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(v2.1.1.9081) HUGE microorganisms update for fungi!

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dr. M.S. (Matthijs) Berends
2024-09-29 22:17:56 +02:00
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commit ac1c40d8bb
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R/data.R
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@@ -64,7 +64,7 @@
#' Synonyms (i.e. trade names) were derived from the PubChem Compound ID (column `cid`) and consequently only available where a CID is available.
#'
#' ### Direct download
#' Like all data sets in this package, these data sets are 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).
#' Like all data sets in this package, these data sets are publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, 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).
#' @source
#'
#' * World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology (WHOCC): <https://atcddd.fhi.no/atc_ddd_index/>
@@ -136,7 +136,7 @@
#' The syntax used to transform the original data to a cleansed \R format, can be [found here](https://github.com/msberends/AMR/blob/main/data-raw/reproduction_of_microorganisms.R).
#'
#' ### Direct download
#' 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).
#' 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, 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).
#' @source
#' Taxonomic entries were imported in this order of importance:
#' 1. `r TAXONOMY_VERSION$LPSN$name`:\cr\cr
@@ -171,7 +171,7 @@
#' - `code`\cr Commonly used code of a microorganism. ***This is a unique identifier.***
#' - `mo`\cr ID of the microorganism in the [microorganisms] data set
#' @details
#' 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).
#' 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, 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).
#' @seealso [as.mo()] [microorganisms]
#' @examples
#' microorganisms.codes
@@ -195,7 +195,7 @@
#' - `mo_group_name`\cr Name of the species group / microbiological complex, as retrieved with [mo_name()]
#' - `mo_name`\cr Name of the microorganism belonging in the species group / microbiological complex, as retrieved with [mo_name()]
#' @details
#' 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).
#' 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, 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).
#' @seealso [as.mo()] [microorganisms]
#' @examples
#' microorganisms.groups
@@ -216,7 +216,7 @@
#' - `mo`\cr ID of microorganism created with [as.mo()], see also the [microorganisms] data set
#' - `PEN:RIF`\cr `r sum(vapply(FUN.VALUE = logical(1), example_isolates, is.sir))` different antibiotics with class [`sir`] (see [as.sir()]); these column names occur in the [antibiotics] data set and can be translated with [set_ab_names()] or [ab_name()]
#' @details
#' 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).
#' 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, 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).
#' @examples
#' example_isolates
"example_isolates"
@@ -231,7 +231,7 @@
#' - `bacteria`\cr info about microorganism that can be transformed with [as.mo()], see also [microorganisms]
#' - `AMX:GEN`\cr 4 different antibiotics that have to be transformed with [as.sir()]
#' @details
#' 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).
#' 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, 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).
#' @examples
#' example_isolates_unclean
"example_isolates_unclean"
@@ -267,7 +267,7 @@
#' - `Date of data entry`\cr [Date] this data was entered in WHONET
#' - `AMP_ND10:CIP_EE`\cr `r sum(vapply(FUN.VALUE = logical(1), WHONET, is.sir))` different antibiotics. You can lookup the abbreviations in the [antibiotics] data set, or use e.g. [`ab_name("AMP")`][ab_name()] to get the official name immediately. Before analysis, you should transform this to a valid antibiotic class, using [as.sir()].
#' @details
#' 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).
#' 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, 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).
#' @examples
#' WHONET
"WHONET"
@@ -310,7 +310,7 @@
#' 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, WHO, developers of WHONET software, and developers of this `AMR` package.
#'
#' ### Download
#' 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.
#' 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, 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.
#'
#' **NOTE:** this `AMR` package (and the WHONET software as well) contains rather complex internal methods to apply the guidelines. 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.
#' @seealso [intrinsic_resistant]
@@ -328,7 +328,7 @@
#' This data set is based on `r format_eucast_version_nr(3.3)`.
#'
#' ### Direct download
#' 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).
#' 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, 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.
#' @examples
@@ -349,7 +349,7 @@
#' - `original_txt`\cr Original text in the PDF file of EUCAST
#' - `eucast_version`\cr Version number of the EUCAST Clinical Breakpoints guideline to which these dosages apply, either `r vector_or(dosage$eucast_version, quotes = FALSE, sort = TRUE, reverse = TRUE)`
#' @details
#' 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).
#' 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, 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).
#' @examples
#' dosage
"dosage"