mirror of https://github.com/msberends/AMR.git
92 lines
8.8 KiB
Markdown
92 lines
8.8 KiB
Markdown
# AMR 2.1.1.9078
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*(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using [the instructions here](https://msberends.github.io/AMR/#latest-development-version).)*
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#### A New Milestone: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental)
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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.
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## Breaking
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* Removed all functions and references that used the deprecated `rsi` class, which were all replaced with their `sir` equivalents over a year ago
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## New
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* One Health implementation
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* Function `as.sir()` now has extensive support for animal breakpoints from CLSI. Use `breakpoint_type = "animal"` and set the `host` argument to a variable that contains animal species names.
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* The `clinical_breakpoints` data set contains all these breakpoints, and can be downloaded on our [download page](https://msberends.github.io/AMR/articles/datasets.html).
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* The `antibiotics` data set contains all veterinary antibiotics, such as pradofloxacin and enrofloxacin. All WHOCC codes for veterinary use have been added as well.
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* `ab_atc()` now supports ATC codes of veterinary antibiotics (that all start with "Q")
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* `ab_url()` now supports retrieving the WHOCC url of their ATCvet pages
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* Clinical breakpoints
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* EUCAST 2024 and CLSI 2024 are now supported, by adding all of their over 4,000 new clinical breakpoints to the `clinical_breakpoints` data set for usage in `as.sir()`. EUCAST 2024 is now the new default guideline for all MIC and disks diffusion interpretations.
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* `as.sir()` 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".
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* MIC plotting and transforming
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* New function group `scale_*_mic()`, namely: `scale_x_mic()`, `scale_y_mic()`, `scale_colour_mic()` and `scale_fill_mic()`. They are advanced ggplot2 extensions to allow easy plotting of MIC values. They allow for manual range definition and plotting missing intermediate log2 levels.
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* New function `rescale_mic()`, which allows to rescale MIC values to a manually set range. This is the powerhouse behind the `scale_*_mic()` functions, but it can be used by users directly to e.g. compare equality in MIC distributions by rescaling them to the same range first.
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* Microbiological taxonomy (`microorganisms` data set) updated to June 2024, with some exciting new features:
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* Added MycoBank as the primary taxonomic source for fungi
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* The `microorganisms` data set now contains additional columns `mycobank`, `mycobank_parent`, and `mycobank_renamed_to`
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* New function `mo_mycobank()` to get the MycoBank record number, analogous to existing functions `mo_lpsn()` and `mo_gbif()`
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* We've welcomed over 2,000 records from 2023, over 900 from 2024, and many thousands of new fungi
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* Improved support for mycologists:
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* The `as.mo()` function now includes a new argument, `only_fungi` (TRUE/FALSE), which limits the results to fungi only. Normally, bacteria are often prioritised by the algorithm, but setting `only_fungi = TRUE` ensures only fungi are returned.
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* You can also set this globally using the new R option `AMR_only_fungi`, e.g., `options(AMR_only_fungi = TRUE)`.
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* Other
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* New function `mo_group_members()` to retrieve the member microorganisms of a microorganism group. For example, `mo_group_members("Strep group C")` returns a vector of all microorganisms that are in that group.
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## Changed
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* SIR interpretation
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* It is now possible to use column names for argument `ab`, `mo`, and `uti`: `as.sir(..., ab = "column1", mo = "column2", uti = "column3")`. This greatly improves the flexibility for users.
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* Users can now set their own criteria (using regular expressions) as to what should be considered S, I, R, SDD, and NI.
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* To get quantitative values, `as.double()` 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()`) are updated to reflect the change to contain NI and SDD.
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* `antibiogram()` function
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* New argument `formatting_type` to set any of the 12 options for the formatting of all 'cells'. This defaults to `10`, changing the output of antibiograms to cells with `5% (15/300)` instead of the previous standard of just `5`.
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* For this reason, `add_total_n` is now `FALSE` at default since the denominators are added to the cells
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* The `ab_transform` argument now defaults to `"name"`, displaying antibiotic column names instead of codes
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* `antibiotics` data set
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* Added "clindamycin inducible screening" as `CLI1`. Since clindamycin is a lincosamide, the antibiotic selector `lincosamides()` now contains the argument `only_treatable = TRUE` (similar to other antibiotic selectors that contain non-treatable drugs)
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* Added Amorolfine (`AMO`, D01AE16), which is now also part of the `antifungals()` selector
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* Antibiotic selectors
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* Added selectors `nitrofurans()` and `rifamycins()`
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* When using antibiotic selectors such as `aminoglycosides()` that exclude non-treatable drugs like gentamicin-high, the function now always returns a warning that these can be included using `only_treatable = FALSE`
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* MICs
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* Added as valid levels: 4096, 6 powers of 0.0625, and 5 powers of 192 (192, 384, 576, 768, 960)
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* Added new argument `keep_operators` to `as.mic()`. This can be `"all"` (default), `"none"`, or `"edges"`. This argument is also available in the new `rescale_mic()` and `scale_*_mic()` functions.
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* 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`.
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* Sorting of MIC values (using `sort()`) was fixed in the same manner; `<0.001` now gets sorted before `0.001`, and `>0.001` gets sorted after `0.001`.
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* Updated `italicise_taxonomy()` to support HTML output
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* `custom_eucast_rules()` now supports multiple antibiotics and antibiotic groups to be affected by a single rule
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* `mo_info()` now contains an extra element `group_members`, with the contents of the new `mo_group_members()` function
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* 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()`, `rowwise()` and `c_across()` 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`.
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* Updated all ATC codes from WHOCC
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* Updated all antibiotic DDDs from WHOCC
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* Fix for using a manual value for `mo_transform` in `antibiogram()`
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* Fix for mapping 'high level' antibiotics in `as.ab()` (amphotericin B-high, gentamicin-high, kanamycin-high, streptomycin-high, tobramycin-high)
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* Improved overall algorithm of `as.ab()` for better performance and accuracy
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* Improved overall algorithm of `as.mo()` 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.
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* Intermediate log2 levels used for MIC plotting are now more common values instead of following a strict dilution range
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* Fixed a bug for when `antibiogram()` returns an empty data set
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## Other
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* Greatly updated and expanded documentation
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* Added Jordan Stull, Matthew Saab, and Javier Sanchez as contributors, to thank them for their valuable input
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# AMR 2.1.1
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* Fix for selecting first isolates using the phenotype-based method
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* This included too many isolates when patients had altering antibiograms within the same bacterial species
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* See for more info [our issue #122](https://github.com/msberends/AMR/issues/122)
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* Added 1,366 LOINC codes to the `antibiotics` data set and updated to the latest version (LOINC v2.76)
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* MICs can now be used in complex number calculations and allow scientific number format as input (e.g., `as.mic("1.28e-2")`)
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* Fix rounding MICs on latest R beta ('R-devel')
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* Removed unneeded note about the used language when option `AMR_locale` is set
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* Fixed non-ASCII characters in documentation, according to CRAN maintainers
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----
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# Older versions
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This changelog only contains changes from AMR v3.0 (October 2024) and later.
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* For prior v2 versions, please see [our v2 archive](https://github.com/msberends/AMR/blob/v2.1.1/NEWS.md).
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* For prior v1 versions, please see [our v1 archive](https://github.com/msberends/AMR/blob/v1.8.2/NEWS.md).
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