints (e.g. cefoxitin against - *E. coli*) +- Translation fixes for Italian CoNS/CoPS names + ([\#256](https://github.com/msberends/AMR/issues/256)), Dutch + antimicrobials, and + [`sir_df()`](https://amr-for-r.org/reference/proportion.md) + foreign-language output + ([\#272](https://github.com/msberends/AMR/issues/272)) #### Updates -- [`as.sir()`](https://amr-for-r.org/reference/as.sir.md) with - `reference_data`: custom guideline names now correctly classify values - as R using EUCAST convention (`> breakpoint_R` for MIC, - `< breakpoint_R` for disk); custom breakpoints with `host = NA` now - serve as a host-agnostic fallback when no host-specific row matches - ([\#239](https://github.com/msberends/AMR/issues/239)) -- Extensive `cli` integration for better message handling and clickable - links in messages and warnings - ([\#191](https://github.com/msberends/AMR/issues/191), - [\#265](https://github.com/msberends/AMR/issues/265)) -- [`mdro()`](https://amr-for-r.org/reference/mdro.md) now infers - resistance for a *missing* base drug column from an *available* - corresponding drug+inhibitor combination showing resistance (e.g., - piperacillin is absent but required, while piperacillin/tazobactam - available and resistant). Can be set with the new argument - `infer_from_combinations`, which defaults to `TRUE` - ([\#209](https://github.com/msberends/AMR/issues/209)). Note that this - can yield a higher MDRO detection (which is a good thing as it has - become more reliable). -- [`susceptibility()`](https://amr-for-r.org/reference/proportion.md) - and [`resistance()`](https://amr-for-r.org/reference/proportion.md) - gained the argument `guideline`, which defaults to EUCAST, for - interpreting the ‘I’ category correctly. -- Added to the `antimicrobials` data set: cefepime/taniborbactam - (`FTA`), ceftibuten/avibactam (`CTA`), clorobiocin (`CLB`), - kasugamycin (`KAS`), ostreogrycin (`OST`), taniborbactam (`TAN`), - thiostrepton (`THS`), xeruborbactam (`XER`), and zorbamycin (`ZOR`) -- [`as.mic()`](https://amr-for-r.org/reference/as.mic.md) and - [`rescale_mic()`](https://amr-for-r.org/reference/as.mic.md) gained - the argument `round_to_next_log2`, which can be set to `TRUE` to round - all values up to the nearest next log2 level - ([\#255](https://github.com/msberends/AMR/issues/255)) -- `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) gained - an argument `all_groups` to return all groups the antimicrobial drug - is in ([\#246](https://github.com/msberends/AMR/issues/246)) -- 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) - ([\#244](https://github.com/msberends/AMR/issues/244)) -- Updated handling of capped MIC values (`<`, `<=`, `>`, `>=`) in - [`as.sir()`](https://amr-for-r.org/reference/as.sir.md) in the - argument `capped_mic_handling`: +- [`custom_eucast_rules()`](https://amr-for-r.org/reference/AMR-deprecated.md) + renamed to + [`custom_interpretive_rules()`](https://amr-for-r.org/reference/custom_interpretive_rules.md); + old name deprecated but still works + ([\#268](https://github.com/msberends/AMR/issues/268)) +- [`mdro()`](https://amr-for-r.org/reference/mdro.md) can now infer + resistance from a drug+inhibitor combination when the base drug column + is absent (e.g. piperacillin inferred from piperacillin/tazobactam); + controlled via new `infer_from_combinations` argument (default `TRUE`) + ([\#209](https://github.com/msberends/AMR/issues/209)) +- [`susceptibility()`](https://amr-for-r.org/reference/proportion.md) / + [`resistance()`](https://amr-for-r.org/reference/proportion.md): new + `guideline` argument (default EUCAST) to ensure the ‘I’ category is + interpreted correctly per guideline +- Capped MIC handling in + [`as.sir()`](https://amr-for-r.org/reference/as.sir.md) reworked into + four clearly defined options: `"none"`, `"conservative"` (new + default), `"standard"`, `"lenient"` ([\#243](https://github.com/msberends/AMR/issues/243)) - - Introduced four clearly defined options: `"none"`, `"conservative"` - (default), `"standard"`, and `"lenient"` - - Interpretation of capped MIC values now consistently returns `"NI"` - (non-interpretable) when the true MIC could be at either side of a - breakpoint, depending on the selected handling mode - - This results in more reliable behaviour compared to previous - versions for capped MIC values - - Removed the `"inverse"` option, which has now become redundant -- [`ab_group()`](https://amr-for-r.org/reference/ab_property.md) now - returns values consist with the AMR selectors +- [`as.mic()`](https://amr-for-r.org/reference/as.mic.md) / + [`rescale_mic()`](https://amr-for-r.org/reference/as.mic.md): new + `round_to_next_log2` argument to round values up to the nearest log2 + dilution level ([\#255](https://github.com/msberends/AMR/issues/255)) +- `antimicrobials$group` now a `list`, so drugs belonging to multiple + groups are fully represented; use `ab_group(all_groups = TRUE)` to + retrieve all groups for a drug ([\#246](https://github.com/msberends/AMR/issues/246)) +- New antimicrobials added: cefepime/taniborbactam (`FTA`), + ceftibuten/avibactam (`CTA`), clorobiocin (`CLB`), kasugamycin + (`KAS`), ostreogrycin (`OST`), taniborbactam (`TAN`), thiostrepton + (`THS`), xeruborbactam (`XER`), zorbamycin (`ZOR`) +- Improved console messages with clickable links throughout, powered by + `cli` ([\#191](https://github.com/msberends/AMR/issues/191), + [\#265](https://github.com/msberends/AMR/issues/265)) ## AMR 3.0.1 @@ -581,7 +496,7 @@ this change. - Updated [`italicise_taxonomy()`](https://amr-for-r.org/reference/italicise_taxonomy.md) to support HTML output -- [`custom_eucast_rules()`](https://amr-for-r.org/reference/custom_eucast_rules.md) +- [`custom_eucast_rules()`](https://amr-for-r.org/reference/AMR-deprecated.md) now supports multiple antimicrobials and antimicrobial groups to be affected by a single rule - [`mo_info()`](https://amr-for-r.org/reference/mo_property.md) now diff --git a/pkgdown.yml b/pkgdown.yml index 349afd8cc..f0f618ec4 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -10,7 +10,7 @@ articles: PCA: PCA.html WHONET: WHONET.html WISCA: WISCA.html -last_built: 2026-04-30T17:47Z +last_built: 2026-05-02T13:01Z 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 9c4ddc908..d16e50ae6 100644 --- a/reference/AMR-deprecated.html +++ b/reference/AMR-deprecated.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9055 + 3.0.1.9057 @@ -55,7 +55,9 @@ Usage - ab_class(...) + custom_eucast_rules(...) + +ab_class(...) ab_selector(...) diff --git a/reference/AMR-deprecated.md b/reference/AMR-deprecated.md index 5356fbea6..44090ab1f 100644 --- a/reference/AMR-deprecated.md +++ b/reference/AMR-deprecated.md @@ -9,6 +9,8 @@ warning with the name of the alternative object it has been replaced by ## Usage ``` r +custom_eucast_rules(...) + ab_class(...) ab_selector(...) diff --git a/reference/AMR-options.html b/reference/AMR-options.html index e4c65da2c..c2a27e34d 100644 --- a/reference/AMR-options.html +++ b/reference/AMR-options.html @@ -9,7 +9,7 @@ options(AMR_guideline = "CLSI")'>AMR (for R) - 3.0.1.9055 + 3.0.1.9057 diff --git a/reference/AMR.html b/reference/AMR.html index 71d2624f4..8bd92ef45 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) - 3.0.1.9055 + 3.0.1.9057 diff --git a/reference/WHOCC.html b/reference/WHOCC.html index 4f949f454..9eba8e75d 100644 --- a/reference/WHOCC.html +++ b/reference/WHOCC.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9055 + 3.0.1.9057 diff --git a/reference/WHONET.html b/reference/WHONET.html index c49a25997..b068db3b4 100644 --- a/reference/WHONET.html +++ b/reference/WHONET.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9055 + 3.0.1.9057 diff --git a/reference/ab_from_text.html b/reference/ab_from_text.html index af64b3da4..e4923049b 100644 --- a/reference/ab_from_text.html +++ b/reference/ab_from_text.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9055 + 3.0.1.9057 diff --git a/reference/ab_property.html b/reference/ab_property.html index 5cb09a1c0..71aaa694c 100644 --- a/reference/ab_property.html +++ b/reference/ab_property.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9055 + 3.0.1.9057 diff --git a/reference/add_custom_antimicrobials.html b/reference/add_custom_antimicrobials.html index 69cf4b81e..9d033e08c 100644 --- a/reference/add_custom_antimicrobials.html +++ b/reference/add_custom_antimicrobials.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9055 + 3.0.1.9057 diff --git a/reference/add_custom_microorganisms.html b/reference/add_custom_microorganisms.html index 4af2b76fe..a03a3847c 100644 --- a/reference/add_custom_microorganisms.html +++ b/reference/add_custom_microorganisms.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9055 + 3.0.1.9057 diff --git a/reference/age.html b/reference/age.html index 252ac559b..6638460d5 100644 --- a/reference/age.html +++ b/reference/age.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9055 + 3.0.1.9057 @@ -112,16 +112,16 @@ df #> birth_date age age_exact age_at_y2k -#> 1 1999-06-30 26 26.83288 0 -#> 2 1968-01-29 58 58.24932 31 -#> 3 1965-12-05 60 60.40000 34 -#> 4 1980-03-01 46 46.16438 19 -#> 5 1949-11-01 76 76.49315 50 -#> 6 1947-02-14 79 79.20548 52 -#> 7 1940-02-19 86 86.19178 59 -#> 8 1988-01-10 38 38.30137 11 -#> 9 1997-08-27 28 28.67397 2 -#> 10 1978-01-26 48 48.25753 21 +#> 1 1999-06-30 26 26.83836 0 +#> 2 1968-01-29 58 58.25479 31 +#> 3 1965-12-05 60 60.40548 34 +#> 4 1980-03-01 46 46.16986 19 +#> 5 1949-11-01 76 76.49863 50 +#> 6 1947-02-14 79 79.21096 52 +#> 7 1940-02-19 86 86.19726 59 +#> 8 1988-01-10 38 38.30685 11 +#> 9 1997-08-27 28 28.67945 2 +#> 10 1978-01-26 48 48.26301 21
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 4 April 2026 09:51:50 UTC. Find more info -about the contents, (scientific) source, and structure of this data set +It was last updated on 2 May 2026 12:56:26 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 421f2d14a..cc92f970d 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 4 April 2026 09:51:50 UTC. Find more info about -the contents, (scientific) source, and structure of this [data set +It was last updated on 2 May 2026 12:56:26 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 eca3e2c8a..d59d3119f 100644 --- a/articles/index.html +++ b/articles/index.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9055 + 3.0.1.9057 diff --git a/authors.html b/authors.html index 49363e23f..afa4c3955 100644 --- a/authors.html +++ b/authors.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9055 + 3.0.1.9057 diff --git a/index.html b/index.html index 5343c6f28..2a5335a91 100644 --- a/index.html +++ b/index.html @@ -33,7 +33,7 @@ AMR (for R) - 3.0.1.9055 + 3.0.1.9057 diff --git a/llms.txt b/llms.txt index 2d147432c..1018552d7 100644 --- a/llms.txt +++ b/llms.txt @@ -606,7 +606,7 @@ from clinical text records, using [`clear_custom_antimicrobials()`](https://amr-for-r.org/reference/add_custom_antimicrobials.md) : Add Custom Antimicrobials -## Preparing data: antimicrobial results +## Interpreting data: antimicrobial results With [`as.mic()`](https://amr-for-r.org/reference/as.mic.md) and [`as.disk()`](https://amr-for-r.org/reference/as.disk.md) you can @@ -615,10 +615,10 @@ transform your raw input to valid MIC or disk diffusion values. Use data to let it only contain “R”, “I” and “S”, or to interpret MIC or disk diffusion values as SIR based on the lastest EUCAST and CLSI guidelines. Afterwards, you can extend antibiotic interpretations by -applying [EUCAST -rules](https://www.eucast.org/expert_rules_and_intrinsic_resistance/) +applying interpretive rules, for example [from +EUCAST](https://www.eucast.org/expert_rules_and_intrinsic_resistance/) with -[`eucast_rules()`](https://amr-for-r.org/reference/interpretive_rules.md). +[`interpretive_rules()`](https://amr-for-r.org/reference/interpretive_rules.md). - [`as.sir()`](https://amr-for-r.org/reference/as.sir.md) [`NA_sir_`](https://amr-for-r.org/reference/as.sir.md) @@ -643,8 +643,8 @@ with [`clsi_rules()`](https://amr-for-r.org/reference/interpretive_rules.md) [`eucast_dosage()`](https://amr-for-r.org/reference/interpretive_rules.md) : Apply Interpretive Rules -- [`custom_eucast_rules()`](https://amr-for-r.org/reference/custom_eucast_rules.md) - : Define Custom EUCAST Rules +- [`custom_interpretive_rules()`](https://amr-for-r.org/reference/custom_interpretive_rules.md) + : Define Custom Interpretive Rules ## Analysing data @@ -955,8 +955,8 @@ and other utilities. Especially the ‘like’ function can be useful: ## Other: statistical tests -Some statistical tests or methods are not part of base R and were added -to this package for convenience. +Some statistical tests or methods usable for AMR analyses are not part +of base R and were added to this package for convenience. - [`g.test()`](https://amr-for-r.org/reference/g.test.md) : @@ -973,7 +973,8 @@ to this package for convenience. These objects are deprecated, meaning that they will still work but show a warning that they will be removed in a future version. -- [`ab_class()`](https://amr-for-r.org/reference/AMR-deprecated.md) +- [`custom_eucast_rules()`](https://amr-for-r.org/reference/AMR-deprecated.md) + [`ab_class()`](https://amr-for-r.org/reference/AMR-deprecated.md) [`ab_selector()`](https://amr-for-r.org/reference/AMR-deprecated.md) : Deprecated Functions, Arguments, or Datasets diff --git a/news/index.html b/news/index.html index 0314470f0..6e08e40e5 100644 --- a/news/index.html +++ b/news/index.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9055 + 3.0.1.9057 @@ -49,96 +49,50 @@
It was last updated on 2 May 2026 12:56:26 UTC. Find more info about +the contents, (scientific) source, and structure of this data set here.
Direct download links:
This will become release v3.1.0, intended for launch end of May.
Planned as v3.1.0, May 2026.
clinical_breakpoints
as.sir()
future
parallel = TRUE
future::plan()
future::plan(future::multisession)
breakpoint_type = "ECOFF"
antibiogram()
wisca()
parallel
future.apply
(group, chunk)
recipes
step_mic_log2()
<mic>
step_sir_numeric()
<sir>
tidyselect
all_sir()
all_sir_predictors()
all_mic()
all_disk()
all_mic_predictors()
esbl_isolates
ionophores()
peptides()
phosphonics()
spiropyrimidinetriones()
all_disk_predictors()
as_wt_nwt
TRUE
susceptibility()
interpretive_rules()
eucast_rules()
add_if_missing
FALSE
NA
overwrite = TRUE
amr_course()
NA_ab_
NA_mo_
NA_character_
NA_integer_
"1"
as.mic()
"1e-3"
e
as.ab()
ETH
MTH
PHE
PHN
STH
THA
THI1
S
I
R
keep_operators = "all"
mutate_at(vars(...), as.mic)
NI
as.sir("<= 0.002; S")
as.mic("S; 0.002")
sir_df()
patient
ward
info = FALSE
1e-3
"<= 0.002; S"
"S; 0.002"
reference_data
> breakpoint_R
< breakpoint_R
host = NA
cli
custom_eucast_rules()
custom_interpretive_rules()
mdro()
infer_from_combinations
resistance()
guideline
FTA
CTA
CLB
KAS
OST
TAN
THS
XER
ZOR
"none"
"conservative"
"standard"
"lenient"
rescale_mic()
round_to_next_log2
antimicrobials$group
list
character
ab_group()
all_groups
<
<=
>
>=
capped_mic_handling
"NI"
"inverse"
ab_group(all_groups = TRUE)
as.disk()
italicise_taxonomy()
mo_info()
rank
group_members
mo_group_members()
ab_class(...) + custom_eucast_rules(...) + +ab_class(...) ab_selector(...)
custom_eucast_rules(...) + +ab_class(...) ab_selector(...)