mirror of
https://github.com/msberends/AMR.git
synced 2025-12-16 17:00:17 +01:00
Built site for AMR@3.0.1.9003: ba30b08
This commit is contained in:
490
news/index.md
Normal file
490
news/index.md
Normal file
@@ -0,0 +1,490 @@
|
||||
# Changelog
|
||||
|
||||
## AMR 3.0.1.9003
|
||||
|
||||
#### Changed
|
||||
|
||||
- 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
|
||||
|
||||
## AMR 3.0.1
|
||||
|
||||
CRAN release: 2025-09-20
|
||||
|
||||
This is a bugfix release following the release of v3.0.0 in June 2025.
|
||||
|
||||
#### Changed
|
||||
|
||||
- Fixed bugs introduced by `ggplot2` v4.0.0
|
||||
([\#236](https://github.com/msberends/AMR/issues/236))
|
||||
- MIC scale functions (such as
|
||||
[`scale_y_mic()`](https://amr-for-r.org/reference/plot.md)) will now
|
||||
be applied automatically when plotting values of class `mic`
|
||||
- SIR scale functions (such as
|
||||
[`scale_x_sir()`](https://amr-for-r.org/reference/plot.md)) will now
|
||||
be applied automatically when plotting values of class `sir`
|
||||
- Fixed a bug in
|
||||
[`antibiogram()`](https://amr-for-r.org/reference/antibiogram.md) for
|
||||
when no antimicrobials are set
|
||||
- Fixed a bug in
|
||||
[`antibiogram()`](https://amr-for-r.org/reference/antibiogram.md) to
|
||||
allow column names containing the `+` character
|
||||
([\#222](https://github.com/msberends/AMR/issues/222))
|
||||
- Fixed a bug in [`as.ab()`](https://amr-for-r.org/reference/as.ab.md)
|
||||
for antimicrobial codes with a number in it if they are preceded by a
|
||||
space
|
||||
- Fixed a bug in
|
||||
[`eucast_rules()`](https://amr-for-r.org/reference/eucast_rules.md)
|
||||
for using specific custom rules
|
||||
- Fixed a bug in [`as.sir()`](https://amr-for-r.org/reference/as.sir.md)
|
||||
to allow any tidyselect language
|
||||
([\#220](https://github.com/msberends/AMR/issues/220))
|
||||
- Fixed a bug in [`as.sir()`](https://amr-for-r.org/reference/as.sir.md)
|
||||
to pick right breakpoint when `uti = FALSE`
|
||||
([\#216](https://github.com/msberends/AMR/issues/216))
|
||||
- Fixed a bug in
|
||||
[`ggplot_sir()`](https://amr-for-r.org/reference/ggplot_sir.md) when
|
||||
using `combine_SI = FALSE`
|
||||
([\#213](https://github.com/msberends/AMR/issues/213))
|
||||
- Fixed a bug in [`mdro()`](https://amr-for-r.org/reference/mdro.md) to
|
||||
make sure all genes specified in arguments are acknowledged
|
||||
- Fixed a bug the `antimicrobials` data set to remove statins
|
||||
([\#229](https://github.com/msberends/AMR/issues/229))
|
||||
- Fixed a bug the `microorganisms` data set for MycoBank IDs and
|
||||
synonyms ([\#233](https://github.com/msberends/AMR/issues/233))
|
||||
- Fixed ATC J01CR05 to map to piperacillin/tazobactam rather than
|
||||
piperacillin/sulbactam
|
||||
([\#230](https://github.com/msberends/AMR/issues/230))
|
||||
- Fixed skimmers (`skimr` package) of class `ab`, `sir`, and `disk`
|
||||
([\#234](https://github.com/msberends/AMR/issues/234))
|
||||
- Fixed all plotting to contain a separate colour for SDD (susceptible
|
||||
dose-dependent) ([\#223](https://github.com/msberends/AMR/issues/223))
|
||||
- Fixed some specific Dutch translations for antimicrobials
|
||||
- Added a warning to
|
||||
[`as.ab()`](https://amr-for-r.org/reference/as.ab.md) if input
|
||||
resembles antiviral codes or names
|
||||
([\#232](https://github.com/msberends/AMR/issues/232))
|
||||
- Added all reasons in verbose output of
|
||||
[`mdro()`](https://amr-for-r.org/reference/mdro.md)
|
||||
([\#227](https://github.com/msberends/AMR/issues/227))
|
||||
- Added `names` to
|
||||
[`age_groups()`](https://amr-for-r.org/reference/age_groups.md) so
|
||||
that custom names can be given
|
||||
([\#215](https://github.com/msberends/AMR/issues/215))
|
||||
- Added note to [`as.sir()`](https://amr-for-r.org/reference/as.sir.md)
|
||||
to make it explicit when higher-level taxonomic breakpoints are used
|
||||
([\#218](https://github.com/msberends/AMR/issues/218))
|
||||
- Added antibiotic codes from the Comprehensive Antibiotic Resistance
|
||||
Database (CARD) to the `antimicrobials` data set
|
||||
([\#225](https://github.com/msberends/AMR/issues/225))
|
||||
- Updated Fosfomycin to be of antibiotic class Phosphonics
|
||||
([\#225](https://github.com/msberends/AMR/issues/225))
|
||||
- Updated [`random_mic()`](https://amr-for-r.org/reference/random.md)
|
||||
and [`random_disk()`](https://amr-for-r.org/reference/random.md) to
|
||||
set skewedness of the distribution and allow multiple microorganisms
|
||||
|
||||
## AMR 3.0.0
|
||||
|
||||
CRAN release: 2025-06-02
|
||||
|
||||
This package now supports not only tools for AMR data analysis in
|
||||
clinical settings, but also for veterinary and environmental
|
||||
microbiology. This was made possible through a collaboration with the
|
||||
[University of Prince Edward Island’s Atlantic Veterinary
|
||||
College](https://www.upei.ca/avc), Canada. To celebrate this great
|
||||
improvement of the package, we also updated the package logo to reflect
|
||||
this change.
|
||||
|
||||
#### Breaking
|
||||
|
||||
- Dataset `antibiotics` has been renamed to `antimicrobials` as the data
|
||||
set contains more than just antibiotics. Using `antibiotics` will
|
||||
still work, but now returns a warning.
|
||||
- Removed all functions and references that used the deprecated `rsi`
|
||||
class, which were all replaced with their `sir` equivalents over two
|
||||
years ago.
|
||||
- Functions
|
||||
[`resistance_predict()`](https://amr-for-r.org/reference/resistance_predict.md)
|
||||
and
|
||||
[`sir_predict()`](https://amr-for-r.org/reference/resistance_predict.md)
|
||||
are now deprecated and will be removed in a future version. Use the
|
||||
`tidymodels` framework instead, for which we [wrote a basic
|
||||
introduction](https://amr-for-r.org/articles/AMR_with_tidymodels.html).
|
||||
|
||||
#### New
|
||||
|
||||
- **One Health implementation**
|
||||
- Function [`as.sir()`](https://amr-for-r.org/reference/as.sir.md) now
|
||||
has extensive support for veterinary breakpoints from CLSI. Use
|
||||
`breakpoint_type = "animal"` and set the `host` argument to a
|
||||
variable that contains animal species names.
|
||||
- The `clinical_breakpoints` data set contains all these breakpoints,
|
||||
and can be downloaded on our [download
|
||||
page](https://amr-for-r.org/articles/datasets.html).
|
||||
- The (new) `antimicrobials` data set contains all veterinary
|
||||
antimicrobials, such as pradofloxacin and enrofloxacin. All WHOCC
|
||||
codes for veterinary use have been added as well.
|
||||
- [`ab_atc()`](https://amr-for-r.org/reference/ab_property.md) now
|
||||
supports ATC codes of veterinary antimicrobials (that all start with
|
||||
“Q”)
|
||||
- [`ab_url()`](https://amr-for-r.org/reference/ab_property.md) now
|
||||
supports retrieving the WHOCC url of their ATCvet pages
|
||||
- **Support for WISCA antibiograms**
|
||||
- The
|
||||
[`antibiogram()`](https://amr-for-r.org/reference/antibiogram.md)
|
||||
function now supports creating true Weighted-Incidence Syndromic
|
||||
Combination Antibiograms (WISCA), a powerful Bayesian method for
|
||||
estimating regimen coverage probabilities using pathogen incidence
|
||||
and antimicrobial susceptibility data. WISCA offers improved
|
||||
precision for syndrome-specific treatment, even in datasets with
|
||||
sparse data. A dedicated
|
||||
[`wisca()`](https://amr-for-r.org/reference/antibiogram.md) function
|
||||
is also available for easy usage.
|
||||
- **More global coverage of languages**
|
||||
- Added full support for 8 new languages: Arabic, Bengali, Hindi,
|
||||
Indonesian, Korean, Swahili, Urdu, and Vietnamese. The `AMR` package
|
||||
is now available in 28 languages.
|
||||
- **Major update to fungal taxonomy and tools for mycologists**
|
||||
- MycoBank has now been integrated as the primary taxonomic source for
|
||||
fungi. The `microorganisms` data set has been enriched with new
|
||||
columns (`mycobank`, `mycobank_parent`, and `mycobank_renamed_to`)
|
||||
that provide detailed information for fungal species.
|
||||
- A remarkable addition of over 20,000 new fungal records
|
||||
- New function
|
||||
[`mo_mycobank()`](https://amr-for-r.org/reference/mo_property.md) to
|
||||
retrieve the MycoBank record number, analogous to existing functions
|
||||
such as
|
||||
[`mo_lpsn()`](https://amr-for-r.org/reference/mo_property.md) and
|
||||
[`mo_gbif()`](https://amr-for-r.org/reference/mo_property.md).
|
||||
- The [`as.mo()`](https://amr-for-r.org/reference/as.mo.md) function
|
||||
and all `mo_*()` functions now include an `only_fungi` argument,
|
||||
allowing users to restrict results solely to fungal species. This
|
||||
ensures fungi are prioritised over bacteria during microorganism
|
||||
identification. This can also be set globally with the new
|
||||
`AMR_only_fungi` option.
|
||||
- Also updated other kingdoms, welcoming a total of 2,149 new records
|
||||
from 2023 and 927 from 2024.
|
||||
- **Updated clinical breakpoints**
|
||||
- Breakpoint of 2024 and 2025 of both CLSI and EUCAST are now
|
||||
supported, by adding all of their over 10,000 new clinical
|
||||
breakpoints to the `clinical_breakpoints` data set for usage in
|
||||
[`as.sir()`](https://amr-for-r.org/reference/as.sir.md). EUCAST 2025
|
||||
is now the new default guideline for all MIC and disk diffusion
|
||||
interpretations.
|
||||
- Added all Expected Resistant Phenotypes from EUCAST (v1.2). The
|
||||
default `rules` for
|
||||
[`eucast_rules()`](https://amr-for-r.org/reference/eucast_rules.md)
|
||||
are now: `c("breakpoints", "expected_phenotypes")`.
|
||||
- Updated the `intrinsic_resistant` data set, which is now based on
|
||||
EUCAST Expected Resistant Phenotypes v1.2
|
||||
- [`as.sir()`](https://amr-for-r.org/reference/as.sir.md) now brings
|
||||
additional factor levels: “NI” for non-interpretable and “SDD” for
|
||||
susceptible dose-dependent. Currently, the `clinical_breakpoints`
|
||||
data set contains 24 breakpoints that can return the value “SDD”
|
||||
instead of “I”.
|
||||
- EUCAST interpretive rules (using
|
||||
[`eucast_rules()`](https://amr-for-r.org/reference/eucast_rules.md))
|
||||
are now available for EUCAST 12 (2022), 13 (2023), 14 (2024), and 15
|
||||
(2025).
|
||||
- EUCAST dosage tables (`dosage` data set) are now available for
|
||||
EUCAST 13 (2023), 14 (2024), and 15 (2025).
|
||||
- **New advanced ggplot2 extensions for MIC and SIR plotting and
|
||||
transforming**
|
||||
- New function group `scale_*_mic()`, namely:
|
||||
[`scale_x_mic()`](https://amr-for-r.org/reference/plot.md),
|
||||
[`scale_y_mic()`](https://amr-for-r.org/reference/plot.md),
|
||||
[`scale_colour_mic()`](https://amr-for-r.org/reference/plot.md) and
|
||||
[`scale_fill_mic()`](https://amr-for-r.org/reference/plot.md). They
|
||||
allow easy plotting of MIC values. They allow for manual range
|
||||
definition and plotting missing intermediate log2 levels.
|
||||
- New function group `scale_*_sir()`, namely:
|
||||
[`scale_x_sir()`](https://amr-for-r.org/reference/plot.md),
|
||||
[`scale_colour_sir()`](https://amr-for-r.org/reference/plot.md) and
|
||||
[`scale_fill_sir()`](https://amr-for-r.org/reference/plot.md). They
|
||||
allow to plot the `sir` class, and translates into the system
|
||||
language at default. They also set colourblind-safe colours to the
|
||||
plots.
|
||||
- New function
|
||||
[`rescale_mic()`](https://amr-for-r.org/reference/as.mic.md), which
|
||||
allows users to rescale MIC values to a manually set range. This is
|
||||
the powerhouse behind the `scale_*_mic()` functions, but it can be
|
||||
used independently to, for instance, compare equality in MIC
|
||||
distributions by rescaling them to the same range first.
|
||||
- **Support for Python**
|
||||
- While using R for the heavy lifting, [our ‘AMR’ Python
|
||||
Package](https://pypi.org/project/AMR/) was developed to run the AMR
|
||||
R package natively in Python. The Python package will always have
|
||||
the same version number as the R package, as it is built
|
||||
automatically with every code change.
|
||||
- **Support for `tidymodels`**
|
||||
- All antimicrobial selectors (such as
|
||||
[`aminoglycosides()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
and
|
||||
[`betalactams()`](https://amr-for-r.org/reference/antimicrobial_selectors.md))
|
||||
are now supported in `tidymodels` packages such as `recipe` and
|
||||
`parsnip`. See for more info [our
|
||||
tutorial](https://amr-for-r.org/articles/AMR_with_tidymodels.html)
|
||||
on using these AMR functions for predictive modelling.
|
||||
- **Other**
|
||||
- New function
|
||||
[`top_n_microorganisms()`](https://amr-for-r.org/reference/top_n_microorganisms.md)
|
||||
to filter a data set to the top *n* of any taxonomic property, e.g.,
|
||||
filter to the top 3 species, filter to any species in the top 5
|
||||
genera, or filter to the top 3 species in each of the top 5 genera
|
||||
- New function
|
||||
[`mo_group_members()`](https://amr-for-r.org/reference/mo_property.md)
|
||||
to retrieve the member microorganisms of a microorganism group. For
|
||||
example, `mo_group_members("Strep group C")` returns a vector of all
|
||||
microorganisms that belong to that group.
|
||||
- New functions
|
||||
[`mic_p50()`](https://amr-for-r.org/reference/as.mic.md) and
|
||||
[`mic_p90()`](https://amr-for-r.org/reference/as.mic.md) to retrieve
|
||||
the 50th and 90th percentile of MIC values.
|
||||
|
||||
#### Changed
|
||||
|
||||
- SIR interpretation
|
||||
- Support for parallel computing to greatly improve speed using the
|
||||
`parallel` package (part of base R). Use
|
||||
`as.sir(your_data, parallel = TRUE)` to run SIR interpretation using
|
||||
multiple cores.
|
||||
- It is now possible to use column names for arguments `guideline`,
|
||||
`ab`, `mo`, and `uti`:
|
||||
`as.sir(..., ab = "column1", mo = "column2", uti = "column3")`. This
|
||||
greatly improves the flexibility for users.
|
||||
- Users can now set their own criteria (using regular expressions) as
|
||||
to what should be considered S, I, R, SDD, and NI.
|
||||
- To get quantitative values,
|
||||
[`as.double()`](https://rdrr.io/r/base/double.html) on a `sir`
|
||||
object will return 1 for S, 2 for SDD/I, and 3 for R (NI will become
|
||||
`NA`). Other functions using `sir` classes (e.g.,
|
||||
[`summary()`](https://rdrr.io/r/base/summary.html)) are updated to
|
||||
reflect the change to contain NI and SDD.
|
||||
- Following CLSI interpretation rules, values outside the
|
||||
log2-dilution range will be rounded upwards to the nearest
|
||||
log2-level before interpretation. Only if using a CLSI guideline.
|
||||
- Combined MIC values (e.g., from CLSI) are now supported
|
||||
- The argument `conserve_capped_values` in
|
||||
[`as.sir()`](https://amr-for-r.org/reference/as.sir.md) has been
|
||||
replaced with `capped_mic_handling`, which allows greater
|
||||
flexibility in handling capped MIC values (`<`, `<=`, `>`, `>=`).
|
||||
The four available options (`"standard"`, `"strict"`, `"relaxed"`,
|
||||
`"inverse"`) provide full control over whether these values should
|
||||
be interpreted conservatively or ignored. Using
|
||||
`conserve_capped_values` is now deprecated and returns a warning.
|
||||
- Added argument `info` to silence all console messages
|
||||
- [`antibiogram()`](https://amr-for-r.org/reference/antibiogram.md)
|
||||
function
|
||||
- Argument `antibiotics` has been renamed to `antimicrobials`. Using
|
||||
`antibiotics` will still work, but now returns a warning.
|
||||
- Added argument `formatting_type` to set any of the 22 options for
|
||||
the formatting of all ‘cells’. This defaults to `18` for non-WISCA
|
||||
and `14` for WISCA, changing the output of antibiograms to cells
|
||||
with more info.
|
||||
- For this reason, `add_total_n` is now deprecated and `FALSE` at
|
||||
default since the denominators are added to the cells dependent on
|
||||
the `formatting_type` setting
|
||||
- The `ab_transform` argument now defaults to `"name"`, displaying
|
||||
antibiotic column names instead of codes
|
||||
- Antimicrobial selectors (previously: *antibiotic selectors*)
|
||||
- ‘Antibiotic selectors’ are now called ‘antimicrobial selectors’
|
||||
since their scope is broader than just antibiotics. All
|
||||
documentation have been updated, and
|
||||
[`ab_class()`](https://amr-for-r.org/reference/AMR-deprecated.md)
|
||||
and
|
||||
[`ab_selector()`](https://amr-for-r.org/reference/AMR-deprecated.md)
|
||||
have been replaced with
|
||||
[`amr_class()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
and
|
||||
[`amr_selector()`](https://amr-for-r.org/reference/antimicrobial_selectors.md).
|
||||
The old functions are now deprecated and will be removed in a future
|
||||
version.
|
||||
- Added selectors
|
||||
[`isoxazolylpenicillins()`](https://amr-for-r.org/reference/antimicrobial_selectors.md),
|
||||
[`monobactams()`](https://amr-for-r.org/reference/antimicrobial_selectors.md),
|
||||
[`nitrofurans()`](https://amr-for-r.org/reference/antimicrobial_selectors.md),
|
||||
[`phenicols()`](https://amr-for-r.org/reference/antimicrobial_selectors.md),
|
||||
[`rifamycins()`](https://amr-for-r.org/reference/antimicrobial_selectors.md),
|
||||
and
|
||||
[`sulfonamides()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
- When using antimicrobial selectors that exclude non-treatable drugs
|
||||
(such as gentamicin-high when using
|
||||
[`aminoglycosides()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)),
|
||||
the function now always returns a warning that these can be included
|
||||
using `only_treatable = FALSE`
|
||||
- Added a new argument `return_all` to all selectors, which defaults
|
||||
to `TRUE` to include any match. With `FALSE`, the old behaviour,
|
||||
only the first hit for each unique antimicrobial is returned.
|
||||
- All selectors can now be run as a separate command to retrieve a
|
||||
vector of all possible antimicrobials that the selector can select
|
||||
- The selectors
|
||||
[`lincosamides()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
and
|
||||
[`macrolides()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
do not overlap anymore - each antibiotic is now classified as either
|
||||
of these and not both
|
||||
- Fixed selector
|
||||
[`fluoroquinolones()`](https://amr-for-r.org/reference/antimicrobial_selectors.md),
|
||||
which now really only selects second-generation quinolones and up
|
||||
(first-generation quinolones do not contain a fluorine group)
|
||||
- `antimicrobials` data set
|
||||
- Added agents used for screening, with an ID all ending with `-S`:
|
||||
benzylpenicillin screening test (`PEN-S`), beta-lactamase screening
|
||||
test (`BLA-S`), cefotaxime screening test (`CTX-S`), clindamycin
|
||||
inducible screening test (`CLI-S`), nalidixic acid screening test
|
||||
(`NAL-S`), norfloxacin screening test (`NOR-S`), oxacillin screening
|
||||
test (`OXA-S`), pefloxacin screening test (`PEF-S`), and
|
||||
tetracycline screening test (`TCY-S`). The ID of cefoxitin screening
|
||||
was renamed from `FOX1` to `FOX-S`, while the old code remains to
|
||||
work.
|
||||
- For this reason, the antimicrobial selectors
|
||||
[`cephalosporins()`](https://amr-for-r.org/reference/antimicrobial_selectors.md),
|
||||
[`cephalosporins_3rd()`](https://amr-for-r.org/reference/antimicrobial_selectors.md),
|
||||
[`lincosamides()`](https://amr-for-r.org/reference/antimicrobial_selectors.md),
|
||||
[`isoxazolylpenicillins()`](https://amr-for-r.org/reference/antimicrobial_selectors.md),
|
||||
[`quinolones()`](https://amr-for-r.org/reference/antimicrobial_selectors.md),
|
||||
[`fluoroquinolones()`](https://amr-for-r.org/reference/antimicrobial_selectors.md),
|
||||
and
|
||||
[`tetracyclines()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
now contain the argument `only_treatable = TRUE` (similar to other
|
||||
antimicrobial selectors that contain non-treatable drugs)
|
||||
- Added amorolfine (`AMO`, D01AE16), an antimycotic, which is now also
|
||||
part of the
|
||||
[`antifungals()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
selector
|
||||
- Added cefepime/enmetazobactam (`FPE`), a 4th gen cephalosporin
|
||||
- Added tigemonam (`TNM`), a monobactam
|
||||
- Added bleomycin (`BLM`), a glycopeptide
|
||||
- Added efflux (`EFF`), to allow mapping to AMRFinderPlus
|
||||
- Updated all ATC codes, trade names, and DDDs
|
||||
- MICs
|
||||
- Added as valid levels: 4096, 6 powers of 0.0625, and 5 powers of 192
|
||||
(192, 384, 576, 768, 960)
|
||||
- Fixed a bug in
|
||||
[`as.mic()`](https://amr-for-r.org/reference/as.mic.md) that failed
|
||||
translation of scientifically formatted numbers
|
||||
- Added new argument `keep_operators` to
|
||||
[`as.mic()`](https://amr-for-r.org/reference/as.mic.md). This can be
|
||||
`"all"` (default), `"none"`, or `"edges"`. This argument is also
|
||||
available in the new
|
||||
[`rescale_mic()`](https://amr-for-r.org/reference/as.mic.md) and
|
||||
`scale_*_mic()` functions.
|
||||
- Comparisons of MIC values are now more strict. For example, `>32` is
|
||||
higher than (and never equal to) `32`. Thus,
|
||||
`as.mic(">32") == as.mic(32)` now returns `FALSE`, and
|
||||
`as.mic(">32") > as.mic(32)` now returns `TRUE`.
|
||||
- Sorting of MIC values (using
|
||||
[`sort()`](https://rdrr.io/r/base/sort.html)) was fixed in the same
|
||||
manner; `<0.001` now gets sorted before `0.001`, and `>0.001` gets
|
||||
sorted after `0.001`.
|
||||
- Intermediate log2 levels used for MIC plotting are now more common
|
||||
values instead of following a strict dilution range
|
||||
- [`is.mic()`](https://amr-for-r.org/reference/as.mic.md) now returns
|
||||
a vector of `TRUE`/`FALSE` if the input is a `data.frame`, just like
|
||||
[`as.sir()`](https://amr-for-r.org/reference/as.sir.md)
|
||||
- [`eucast_rules()`](https://amr-for-r.org/reference/eucast_rules.md)
|
||||
now has an argument `overwrite` (default: `FALSE`) to indicate whether
|
||||
non-`NA` values should be overwritten
|
||||
- Disks of 0 to 5 mm are now allowed, the newly allowed range for disk
|
||||
diffusion ([`as.disk()`](https://amr-for-r.org/reference/as.disk.md))
|
||||
is now between 0 and 50 mm
|
||||
- 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)
|
||||
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
|
||||
contains an extra element `rank` and `group_members` (with the
|
||||
contents of the new
|
||||
[`mo_group_members()`](https://amr-for-r.org/reference/mo_property.md)
|
||||
function)
|
||||
- Updated all ATC codes from WHOCC
|
||||
- Updated all antimicrobial DDDs from WHOCC
|
||||
- Fix for using a manual value for `mo_transform` in
|
||||
[`antibiogram()`](https://amr-for-r.org/reference/antibiogram.md)
|
||||
- Fixed a bug for when
|
||||
[`antibiogram()`](https://amr-for-r.org/reference/antibiogram.md)
|
||||
returns an empty data set
|
||||
- Argument `only_sir_columns` now defaults to `TRUE` if any column of a
|
||||
data set contains a class ‘sir’ (functions
|
||||
[`eucast_rules()`](https://amr-for-r.org/reference/eucast_rules.md),
|
||||
[`key_antimicrobials()`](https://amr-for-r.org/reference/key_antimicrobials.md),
|
||||
[`mdro()`](https://amr-for-r.org/reference/mdro.md), etc.)
|
||||
- Added Sensititre codes for animals, antimicrobials and microorganisms
|
||||
- Fix for mapping ‘high level’ antimicrobials in
|
||||
[`as.ab()`](https://amr-for-r.org/reference/as.ab.md) (amphotericin
|
||||
B-high, gentamicin-high, kanamycin-high, streptomycin-high,
|
||||
tobramycin-high)
|
||||
- Improved overall algorithm of
|
||||
[`as.ab()`](https://amr-for-r.org/reference/as.ab.md) for better
|
||||
performance and accuracy, including the new function
|
||||
`as_reset_session()` to remove earlier coercions.
|
||||
- Improved overall algorithm of
|
||||
[`as.mo()`](https://amr-for-r.org/reference/as.mo.md) for better
|
||||
performance and accuracy, specifically:
|
||||
- More weight is given to genus and species combinations in cases
|
||||
where the subspecies is miswritten, so that the result will be the
|
||||
correct genus and species
|
||||
- Genera from the World Health Organization’s (WHO) Priority Pathogen
|
||||
List now have the highest prevalence
|
||||
- Fixed a bug for
|
||||
[`sir_confidence_interval()`](https://amr-for-r.org/reference/proportion.md)
|
||||
when there are no isolates available
|
||||
- Updated the prevalence calculation to include genera from the World
|
||||
Health Organization’s (WHO) Priority Pathogen List
|
||||
- Improved algorithm of
|
||||
[`first_isolate()`](https://amr-for-r.org/reference/first_isolate.md)
|
||||
when using the phenotype-based method, to prioritise records with the
|
||||
highest availability of SIR values
|
||||
- [`scale_y_percent()`](https://amr-for-r.org/reference/plot.md) can now
|
||||
cope with ranges outside the 0-100% range
|
||||
- MDRO determination (using
|
||||
[`mdro()`](https://amr-for-r.org/reference/mdro.md))
|
||||
- The Verbose Mode (`verbose = TRUE`) now includes the guideline name
|
||||
- Implemented the new Dutch national MDRO guideline (SRI-richtlijn
|
||||
BRMO, Nov 2024)
|
||||
- Added arguments `esbl`, `carbapenemase`, `mecA`, `mecC`, `vanA`,
|
||||
`vanB` to denote column names or logical values indicating presence
|
||||
of these genes (or production of their proteins)
|
||||
- Added upport for antimicrobial selectors to use as as a custom rule
|
||||
([`custom_mdro_guideline()`](https://amr-for-r.org/reference/custom_mdro_guideline.md))
|
||||
- Added console colours support of `sir` class for Positron
|
||||
|
||||
#### Other
|
||||
|
||||
- New website domain: <https://amr-for-r.org>! The old domain will
|
||||
remain to work.
|
||||
- Added Dr. Larisse Bolton and Aislinn Cook as contributors for their
|
||||
fantastic implementation of WISCA in a mathematically solid way
|
||||
- Added Matthew Saab, Dr. Jordan Stull, and Prof. Javier Sanchez as
|
||||
contributors for their tremendous input on veterinary breakpoints and
|
||||
interpretations
|
||||
- Added Prof. Kathryn Holt, Dr. Jane Hawkey, and Dr. Natacha Couto as
|
||||
contributors for their many suggestions, ideas and bugfixes
|
||||
- Greatly improved `vctrs` integration, a Tidyverse package working in
|
||||
the background for many Tidyverse functions. For users, this means
|
||||
that functions such as `dplyr`’s
|
||||
[`bind_rows()`](https://dplyr.tidyverse.org/reference/bind_rows.html),
|
||||
[`rowwise()`](https://dplyr.tidyverse.org/reference/rowwise.html) and
|
||||
[`c_across()`](https://dplyr.tidyverse.org/reference/c_across.html)
|
||||
are now supported for e.g. columns of class `mic`. Despite this, this
|
||||
`AMR` package is still zero-dependent on any other package, including
|
||||
`dplyr` and `vctrs`.
|
||||
- Greatly updated and expanded documentation
|
||||
- Stopped support for SAS (`.xpt`) files, since their file structure and
|
||||
extremely inefficient and requires more disk space than GitHub allows
|
||||
in a single commit.
|
||||
|
||||
### Older Versions
|
||||
|
||||
This changelog only contains changes from AMR v3.0 (June 2025) and
|
||||
later.
|
||||
|
||||
- For prior v2 versions, please see [our v2
|
||||
archive](https://github.com/msberends/AMR/blob/v2.1.1/NEWS.md).
|
||||
- For prior v1 versions, please see [our v1
|
||||
archive](https://github.com/msberends/AMR/blob/v1.8.2/NEWS.md).
|
||||
Reference in New Issue
Block a user