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Package: AMR
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Version: 2.0.0.9040
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Version: 2.0.0.9041
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Date: 2023-07-12
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Title: Antimicrobial Resistance Data Analysis
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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7
NEWS.md
7
NEWS.md
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# AMR 2.0.0.9040
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# AMR 2.0.0.9041
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## New
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* Clinical breakpoints and intrinsic resistance of EUCAST 2023 and CLSI 2023 have been added for `as.sir()`. EUCAST 2023 (v13.0) is now the new default guideline for all MIC and disks diffusion interpretations
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* The EUCAST dosage guideline of v13.0 has been added to the `dosage` data set
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* ECOFF: the `clinical_breakpoints` data set now contains epidemiological cut-off (ECOFF) values. These ECOFFs can be used for MIC/disk interpretation using `as.sir(..., breakpoint_type = "ECOFF")`, which is an important new addition for veterinary microbiology.
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* Added support for 29 species groups / complexes. They are gathered in a new data set `microorganisms.groups` and are used in clinical breakpoint interpretation. For example, CLSI 2023 contains breakpoints for the RGM group (Rapidly Growing Mycobacterium, containing over 80 species) which is now supported by our package.
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* ECOFF and animal breakpoints: the `clinical_breakpoints` data set now contains epidemiological cut-off (ECOFF) values and CLSI animal breakpoints. These two new breakpoint types can be used for MIC/disk interpretation using `as.sir(..., breakpoint_type = "ECOFF")` or`as.sir(..., breakpoint_type = "animal")`, which is an important new addition for veterinary microbiology.
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* Added support for 30 species groups / complexes. They are gathered in a new data set `microorganisms.groups` and are used in clinical breakpoint interpretation. For example, CLSI 2023 contains breakpoints for the RGM group (Rapidly Growing Mycobacterium, containing over 80 species) which is now supported by our package.
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* Added oxygen tolerance from BacDive to over 25,000 bacteria in the `microorganisms` data set
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* Added `mo_oxygen_tolerance()` to retrieve the values
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* Added `mo_is_anaerobic()` to determine which genera/species are obligate anaerobic bacteria
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@ -14,6 +14,7 @@
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## Changed
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* Updated algorithm of `as.mo()` by giving more weight to fungi
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* Fixed clinical breakpoints errors introduced by the source we import the rules from
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* `mo_rank()` now returns `NA` for 'unknown' microorganisms (`B_ANAER`, `B_ANAER-NEG`, `B_ANAER-POS`, `B_GRAMN`, `B_GRAMP`, `F_FUNGUS`, `F_YEAST`, and `UNKNOWN`)
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* When printing microorganism or antibiotic codes in a tibble, a mouse-hover now shows the full name of the code
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* Plots for MIC and disk diffusion values:
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20
R/data.R
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R/data.R
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#' Two data sets containing all antibiotics/antimycotics and antivirals. Use [as.ab()] or one of the [`ab_*`][ab_property()] functions to retrieve values from the [antibiotics] data set. Three identifiers are included in this data set: an antibiotic ID (`ab`, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (`atc`) as defined by the WHO, and a Compound ID (`cid`) as found in PubChem. Other properties in this data set are derived from one or more of these codes. Note that some drugs have multiple ATC codes.
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#' @format
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#' ### For the [antibiotics] data set: a [tibble][tibble::tibble] with `r nrow(antibiotics)` observations and `r ncol(antibiotics)` variables:
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#' - `ab`\cr Antibiotic ID as used in this package (such as `AMC`), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available
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#' - `cid`\cr Compound ID as found in PubChem
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#' - `name`\cr Official name as used by WHONET/EARS-Net or the WHO
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#' - `ab`\cr Antibiotic ID as used in this package (such as `AMC`), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available. *This is a unique identifier.*
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#' - `cid`\cr Compound ID as found in PubChem. *This is a unique identifier.*
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#' - `name`\cr Official name as used by WHONET/EARS-Net or the WHO. *This is a unique identifier.*
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#' - `group`\cr A short and concise group name, based on WHONET and WHOCC definitions
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#' - `atc`\cr ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC, like `J01CR02`
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#' - `atc_group1`\cr Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC, like `"Macrolides, lincosamides and streptogramins"`
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#' - `loinc`\cr All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the name of the antimicrobial drug. Use [ab_loinc()] to retrieve them quickly, see [ab_property()].
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#'
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#' ### For the [antivirals] data set: a [tibble][tibble::tibble] with `r nrow(antivirals)` observations and `r ncol(antivirals)` variables:
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#' - `av`\cr Antibiotic ID as used in this package (such as `AMC`), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available
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#' - `name`\cr Official name as used by WHONET/EARS-Net or the WHO
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#' - `av`\cr Antibiotic ID as used in this package (such as `AMC`), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available. *This is a unique identifier.*
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#' - `name`\cr Official name as used by WHONET/EARS-Net or the WHO. *This is a unique identifier.*
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#' - `atc`\cr ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC
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#' - `cid`\cr Compound ID as found in PubChem
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#' - `cid`\cr Compound ID as found in PubChem. *This is a unique identifier.*
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#' - `atc_group`\cr Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC
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#' - `synonyms`\cr Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID
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#' - `oral_ddd`\cr Defined Daily Dose (DDD), oral treatment
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#'
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#' A data set containing the full microbial taxonomy (**last updated: `r documentation_date(max(TAXONOMY_VERSION$GBIF$accessed_date, TAXONOMY_VERSION$LPSN$accessed_date))`**) of `r nr2char(length(unique(microorganisms$kingdom[!microorganisms$kingdom %like% "unknown"])))` kingdoms from the List of Prokaryotic names with Standing in Nomenclature (LPSN) and the Global Biodiversity Information Facility (GBIF). This data set is the backbone of this `AMR` package. MO codes can be looked up using [as.mo()].
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#' @format A [tibble][tibble::tibble] with `r format(nrow(microorganisms), big.mark = " ")` observations and `r ncol(microorganisms)` variables:
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#' - `mo`\cr ID of microorganism as used by this package
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#' - `fullname`\cr Full name, like `"Escherichia coli"`. For the taxonomic ranks genus, species and subspecies, this is the 'pasted' text of genus, species, and subspecies. For all taxonomic ranks higher than genus, this is the name of the taxon.
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#' - `mo`\cr ID of microorganism as used by this package. *This is a unique identifier.*
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#' - `fullname`\cr Full name, like `"Escherichia coli"`. For the taxonomic ranks genus, species and subspecies, this is the 'pasted' text of genus, species, and subspecies. For all taxonomic ranks higher than genus, this is the name of the taxon. *This is a unique identifier.*
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#' - `status` \cr Status of the taxon, either `r vector_or(microorganisms$status)`
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#' - `kingdom`, `phylum`, `class`, `order`, `family`, `genus`, `species`, `subspecies`\cr Taxonomic rank of the microorganism
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#' - `rank`\cr Text of the taxonomic rank of the microorganism, such as `"species"` or `"genus"`
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#'
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#' A data set containing commonly used codes for microorganisms, from laboratory systems and [WHONET](https://whonet.org). Define your own with [set_mo_source()]. They will all be searched when using [as.mo()] and consequently all the [`mo_*`][mo_property()] functions.
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#' @format A [tibble][tibble::tibble] with `r format(nrow(microorganisms.codes), big.mark = " ")` observations and `r ncol(microorganisms.codes)` variables:
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#' - `code`\cr Commonly used code of a microorganism
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#' - `code`\cr Commonly used code of a microorganism. *This is a unique identifier.*
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#' - `mo`\cr ID of the microorganism in the [microorganisms] data set
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#' @details
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#' Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. Please visit [our website for the download links](https://msberends.github.io/AMR/articles/datasets.html). The actual files are of course available on [our GitHub repository](https://github.com/msberends/AMR/tree/main/data-raw).
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#' Clinical breakpoints in this package were validated through and imported from [WHONET](https://whonet.org), a free desktop Windows application developed and supported by the WHO Collaborating Centre for Surveillance of Antimicrobial Resistance. More can be read on [their website](https://whonet.org). The developers of WHONET and this `AMR` package have been in contact about sharing their work. We highly appreciate their development on the WHONET software.
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#'
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#' ### Response from CLSI and EUCAST
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#' The CEO of CLSI and the chairman of EUCAST have endorsed the work and public use of this `AMR` package in June 2023, when future development of distributing clinical breakpoints was discussed in a meeting between CLSI, EUCAST, the WHO, and developers of WHONET and the `AMR` package.
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#' The CEO of CLSI and the chairman of EUCAST have endorsed the work and public use of this `AMR` package (and consequently the use of their breakpoints) in June 2023, when future development of distributing clinical breakpoints was discussed in a meeting between CLSI, EUCAST, the WHO, and developers of WHONET and the `AMR` package.
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#'
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#' ### Download
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#' Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. Please visit [our website for the download links](https://msberends.github.io/AMR/articles/datasets.html). The actual files are of course available on [our GitHub repository](https://github.com/msberends/AMR/tree/main/data-raw). They allow for machine reading EUCAST and CLSI guidelines, which is almost impossible with the MS Excel and PDF files distributed by EUCAST and CLSI, though initiatives have started to overcome these burdens.
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\format{
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\subsection{For the \link{antibiotics} data set: a \link[tibble:tibble]{tibble} with 483 observations and 14 variables:}{
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\itemize{
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\item \code{ab}\cr Antibiotic ID as used in this package (such as \code{AMC}), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available
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\item \code{cid}\cr Compound ID as found in PubChem
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\item \code{name}\cr Official name as used by WHONET/EARS-Net or the WHO
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\item \code{ab}\cr Antibiotic ID as used in this package (such as \code{AMC}), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available. \emph{This is a unique identifier.}
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\item \code{cid}\cr Compound ID as found in PubChem. \emph{This is a unique identifier.}
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\item \code{name}\cr Official name as used by WHONET/EARS-Net or the WHO. \emph{This is a unique identifier.}
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\item \code{group}\cr A short and concise group name, based on WHONET and WHOCC definitions
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\item \code{atc}\cr ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC, like \code{J01CR02}
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\item \code{atc_group1}\cr Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC, like \code{"Macrolides, lincosamides and streptogramins"}
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\subsection{For the \link{antivirals} data set: a \link[tibble:tibble]{tibble} with 120 observations and 11 variables:}{
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\itemize{
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\item \code{av}\cr Antibiotic ID as used in this package (such as \code{AMC}), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available
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\item \code{name}\cr Official name as used by WHONET/EARS-Net or the WHO
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\item \code{av}\cr Antibiotic ID as used in this package (such as \code{AMC}), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available. \emph{This is a unique identifier.}
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\item \code{name}\cr Official name as used by WHONET/EARS-Net or the WHO. \emph{This is a unique identifier.}
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\item \code{atc}\cr ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC
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\item \code{cid}\cr Compound ID as found in PubChem
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\item \code{cid}\cr Compound ID as found in PubChem. \emph{This is a unique identifier.}
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\item \code{atc_group}\cr Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC
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\item \code{synonyms}\cr Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID
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\item \code{oral_ddd}\cr Defined Daily Dose (DDD), oral treatment
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\subsection{Response from CLSI and EUCAST}{
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The CEO of CLSI and the chairman of EUCAST have endorsed the work and public use of this \code{AMR} package in June 2023, when future development of distributing clinical breakpoints was discussed in a meeting between CLSI, EUCAST, the WHO, and developers of WHONET and the \code{AMR} package.
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The CEO of CLSI and the chairman of EUCAST have endorsed the work and public use of this \code{AMR} package (and consequently the use of their breakpoints) in June 2023, when future development of distributing clinical breakpoints was discussed in a meeting between CLSI, EUCAST, the WHO, and developers of WHONET and the \code{AMR} package.
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}
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\subsection{Download}{
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\format{
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A \link[tibble:tibble]{tibble} with 52 169 observations and 23 variables:
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\itemize{
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\item \code{mo}\cr ID of microorganism as used by this package
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\item \code{fullname}\cr Full name, like \code{"Escherichia coli"}. For the taxonomic ranks genus, species and subspecies, this is the 'pasted' text of genus, species, and subspecies. For all taxonomic ranks higher than genus, this is the name of the taxon.
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\item \code{mo}\cr ID of microorganism as used by this package. \emph{This is a unique identifier.}
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\item \code{fullname}\cr Full name, like \code{"Escherichia coli"}. For the taxonomic ranks genus, species and subspecies, this is the 'pasted' text of genus, species, and subspecies. For all taxonomic ranks higher than genus, this is the name of the taxon. \emph{This is a unique identifier.}
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\item \code{status} \cr Status of the taxon, either "accepted" or "synonym"
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\item \code{kingdom}, \code{phylum}, \code{class}, \code{order}, \code{family}, \code{genus}, \code{species}, \code{subspecies}\cr Taxonomic rank of the microorganism
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\item \code{rank}\cr Text of the taxonomic rank of the microorganism, such as \code{"species"} or \code{"genus"}
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\format{
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A \link[tibble:tibble]{tibble} with 4 957 observations and 2 variables:
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\itemize{
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\item \code{code}\cr Commonly used code of a microorganism
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\item \code{code}\cr Commonly used code of a microorganism. \emph{This is a unique identifier.}
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\item \code{mo}\cr ID of the microorganism in the \link{microorganisms} data set
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}
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}
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@ -221,6 +221,12 @@ This data set is in R available as `clinical_breakpoints`, after you load the `A
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This data set contains interpretation rules for MIC values and disk diffusion diameters. Included guidelines are CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "CLSI")$guideline)))`) and EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`).
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Clinical breakpoints in this package were validated through and imported from [WHONET](https://whonet.org), a free desktop Windows application developed and supported by the WHO Collaborating Centre for Surveillance of Antimicrobial Resistance. More can be read on [their website](https://whonet.org). The developers of WHONET and this `AMR` package have been in contact about sharing their work. We highly appreciate their development on the WHONET software.
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The CEO of CLSI and the chairman of EUCAST have endorsed the work and public use of this `AMR` package (and consequently the use of their breakpoints) in June 2023, when future development of distributing clinical breakpoints was discussed in a meeting between CLSI, EUCAST, the WHO, and developers of WHONET and the `AMR` package.
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**NOTE:** this `AMR` package (and the WHONET software as well) contains internal methods to apply the guidelines, which is rather complex. For example, some breakpoints must be applied on certain species groups (which are in case of this package available through the `microorganisms.groups` data set). It is important that this is considered when using the breakpoints for own use.
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### Example content
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```{r, echo = FALSE}
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