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support veterinary MIC/disk translation

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dr. M.S. (Matthijs) Berends
2024-02-24 15:16:52 +01:00
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20
man/AMR-options.Rd
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@ -9,17 +9,17 @@ This is an overview of all the package-specific \code{\link[=options]{options()}
\section{Options}{
\itemize{
\item \code{AMR_custom_ab} \cr Allows to use custom antimicrobial drugs with this package. This is explained in \code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}}.
\item \code{AMR_custom_mo} \cr Allows to use custom microorganisms with this package. This is explained in \code{\link[=add_custom_microorganisms]{add_custom_microorganisms()}}.
\item \code{AMR_eucastrules} \cr Used for setting the default types of rules for \code{\link[=eucast_rules]{eucast_rules()}} function, must be one or more of: \code{"breakpoints"}, \code{"expert"}, \code{"other"}, \code{"custom"}, \code{"all"}, and defaults to \code{c("breakpoints", "expert")}.
\item \code{AMR_guideline} \cr Used for setting the default guideline for interpreting MIC values and disk diffusion diameters with \code{\link[=as.sir]{as.sir()}}. Can be only the guideline name (e.g., \code{"CLSI"}) or the name with a year (e.g. \code{"CLSI 2019"}). The default to the latest implemented EUCAST guideline, currently \code{"EUCAST 2023"}. Supported guideline are currently EUCAST (2011-2023) and CLSI (2011-2023).
\item \code{AMR_breakpoint_type} \cr A \link{character} to use in \code{\link[=as.sir]{as.sir()}}, to indicate which breakpoint type to use. This must be either "ECOFF", "animal", or "human".
\item \code{AMR_cleaning_regex} \cr A \link[base:regex]{regular expression} (case-insensitive) to use in \code{\link[=as.mo]{as.mo()}} and all \code{\link[=mo_property]{mo_*}} functions, to clean the user input. The default is the outcome of \code{\link[=mo_cleaning_regex]{mo_cleaning_regex()}}, which removes texts between brackets and texts such as "species" and "serovar".
\item \code{AMR_custom_ab} \cr A file location to an RDS file, to use custom antimicrobial drugs with this package. This is explained in \code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}}.
\item \code{AMR_custom_mo} \cr A file location to an RDS file, to use custom microorganisms with this package. This is explained in \code{\link[=add_custom_microorganisms]{add_custom_microorganisms()}}.
\item \code{AMR_eucastrules} \cr A \link{character} to set the default types of rules for \code{\link[=eucast_rules]{eucast_rules()}} function, must be one or more of: \code{"breakpoints"}, \code{"expert"}, \code{"other"}, \code{"custom"}, \code{"all"}, and defaults to \code{c("breakpoints", "expert")}.
\item \code{AMR_guideline} \cr A \link{character} to set the default guideline for interpreting MIC values and disk diffusion diameters with \code{\link[=as.sir]{as.sir()}}. Can be only the guideline name (e.g., \code{"CLSI"}) or the name with a year (e.g. \code{"CLSI 2019"}). The default to the latest implemented EUCAST guideline, currently \code{"EUCAST 2023"}. Supported guideline are currently EUCAST (2011-2023) and CLSI (2011-2023).
\item \code{AMR_ignore_pattern} \cr A \link[base:regex]{regular expression} to ignore (i.e., make \code{NA}) any match given in \code{\link[=as.mo]{as.mo()}} and all \code{\link[=mo_property]{mo_*}} functions.
\item \code{AMR_include_PKPD} \cr A \link{logical} to use in \code{\link[=as.sir]{as.sir()}}, to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is \code{TRUE}.
\item \code{AMR_ecoff} \cr A \link{logical} use in \code{\link[=as.sir]{as.sir()}}, to indicate that ECOFF (Epidemiological Cut-Off) values must be used - the default is \code{FALSE}.
\item \code{AMR_include_screening} \cr A \link{logical} to use in \code{\link[=as.sir]{as.sir()}}, to indicate that clinical breakpoints for screening are allowed - the default is \code{FALSE}.
\item \code{AMR_keep_synonyms} \cr A \link{logical} to use in \code{\link[=as.mo]{as.mo()}} and all \code{\link[=mo_property]{mo_*}} functions, to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. The default is \code{FALSE}.
\item \code{AMR_cleaning_regex} \cr A \link[base:regex]{regular expression} (case-insensitive) to use in \code{\link[=as.mo]{as.mo()}} and all \code{\link[=mo_property]{mo_*}} functions, to clean the user input. The default is the outcome of \code{\link[=mo_cleaning_regex]{mo_cleaning_regex()}}, which removes texts between brackets and texts such as "species" and "serovar".
\item \code{AMR_locale} \cr A language to use for the \code{AMR} package, can be one of these supported language names or ISO-639-1 codes: English (en), Chinese (zh), Czech (cs), Danish (da), Dutch (nl), Finnish (fi), French (fr), German (de), Greek (el), Italian (it), Japanese (ja), Norwegian (no), Polish (pl), Portuguese (pt), Romanian (ro), Russian (ru), Spanish (es), Swedish (sv), Turkish (tr), or Ukrainian (uk). The default is the current system language (if supported).
\item \code{AMR_locale} \cr A \link{character} to set the language for the \code{AMR} package, can be one of these supported language names or ISO-639-1 codes: English (en), Chinese (zh), Czech (cs), Danish (da), Dutch (nl), Finnish (fi), French (fr), German (de), Greek (el), Italian (it), Japanese (ja), Norwegian (no), Polish (pl), Portuguese (pt), Romanian (ro), Russian (ru), Spanish (es), Swedish (sv), Turkish (tr), or Ukrainian (uk). The default is the current system language (if supported, English otherwise).
\item \code{AMR_mo_source} \cr A file location for a manual code list to be used in \code{\link[=as.mo]{as.mo()}} and all \code{\link[=mo_property]{mo_*}} functions. This is explained in \code{\link[=set_mo_source]{set_mo_source()}}.
}
}
@ -31,16 +31,16 @@ Settings in \R are not saved globally and are thus lost when \R is exited. You c
\if{html}{\out{<div class="sourceCode r">}}\preformatted{ utils::file.edit("~/.Rprofile")
}\if{html}{\out{</div>}}
In this file, you can set options such as:
In this file, you can set options such as...
\if{html}{\out{<div class="sourceCode r">}}\preformatted{ options(AMR_locale = "pt")
options(AMR_include_PKPD = TRUE)
}\if{html}{\out{</div>}}
to add Portuguese language support of antibiotics, and allow PK/PD rules when interpreting MIC values with \code{\link[=as.sir]{as.sir()}}.
...to add Portuguese language support of antibiotics, and allow PK/PD rules when interpreting MIC values with \code{\link[=as.sir]{as.sir()}}.
\subsection{Share Options Within Team}{
For a more global approach, e.g. within a data team, save an options file to a remote file location, such as a shared network drive. This would work in this way:
For a more global approach, e.g. within a (data) team, save an options file to a remote file location, such as a shared network drive, and have each user read in this file automatically at start-up. This would work in this way:
\enumerate{
\item Save a plain text file to e.g. "X:/team_folder/R_options.R" and fill it with preferred settings.
\item For each user, open the \code{.Rprofile} file using \code{utils::file.edit("~/.Rprofile")} and put in there:

9
man/AMR.Rd
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@ -2,8 +2,8 @@
% Please edit documentation in R/aa_amr-package.R
\docType{package}
\name{AMR}
\alias{AMR}
\alias{AMR-package}
\alias{AMR}
\title{The \code{AMR} Package}
\source{
To cite AMR in publications use:
@ -32,7 +32,7 @@ The \code{AMR} package is a \href{https://msberends.github.io/AMR/#copyright}{fr
This work was published in the Journal of Statistical Software (Volume 104(3); \doi{10.18637/jss.v104.i03}) and formed the basis of two PhD theses (\doi{10.33612/diss.177417131} and \doi{10.33612/diss.192486375}).
After installing this package, R knows \href{https://msberends.github.io/AMR/reference/microorganisms.html}{\strong{~52 000 microorganisms}} (updated december 2022) and all \href{https://msberends.github.io/AMR/reference/antibiotics.html}{\strong{~600 antibiotic, antimycotic and antiviral drugs}} by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). \strong{It was designed to work in any setting, including those with very limited resources}. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the public \href{https://www.rug.nl}{University of Groningen}, in collaboration with non-profit organisations \href{https://www.certe.nl}{Certe Medical Diagnostics and Advice Foundation} and \href{https://www.umcg.nl}{University Medical Center Groningen}.
After installing this package, R knows \href{https://msberends.github.io/AMR/reference/microorganisms.html}{\strong{~52 000 microorganisms}} (updated January 2024) and all \href{https://msberends.github.io/AMR/reference/antibiotics.html}{\strong{~600 antibiotic, antimycotic and antiviral drugs}} by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). \strong{It was designed to work in any setting, including those with very limited resources}. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the public \href{https://www.rug.nl}{University of Groningen}, in collaboration with non-profit organisations \href{https://www.certe.nl}{Certe Medical Diagnostics and Advice Foundation} and \href{https://www.umcg.nl}{University Medical Center Groningen}.
The \code{AMR} package is available in English, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish, Turkish, and Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.
}
@ -55,7 +55,6 @@ Useful links:
Authors:
\itemize{
\item Christian F. Luz (\href{https://orcid.org/0000-0001-5809-5995}{ORCID}) [contributor]
\item Dennis Souverein (\href{https://orcid.org/0000-0003-0455-0336}{ORCID}) [contributor]
\item Erwin E. A. Hassing [contributor]
}
@ -70,14 +69,18 @@ Other contributors:
\item Eric H. L. C. M. Hazenberg [contributor]
\item Gwen Knight (\href{https://orcid.org/0000-0002-7263-9896}{ORCID}) [contributor]
\item Annick Lenglet (\href{https://orcid.org/0000-0003-2013-8405}{ORCID}) [contributor]
\item Christian F. Luz (\href{https://orcid.org/0000-0001-5809-5995}{ORCID}) [contributor]
\item Bart C. Meijer [contributor]
\item Dmytro Mykhailenko [contributor]
\item Anton Mymrikov [contributor]
\item Andrew P. Norgan (\href{https://orcid.org/0000-0002-2955-2066}{ORCID}) [contributor]
\item Sofia Ny (\href{https://orcid.org/0000-0002-2017-1363}{ORCID}) [contributor]
\item Matthew Saab [contributor]
\item Jonas Salm [contributor]
\item Javier Sanchez (\href{https://orcid.org/0000-0003-2605-8094}{ORCID}) [contributor]
\item Rogier P. Schade [contributor]
\item Bhanu N. M. Sinha (\href{https://orcid.org/0000-0003-1634-0010}{ORCID}) [thesis advisor]
\item Jason Stull (\href{https://orcid.org/0000-0002-9028-8153}{ORCID}) [contributor]
\item Anthony Underwood (\href{https://orcid.org/0000-0002-8547-4277}{ORCID}) [contributor]
\item Anita Williams (\href{https://orcid.org/0000-0002-5295-8451}{ORCID}) [contributor]
}

4
man/antibiotics.Rd
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@ -17,9 +17,9 @@
\item \code{atc_group2}\cr Official chemical subgroup (4th level ATC code) as defined by the WHOCC, like \code{"Macrolides"}
\item \code{abbr}\cr List of abbreviations as used in many countries, also for antibiotic susceptibility testing (AST)
\item \code{synonyms}\cr Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID
\item \code{oral_ddd}\cr Defined Daily Dose (DDD), oral treatment, currently available for 174 drugs
\item \code{oral_ddd}\cr Defined Daily Dose (DDD), oral treatment, currently available for 179 drugs
\item \code{oral_units}\cr Units of \code{oral_ddd}
\item \code{iv_ddd}\cr Defined Daily Dose (DDD), parenteral (intravenous) treatment, currently available for 146 drugs
\item \code{iv_ddd}\cr Defined Daily Dose (DDD), parenteral (intravenous) treatment, currently available for 153 drugs
\item \code{iv_units}\cr Units of \code{iv_ddd}
\item \code{loinc}\cr All codes associated with the name of the antimicrobial drug from Logical Observation Identifiers Names and Codes (LOINC), Version 2.76 (18 September, 2023). Use \code{\link[=ab_loinc]{ab_loinc()}} to retrieve them quickly, see \code{\link[=ab_property]{ab_property()}}.
}

16
man/as.mic.Rd
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@ -6,7 +6,7 @@
\alias{mic}
\alias{is.mic}
\alias{NA_mic_}
\alias{rescale_mic}
\alias{limit_mic_range}
\alias{droplevels.mic}
\title{Transform Input to Minimum Inhibitory Concentrations (MIC)}
\usage{
@ -16,7 +16,7 @@ is.mic(x)
NA_mic_
rescale_mic(x, mic_range, keep_operators = "edges", as.mic = TRUE)
limit_mic_range(x, mic_range, keep_operators = "edges", as.mic = TRUE)
\method{droplevels}{mic}(x, as.mic = FALSE, ...)
}
@ -27,14 +27,14 @@ rescale_mic(x, mic_range, keep_operators = "edges", as.mic = TRUE)
\item{keep_operators}{a \link{character} specifying how to handle operators (such as \code{>} and \code{<=}) in the input. Accepts one of three values: \code{"all"} (or \code{TRUE}) to keep all operators, \code{"none"} (or \code{FALSE}) to remove all operators, or \code{"edges"} to keep operators only at both ends of the range.}
\item{mic_range}{a manual range to plot the MIC values, e.g., \code{mic_range = c(0.001, 32)}. Use \code{NA} to set no limit on one side, e.g., \code{mic_range = c(NA, 32)}.}
\item{mic_range}{a manual range to limit the MIC values, e.g., \code{mic_range = c(0.001, 32)}. Use \code{NA} to set no limit on one side, e.g., \code{mic_range = c(NA, 32)}.}
\item{as.mic}{a \link{logical} to indicate whether the \code{mic} class should be kept - the default is \code{FALSE}}
\item{...}{arguments passed on to methods}
}
\value{
Ordered \link{factor} with additional class \code{\link{mic}}, that in mathematical operations acts as decimal numbers. Bare in mind that the outcome of any mathematical operation on MICs will return a \link{numeric} value.
Ordered \link{factor} with additional class \code{\link{mic}}, that in mathematical operations acts as a \link{numeric} vector. Bear in mind that the outcome of any mathematical operation on MICs will return a \link{numeric} value.
}
\description{
This transforms vectors to a new class \code{\link{mic}}, which treats the input as decimal numbers, while maintaining operators (such as ">=") and only allowing valid MIC values known to the field of (medical) microbiology.
@ -76,13 +76,13 @@ subset(df, x > 4) # or with dplyr: df \%>\% filter(x > 4)
#> 10 16 A
}\if{html}{\out{</div>}}
The following \link[=groupGeneric]{generic functions} are implemented for the MIC class: \code{!}, \code{!=}, \code{\%\%}, \code{\%/\%}, \code{&}, \code{*}, \code{+}, \code{-}, \code{/}, \code{<}, \code{<=}, \code{==}, \code{>}, \code{>=}, \code{^}, \code{|}, \code{\link[=abs]{abs()}}, \code{\link[=acos]{acos()}}, \code{\link[=acosh]{acosh()}}, \code{\link[=all]{all()}}, \code{\link[=any]{any()}}, \code{\link[=asin]{asin()}}, \code{\link[=asinh]{asinh()}}, \code{\link[=atan]{atan()}}, \code{\link[=atanh]{atanh()}}, \code{\link[=ceiling]{ceiling()}}, \code{\link[=cos]{cos()}}, \code{\link[=cosh]{cosh()}}, \code{\link[=cospi]{cospi()}}, \code{\link[=cummax]{cummax()}}, \code{\link[=cummin]{cummin()}}, \code{\link[=cumprod]{cumprod()}}, \code{\link[=cumsum]{cumsum()}}, \code{\link[=digamma]{digamma()}}, \code{\link[=exp]{exp()}}, \code{\link[=expm1]{expm1()}}, \code{\link[=floor]{floor()}}, \code{\link[=gamma]{gamma()}}, \code{\link[=lgamma]{lgamma()}}, \code{\link[=log]{log()}}, \code{\link[=log1p]{log1p()}}, \code{\link[=log2]{log2()}}, \code{\link[=log10]{log10()}}, \code{\link[=max]{max()}}, \code{\link[=mean]{mean()}}, \code{\link[=min]{min()}}, \code{\link[=prod]{prod()}}, \code{\link[=range]{range()}}, \code{\link[=round]{round()}}, \code{\link[=sign]{sign()}}, \code{\link[=signif]{signif()}}, \code{\link[=sin]{sin()}}, \code{\link[=sinh]{sinh()}}, \code{\link[=sinpi]{sinpi()}}, \code{\link[=sqrt]{sqrt()}}, \code{\link[=sum]{sum()}}, \code{\link[=tan]{tan()}}, \code{\link[=tanh]{tanh()}}, \code{\link[=tanpi]{tanpi()}}, \code{\link[=trigamma]{trigamma()}} and \code{\link[=trunc]{trunc()}}. Some functions of the \code{stats} package are also implemented: \code{\link[=median]{median()}}, \code{\link[=quantile]{quantile()}}, \code{\link[=mad]{mad()}}, \code{\link[=IQR]{IQR()}}, \code{\link[=fivenum]{fivenum()}}. Also, \code{\link[=boxplot.stats]{boxplot.stats()}} is supported. Since \code{\link[=sd]{sd()}} and \code{\link[=var]{var()}} are non-generic functions, these could not be extended. Use \code{\link[=mad]{mad()}} as an alternative, or use e.g. \code{sd(as.numeric(x))} where \code{x} is your vector of MIC values.
All so-called \link[=groupGeneric]{group generic functions} are implemented for the MIC class (such as \code{!}, \code{!=}, \code{<}, \code{>=}, \code{\link[=exp]{exp()}}, \code{\link[=log2]{log2()}}). Some functions of the \code{stats} package are also implemented (such as \code{\link[=quantile]{quantile()}}, \code{\link[=median]{median()}}, \code{\link[=fivenum]{fivenum()}}). Since \code{\link[=sd]{sd()}} and \code{\link[=var]{var()}} are non-generic functions, these could not be extended. Use \code{\link[=mad]{mad()}} as an alternative, or use e.g. \code{sd(as.numeric(x))} where \code{x} is your vector of MIC values.
Using \code{\link[=as.double]{as.double()}} or \code{\link[=as.numeric]{as.numeric()}} on MIC values will remove the operators and return a numeric vector. Do \strong{not} use \code{\link[=as.integer]{as.integer()}} on MIC values as by the \R convention on \link{factor}s, it will return the index of the factor levels (which is often useless for regular users).
Use \code{\link[=droplevels]{droplevels()}} to drop unused levels. At default, it will return a plain factor. Use \code{droplevels(..., as.mic = TRUE)} to maintain the \code{mic} class.
With \code{\link[=rescale_mic]{rescale_mic()}}, existing MIC ranges can be rescaled to a defined range of MIC values. This can be useful to better compare MIC distributions.
With \code{\link[=limit_mic_range]{limit_mic_range()}}, existing MIC ranges can be limited to a defined range of MIC values. This can be useful to better compare MIC distributions.
For \code{ggplot2}, use one of the \code{\link[=scale_x_mic]{scale_*_mic()}} functions to plot MIC values. They allows custom MIC ranges and to plot intermediate log2 levels for missing MIC values.
@ -101,8 +101,8 @@ fivenum(mic_data)
quantile(mic_data)
all(mic_data < 512)
# rescale MICs using rescale_mic()
rescale_mic(mic_data, mic_range = c(4, 16))
# limit MICs using limit_mic_range()
limit_mic_range(mic_data, mic_range = c(4, 16))
# interpret MIC values
as.sir(

4
man/as.mo.Rd
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@ -125,7 +125,7 @@ The coercion rules consider the prevalence of microorganisms in humans, which is
\item Lancefield RC (1933). \strong{A serological differentiation of human and other groups of hemolytic streptococci.} \emph{J Exp Med.} 57(4): 571-95; \doi{10.1084/jem.57.4.571}
\item Berends MS \emph{et al.} (2022). \strong{Trends in Occurrence and Phenotypic Resistance of Coagulase-Negative Staphylococci (CoNS) Found in Human Blood in the Northern Netherlands between 2013 and 2019/} \emph{Micro.rganisms} 10(9), 1801; \doi{10.3390/microorganisms10091801}
\item Parte, AC \emph{et al.} (2020). \strong{List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ.} International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; \doi{10.1099/ijsem.0.004332}. Accessed from \url{https://lpsn.dsmz.de} on December 11th, 2022.
\item GBIF Secretariat (2022). GBIF Backbone Taxonomy. Checklist dataset \doi{10.15468/39omei}. Accessed from \url{https://www.gbif.org} on December 11th, 2022.
\item GBIF Secretariat (2023). GBIF Backbone Taxonomy. Checklist dataset \doi{10.15468/39omei}. Accessed from \url{https://www.gbif.org} on January 8th, 2024.
\item Reimer, LC \emph{et al.} (2022). \strong{\emph{BacDive} in 2022: the knowledge base for standardized bacterial and archaeal data.} Nucleic Acids Res., 50(D1):D741-D74; \doi{10.1093/nar/gkab961}. Accessed from \url{https://bacdive.dsmz.de} on May 12th, 2023.
\item Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value Set Name 'Microorganism', OID 2.16.840.1.114222.4.11.1009 (v12). URL: \url{https://phinvads.cdc.gov}
\item Bartlett A \emph{et al.} (2022). \strong{A comprehensive list of bacterial pathogens infecting humans} \emph{Microbiology} 168:001269; \doi{10.1099/mic.0.001269}
@ -161,7 +161,7 @@ Furthermore,
\item Any genus present in the \strong{established} list also has \code{prevalence = 1.0} in the \link{microorganisms} data set;
\item Any other genus present in the \strong{putative} list has \code{prevalence = 1.25} in the \link{microorganisms} data set;
\item Any other species or subspecies of which the genus is present in the two aforementioned groups, has \code{prevalence = 1.5} in the \link{microorganisms} data set;
\item Any \emph{non-bacterial} genus, species or subspecies of which the genus is present in the following list, has \code{prevalence = 1.25} in the \link{microorganisms} data set: \emph{Absidia}, \emph{Acanthamoeba}, \emph{Acremonium}, \emph{Aedes}, \emph{Alternaria}, \emph{Amoeba}, \emph{Ancylostoma}, \emph{Angiostrongylus}, \emph{Anisakis}, \emph{Anopheles}, \emph{Apophysomyces}, \emph{Aspergillus}, \emph{Aureobasidium}, \emph{Basidiobolus}, \emph{Beauveria}, \emph{Blastocystis}, \emph{Blastomyces}, \emph{Candida}, \emph{Capillaria}, \emph{Chaetomium}, \emph{Chrysonilia}, \emph{Cladophialophora}, \emph{Cladosporium}, \emph{Conidiobolus}, \emph{Contracaecum}, \emph{Cordylobia}, \emph{Cryptococcus}, \emph{Curvularia}, \emph{Demodex}, \emph{Dermatobia}, \emph{Dientamoeba}, \emph{Diphyllobothrium}, \emph{Dirofilaria}, \emph{Echinostoma}, \emph{Entamoeba}, \emph{Enterobius}, \emph{Exophiala}, \emph{Exserohilum}, \emph{Fasciola}, \emph{Fonsecaea}, \emph{Fusarium}, \emph{Giardia}, \emph{Haloarcula}, \emph{Halobacterium}, \emph{Halococcus}, \emph{Hendersonula}, \emph{Heterophyes}, \emph{Histomonas}, \emph{Histoplasma}, \emph{Hymenolepis}, \emph{Hypomyces}, \emph{Hysterothylacium}, \emph{Leishmania}, \emph{Malassezia}, \emph{Malbranchea}, \emph{Metagonimus}, \emph{Meyerozyma}, \emph{Microsporidium}, \emph{Microsporum}, \emph{Mortierella}, \emph{Mucor}, \emph{Mycocentrospora}, \emph{Necator}, \emph{Nectria}, \emph{Ochroconis}, \emph{Oesophagostomum}, \emph{Oidiodendron}, \emph{Opisthorchis}, \emph{Pediculus}, \emph{Penicillium}, \emph{Phlebotomus}, \emph{Phoma}, \emph{Pichia}, \emph{Piedraia}, \emph{Pithomyces}, \emph{Pityrosporum}, \emph{Pneumocystis}, \emph{Pseudallescheria}, \emph{Pseudoterranova}, \emph{Pulex}, \emph{Rhizomucor}, \emph{Rhizopus}, \emph{Rhodotorula}, \emph{Saccharomyces}, \emph{Sarcoptes}, \emph{Scolecobasidium}, \emph{Scopulariopsis}, \emph{Scytalidium}, \emph{Spirometra}, \emph{Sporobolomyces}, \emph{Stachybotrys}, \emph{Strongyloides}, \emph{Syngamus}, \emph{Taenia}, \emph{Talaromyces}, \emph{Toxocara}, \emph{Trichinella}, \emph{Trichobilharzia}, \emph{Trichoderma}, \emph{Trichomonas}, \emph{Trichophyton}, \emph{Trichosporon}, \emph{Trichostrongylus}, \emph{Trichuris}, \emph{Tritirachium}, \emph{Trombicula}, \emph{Trypanosoma}, \emph{Tunga}, or \emph{Wuchereria};
\item Any \emph{non-bacterial} genus, species or subspecies of which the genus is present in the following list, has \code{prevalence = 1.25} in the \link{microorganisms} data set: \emph{Absidia}, \emph{Acanthamoeba}, \emph{Acremonium}, \emph{Aedes}, \emph{Alternaria}, \emph{Amoeba}, \emph{Ancylostoma}, \emph{Angiostrongylus}, \emph{Anisakis}, \emph{Anopheles}, \emph{Apophysomyces}, \emph{Arthroderma}, \emph{Aspergillus}, \emph{Aureobasidium}, \emph{Basidiobolus}, \emph{Beauveria}, \emph{Blastocystis}, \emph{Blastomyces}, \emph{Candida}, \emph{Capillaria}, \emph{Chaetomium}, \emph{Chrysonilia}, \emph{Chrysosporium}, \emph{Cladophialophora}, \emph{Cladosporium}, \emph{Conidiobolus}, \emph{Contracaecum}, \emph{Cordylobia}, \emph{Cryptococcus}, \emph{Curvularia}, \emph{Demodex}, \emph{Dermatobia}, \emph{Dientamoeba}, \emph{Diphyllobothrium}, \emph{Dirofilaria}, \emph{Echinostoma}, \emph{Entamoeba}, \emph{Enterobius}, \emph{Exophiala}, \emph{Exserohilum}, \emph{Fasciola}, \emph{Fonsecaea}, \emph{Fusarium}, \emph{Geotrichum}, \emph{Giardia}, \emph{Haloarcula}, \emph{Halobacterium}, \emph{Halococcus}, \emph{Hendersonula}, \emph{Heterophyes}, \emph{Histomonas}, \emph{Histoplasma}, \emph{Hymenolepis}, \emph{Hypomyces}, \emph{Hysterothylacium}, \emph{Kloeckera}, \emph{Kodamaea}, \emph{Leishmania}, \emph{Lichtheimia}, \emph{Lodderomyces}, \emph{Malassezia}, \emph{Malbranchea}, \emph{Metagonimus}, \emph{Meyerozyma}, \emph{Microsporidium}, \emph{Microsporum}, \emph{Millerozyma}, \emph{Mortierella}, \emph{Mucor}, \emph{Mycocentrospora}, \emph{Necator}, \emph{Nectria}, \emph{Ochroconis}, \emph{Oesophagostomum}, \emph{Oidiodendron}, \emph{Opisthorchis}, \emph{Paecilomyces}, \emph{Pediculus}, \emph{Penicillium}, \emph{Phlebotomus}, \emph{Phoma}, \emph{Pichia}, \emph{Piedraia}, \emph{Pithomyces}, \emph{Pityrosporum}, \emph{Pneumocystis}, \emph{Pseudallescheria}, \emph{Pseudoterranova}, \emph{Pulex}, \emph{Rhizomucor}, \emph{Rhizopus}, \emph{Rhodotorula}, \emph{Saccharomyces}, \emph{Saprochaete}, \emph{Sarcoptes}, \emph{Scedosporium}, \emph{Scolecobasidium}, \emph{Scopulariopsis}, \emph{Scytalidium}, \emph{Spirometra}, \emph{Sporobolomyces}, \emph{Sporotrichum}, \emph{Stachybotrys}, \emph{Strongyloides}, \emph{Syngamus}, \emph{Taenia}, \emph{Talaromyces}, \emph{Toxocara}, \emph{Trichinella}, \emph{Trichobilharzia}, \emph{Trichoderma}, \emph{Trichomonas}, \emph{Trichophyton}, \emph{Trichosporon}, \emph{Trichostrongylus}, \emph{Trichuris}, \emph{Tritirachium}, \emph{Trombicula}, \emph{Trypanosoma}, \emph{Tunga}, \emph{Verticillium}, or \emph{Wuchereria};
\item All other records have \code{prevalence = 2.0} in the \link{microorganisms} data set.
}

48
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@ -12,15 +12,13 @@
\alias{as.sir.data.frame}
\alias{sir_interpretation_history}
\title{Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data}
\format{
An object of class \code{sir} (inherits from \code{ordered}, \code{factor}) of length 1.
}
\source{
For interpretations of minimum inhibitory concentration (MIC) values and disk diffusion diameters:
\itemize{
\item \strong{M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data}, 2011-2023, \emph{Clinical and Laboratory Standards Institute} (CLSI). \url{https://clsi.org/standards/products/microbiology/documents/m39/}.
\item \strong{M100 Performance Standard for Antimicrobial Susceptibility Testing}, 2011-2023, \emph{Clinical and Laboratory Standards Institute} (CLSI). \url{https://clsi.org/standards/products/microbiology/documents/m100/}.
\item \strong{Breakpoint tables for interpretation of MICs and zone diameters}, 2011-2023, \emph{European Committee on Antimicrobial Susceptibility Testing} (EUCAST). \url{https://www.eucast.org/clinical_breakpoints}.
\item \strong{CLSI M39: Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data}, 2011-2023, \emph{Clinical and Laboratory Standards Institute} (CLSI). \url{https://clsi.org/standards/products/microbiology/documents/m39/}.
\item \strong{CLSI M100: Performance Standard for Antimicrobial Susceptibility Testing}, 2011-2023, \emph{Clinical and Laboratory Standards Institute} (CLSI). \url{https://clsi.org/standards/products/microbiology/documents/m100/}.
\item \strong{CLSI VET01: Performance Standards for Antimicrobial Disk and Dilution Susceptibility Tests for Bacteria Isolated From Animals}, 2019-2023, \emph{Clinical and Laboratory Standards Institute} (CLSI). \url{https://clsi.org/standards/products/veterinary-medicine/documents/vet01//}.
\item \strong{EUCAST Breakpoint tables for interpretation of MICs and zone diameters}, 2011-2023, \emph{European Committee on Antimicrobial Susceptibility Testing} (EUCAST). \url{https://www.eucast.org/clinical_breakpoints}.
}
}
\usage{
@ -44,6 +42,7 @@ is_sir_eligible(x, threshold = 0.05)
include_screening = getOption("AMR_include_screening", FALSE),
include_PKPD = getOption("AMR_include_PKPD", TRUE),
breakpoint_type = getOption("AMR_breakpoint_type", "human"),
host = NULL,
...
)
@ -58,6 +57,7 @@ is_sir_eligible(x, threshold = 0.05)
include_screening = getOption("AMR_include_screening", FALSE),
include_PKPD = getOption("AMR_include_PKPD", TRUE),
breakpoint_type = getOption("AMR_breakpoint_type", "human"),
host = NULL,
...
)
@ -72,7 +72,8 @@ is_sir_eligible(x, threshold = 0.05)
reference_data = AMR::clinical_breakpoints,
include_screening = getOption("AMR_include_screening", FALSE),
include_PKPD = getOption("AMR_include_PKPD", TRUE),
breakpoint_type = getOption("AMR_breakpoint_type", "human")
breakpoint_type = getOption("AMR_breakpoint_type", "human"),
host = NULL
)
sir_interpretation_history(clean = FALSE)
@ -102,7 +103,9 @@ sir_interpretation_history(clean = FALSE)
\item{include_PKPD}{a \link{logical} to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is \code{TRUE}. Can also be set with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_include_PKPD}}.}
\item{breakpoint_type}{the type of breakpoints to use, either "ECOFF", "animal", or "human". ECOFF stands for Epidemiological Cut-Off values. The default is \code{"human"}, which can also be set with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_breakpoint_type}}.}
\item{breakpoint_type}{the type of breakpoints to use, either "ECOFF", "animal", or "human". ECOFF stands for Epidemiological Cut-Off values. The default is \code{"human"}, which can also be set with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_breakpoint_type}}. If \code{host} is set to values of veterinary species, this will automatically be set to \code{"animal"}.}
\item{host}{a vector (or column name) with \link{character}s to indicate the host. Only useful for veterinary breakpoints, as it requires \code{breakpoint_type = "animal"}. The values can be any text resembling the animal species, even in any of the 20 supported languages of this package. For foreign languages, be sure to set the language with \code{\link[=set_AMR_locale]{set_AMR_locale()}} (though it will be automatically guessed based on the system language).}
\item{col_mo}{column name of the names or codes of the microorganisms (see \code{\link[=as.mo]{as.mo()}}) - the default is the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
@ -112,17 +115,22 @@ sir_interpretation_history(clean = FALSE)
Ordered \link{factor} with new class \code{sir}
}
\description{
Interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing SIR values. This transforms the input to a new class \code{\link{sir}}, which is an ordered \link{factor} with levels \verb{S < I < R}.
Clean up existing SIR values, or interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI. \code{\link[=as.sir]{as.sir()}} transforms the input to a new class \code{\link{sir}}, which is an ordered \link{factor} with levels \verb{S < I < R}.
Currently available \strong{breakpoint guidelines} are EUCAST 2011-2023 and CLSI 2011-2023, and available \strong{breakpoint types} are "ECOFF", "animal", and "human".
Currently breakpoints are available:
\itemize{
\item For \strong{clinical microbiology} from EUCAST 2011-2023 and CLSI 2011-2023;
\item For \strong{veterinary microbiology} from EUCAST 2021-2023 and CLSI 2019-2023;
\item ECOFFs (Epidemiological cut-off values) from EUCAST 2020-2023 and CLSI 2022-2023.
}
All breakpoints used for interpretation are publicly available in the \link{clinical_breakpoints} data set.
}
\details{
\emph{Note: The clinical breakpoints in this package were validated through and imported from \href{https://whonet.org}{WHONET} and the public use of this \code{AMR} package has been endorsed by CLSI and EUCAST, please see \link{clinical_breakpoints} for more information.}
\emph{Note: The clinical breakpoints in this package were validated through, and imported from, \href{https://whonet.org}{WHONET}. The public use of this \code{AMR} package has been endorsed by both CLSI and EUCAST. See \link{clinical_breakpoints} for more information.}
\subsection{How it Works}{
The \code{\link[=as.sir]{as.sir()}} function works in four ways:
The \code{\link[=as.sir]{as.sir()}} function can work in four ways:
\enumerate{
\item For \strong{cleaning raw / untransformed data}. The data will be cleaned to only contain values S, I and R and will try its best to determine this with some intelligence. For example, mixed values with SIR interpretations and MIC values such as \code{"<0.25; S"} will be coerced to \code{"S"}. Combined interpretations for multiple test methods (as seen in laboratory records) such as \code{"S; S"} will be coerced to \code{"S"}, but a value like \code{"S; I"} will return \code{NA} with a warning that the input is unclear.
\item For \strong{interpreting minimum inhibitory concentration (MIC) values} according to EUCAST or CLSI. You must clean your MIC values first using \code{\link[=as.mic]{as.mic()}}, that also gives your columns the new data class \code{\link{mic}}. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the \code{mo} argument.
@ -131,6 +139,9 @@ The \code{\link[=as.sir]{as.sir()}} function works in four ways:
\if{html}{\out{<div class="sourceCode">}}\preformatted{your_data \%>\% mutate_if(is.mic, as.sir)
your_data \%>\% mutate(across(where(is.mic), as.sir))
# for veterinary breakpoints, also set `host`:
your_data \%>\% mutate_if(is.mic, as.sir, host = "column_with_animal_hosts", guideline = "CLSI")
}\if{html}{\out{</div>}}
\item Operators like "<=" will be stripped before interpretation. When using \code{conserve_capped_values = TRUE}, an MIC value of e.g. ">2" will always return "R", even if the breakpoint according to the chosen guideline is ">=4". This is to prevent that capped values from raw laboratory data would not be treated conservatively. The default behaviour (\code{conserve_capped_values = FALSE}) considers ">2" to be lower than ">=4" and might in this case return "S" or "I".
}
@ -140,6 +151,9 @@ your_data \%>\% mutate(across(where(is.mic), as.sir))
\if{html}{\out{<div class="sourceCode">}}\preformatted{your_data \%>\% mutate_if(is.disk, as.sir)
your_data \%>\% mutate(across(where(is.disk), as.sir))
# for veterinary breakpoints, also set `host`:
your_data \%>\% mutate_if(is.disk, as.sir, host = "column_with_animal_hosts", guideline = "CLSI")
}\if{html}{\out{</div>}}
}
\item For \strong{interpreting a complete data set}, with automatic determination of MIC values, disk diffusion diameters, microorganism names or codes, and antimicrobial test results. This is done very simply by running \code{as.sir(your_data)}.
@ -150,7 +164,7 @@ your_data \%>\% mutate(across(where(is.disk), as.sir))
\subsection{Supported Guidelines}{
For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are EUCAST (2011-2023) and CLSI (2011-2023).
For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are for \strong{clinical microbiology}: EUCAST 2011-2023 and CLSI 2011-2023, and for \strong{veterinary microbiology}: EUCAST 2021-2023 and CLSI 2019-2023.
Thus, the \code{guideline} argument must be set to e.g., \code{"EUCAST 2023"} or \code{"CLSI 2023"}. By simply using \code{"EUCAST"} (the default) or \code{"CLSI"} as input, the latest included version of that guideline will automatically be selected. You can set your own data set using the \code{reference_data} argument. The \code{guideline} argument will then be ignored.
@ -162,6 +176,12 @@ You can set the default guideline with the \link[=AMR-options]{package option} \
# or to reset:
options(AMR_guideline = NULL)
}\if{html}{\out{</div>}}
For veterinary guidelines, these might be the best options:
\if{html}{\out{<div class="sourceCode">}}\preformatted{ options(AMR_guideline = "CLSI")
options(AMR_breakpoint_type = "animal")
}\if{html}{\out{</div>}}
}
\subsection{After Interpretation}{
@ -171,7 +191,7 @@ After using \code{\link[=as.sir]{as.sir()}}, you can use the \code{\link[=eucast
\subsection{Machine-Readable Clinical Breakpoints}{
The repository of this package \href{https://github.com/msberends/AMR/blob/main/data-raw/clinical_breakpoints.txt}{contains a machine-readable version} of all guidelines. This is a CSV file consisting of 29 747 rows and 12 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial drug and the microorganism. \strong{This allows for easy implementation of these rules in laboratory information systems (LIS)}. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.
The repository of this package \href{https://github.com/msberends/AMR/blob/main/data-raw/clinical_breakpoints.txt}{contains a machine-readable version} of all guidelines. This is a CSV file consisting of 29 883 rows and 13 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial drug and the microorganism. \strong{This allows for easy implementation of these rules in laboratory information systems (LIS)}. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.
}
\subsection{Other}{

11
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@ -5,10 +5,11 @@
\alias{clinical_breakpoints}
\title{Data Set with Clinical Breakpoints for SIR Interpretation}
\format{
A \link[tibble:tibble]{tibble} with 29 747 observations and 12 variables:
A \link[tibble:tibble]{tibble} with 29 883 observations and 13 variables:
\itemize{
\item \code{guideline}\cr Name of the guideline
\item \code{type}\cr Breakpoint type, either "ECOFF", "animal", or "human"
\item \code{host}\cr Host of infectious agent. This is mostly useful for veterinary breakpoints and is either "ECOFF", "aquatic", "cats", "cattle", "dogs", "horse", "human", "poultry", or "swine"
\item \code{method}\cr Testing method, either "DISK" or "MIC"
\item \code{site}\cr Body site for which the breakpoint must be applied, e.g. "Oral" or "Respiratory"
\item \code{mo}\cr Microbial ID, see \code{\link[=as.mo]{as.mo()}}
@ -25,7 +26,13 @@ A \link[tibble:tibble]{tibble} with 29 747 observations and 12 variables:
clinical_breakpoints
}
\description{
Data set containing clinical breakpoints to interpret MIC and disk diffusion to SIR values, according to international guidelines. Currently implemented guidelines are EUCAST (2011-2023) and CLSI (2011-2023). Use \code{\link[=as.sir]{as.sir()}} to transform MICs or disks measurements to SIR values.
Data set containing clinical breakpoints to interpret MIC and disk diffusion to SIR values, according to international guidelines. This dataset contain breakpoints for humans, 7 different animal groups, and ECOFFs.
Currently available breakpoint guidelines for \strong{clinical microbiology} are EUCAST 2011-2023 and CLSI 2011-2023.
Currently available breakpoint guidelines for \strong{veterinary microbiology} are EUCAST 2021-2023 and CLSI 2019-2023.
Use \code{\link[=as.sir]{as.sir()}} to transform MICs or disks measurements to SIR values.
}
\details{
\subsection{Different types of breakpoints}{

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@ -21,14 +21,14 @@ A \link[tibble:tibble]{tibble} with 52 171 observations and 23 variables:
\item \code{gbif_parent}\cr GBIF identifier of the parent taxon
\item \code{gbif_renamed_to}\cr GBIF identifier of the currently valid taxon
\item \code{source}\cr Either "GBIF", "LPSN", or "manually added" (see \emph{Source})
\item \code{prevalence}\cr Prevalence of the microorganism according to Bartlett \emph{et al.} (2022, \doi{10.1099/mic.0.001269}), see \code{\link[=mo_matching_score]{mo_matching_score()}} for the full explanation
\item \code{prevalence}\cr Prevalence of the microorganism based on Bartlett \emph{et al.} (2022, \doi{10.1099/mic.0.001269}), see \code{\link[=mo_matching_score]{mo_matching_score()}} for the full explanation
\item \code{snomed}\cr Systematized Nomenclature of Medicine (SNOMED) code of the microorganism, version of July 1st, 2021 (see \emph{Source}). Use \code{\link[=mo_snomed]{mo_snomed()}} to retrieve it quickly, see \code{\link[=mo_property]{mo_property()}}.
}
}
\source{
\itemize{
\item Parte, AC \emph{et al.} (2020). \strong{List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ.} International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; \doi{10.1099/ijsem.0.004332}. Accessed from \url{https://lpsn.dsmz.de} on December 11th, 2022.
\item GBIF Secretariat (2022). GBIF Backbone Taxonomy. Checklist dataset \doi{10.15468/39omei}. Accessed from \url{https://www.gbif.org} on December 11th, 2022.
\item GBIF Secretariat (2023). GBIF Backbone Taxonomy. Checklist dataset \doi{10.15468/39omei}. Accessed from \url{https://www.gbif.org} on January 8th, 2024.
\item Reimer, LC \emph{et al.} (2022). \strong{\emph{BacDive} in 2022: the knowledge base for standardized bacterial and archaeal data.} Nucleic Acids Res., 50(D1):D741-D74; \doi{10.1093/nar/gkab961}. Accessed from \url{https://bacdive.dsmz.de} on May 12th, 2023.
\item Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value Set Name 'Microorganism', OID 2.16.840.1.114222.4.11.1009 (v12). URL: \url{https://phinvads.cdc.gov}
\item Grimont \emph{et al.} (2007). Antigenic Formulae of the Salmonella Serovars, 9th Edition. WHO Collaborating Centre for Reference and Research on \emph{Salmonella} (WHOCC-SALM).
@ -39,7 +39,7 @@ A \link[tibble:tibble]{tibble} with 52 171 observations and 23 variables:
microorganisms
}
\description{
A data set containing the full microbial taxonomy (\strong{last updated: December 11th, 2022}) of five 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 \code{AMR} package. MO codes can be looked up using \code{\link[=as.mo]{as.mo()}}.
A data set containing the full microbial taxonomy (\strong{last updated: January 8th, 2024}) of five 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 \code{AMR} package. MO codes can be looked up using \code{\link[=as.mo]{as.mo()}}.
}
\details{
Please note that entries are only based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and the Global Biodiversity Information Facility (GBIF) (see below). Since these sources incorporate entries based on (recent) publications in the International Journal of Systematic and Evolutionary Microbiology (IJSEM), it can happen that the year of publication is sometimes later than one might expect.

2
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@ -48,7 +48,7 @@ Furthermore,
\item Any genus present in the \strong{established} list also has \code{prevalence = 1.0} in the \link{microorganisms} data set;
\item Any other genus present in the \strong{putative} list has \code{prevalence = 1.25} in the \link{microorganisms} data set;
\item Any other species or subspecies of which the genus is present in the two aforementioned groups, has \code{prevalence = 1.5} in the \link{microorganisms} data set;
\item Any \emph{non-bacterial} genus, species or subspecies of which the genus is present in the following list, has \code{prevalence = 1.25} in the \link{microorganisms} data set: \emph{Absidia}, \emph{Acanthamoeba}, \emph{Acremonium}, \emph{Aedes}, \emph{Alternaria}, \emph{Amoeba}, \emph{Ancylostoma}, \emph{Angiostrongylus}, \emph{Anisakis}, \emph{Anopheles}, \emph{Apophysomyces}, \emph{Aspergillus}, \emph{Aureobasidium}, \emph{Basidiobolus}, \emph{Beauveria}, \emph{Blastocystis}, \emph{Blastomyces}, \emph{Candida}, \emph{Capillaria}, \emph{Chaetomium}, \emph{Chrysonilia}, \emph{Cladophialophora}, \emph{Cladosporium}, \emph{Conidiobolus}, \emph{Contracaecum}, \emph{Cordylobia}, \emph{Cryptococcus}, \emph{Curvularia}, \emph{Demodex}, \emph{Dermatobia}, \emph{Dientamoeba}, \emph{Diphyllobothrium}, \emph{Dirofilaria}, \emph{Echinostoma}, \emph{Entamoeba}, \emph{Enterobius}, \emph{Exophiala}, \emph{Exserohilum}, \emph{Fasciola}, \emph{Fonsecaea}, \emph{Fusarium}, \emph{Giardia}, \emph{Haloarcula}, \emph{Halobacterium}, \emph{Halococcus}, \emph{Hendersonula}, \emph{Heterophyes}, \emph{Histomonas}, \emph{Histoplasma}, \emph{Hymenolepis}, \emph{Hypomyces}, \emph{Hysterothylacium}, \emph{Leishmania}, \emph{Malassezia}, \emph{Malbranchea}, \emph{Metagonimus}, \emph{Meyerozyma}, \emph{Microsporidium}, \emph{Microsporum}, \emph{Mortierella}, \emph{Mucor}, \emph{Mycocentrospora}, \emph{Necator}, \emph{Nectria}, \emph{Ochroconis}, \emph{Oesophagostomum}, \emph{Oidiodendron}, \emph{Opisthorchis}, \emph{Pediculus}, \emph{Penicillium}, \emph{Phlebotomus}, \emph{Phoma}, \emph{Pichia}, \emph{Piedraia}, \emph{Pithomyces}, \emph{Pityrosporum}, \emph{Pneumocystis}, \emph{Pseudallescheria}, \emph{Pseudoterranova}, \emph{Pulex}, \emph{Rhizomucor}, \emph{Rhizopus}, \emph{Rhodotorula}, \emph{Saccharomyces}, \emph{Sarcoptes}, \emph{Scolecobasidium}, \emph{Scopulariopsis}, \emph{Scytalidium}, \emph{Spirometra}, \emph{Sporobolomyces}, \emph{Stachybotrys}, \emph{Strongyloides}, \emph{Syngamus}, \emph{Taenia}, \emph{Talaromyces}, \emph{Toxocara}, \emph{Trichinella}, \emph{Trichobilharzia}, \emph{Trichoderma}, \emph{Trichomonas}, \emph{Trichophyton}, \emph{Trichosporon}, \emph{Trichostrongylus}, \emph{Trichuris}, \emph{Tritirachium}, \emph{Trombicula}, \emph{Trypanosoma}, \emph{Tunga}, or \emph{Wuchereria};
\item Any \emph{non-bacterial} genus, species or subspecies of which the genus is present in the following list, has \code{prevalence = 1.25} in the \link{microorganisms} data set: \emph{Absidia}, \emph{Acanthamoeba}, \emph{Acremonium}, \emph{Aedes}, \emph{Alternaria}, \emph{Amoeba}, \emph{Ancylostoma}, \emph{Angiostrongylus}, \emph{Anisakis}, \emph{Anopheles}, \emph{Apophysomyces}, \emph{Arthroderma}, \emph{Aspergillus}, \emph{Aureobasidium}, \emph{Basidiobolus}, \emph{Beauveria}, \emph{Blastocystis}, \emph{Blastomyces}, \emph{Candida}, \emph{Capillaria}, \emph{Chaetomium}, \emph{Chrysonilia}, \emph{Chrysosporium}, \emph{Cladophialophora}, \emph{Cladosporium}, \emph{Conidiobolus}, \emph{Contracaecum}, \emph{Cordylobia}, \emph{Cryptococcus}, \emph{Curvularia}, \emph{Demodex}, \emph{Dermatobia}, \emph{Dientamoeba}, \emph{Diphyllobothrium}, \emph{Dirofilaria}, \emph{Echinostoma}, \emph{Entamoeba}, \emph{Enterobius}, \emph{Exophiala}, \emph{Exserohilum}, \emph{Fasciola}, \emph{Fonsecaea}, \emph{Fusarium}, \emph{Geotrichum}, \emph{Giardia}, \emph{Haloarcula}, \emph{Halobacterium}, \emph{Halococcus}, \emph{Hendersonula}, \emph{Heterophyes}, \emph{Histomonas}, \emph{Histoplasma}, \emph{Hymenolepis}, \emph{Hypomyces}, \emph{Hysterothylacium}, \emph{Kloeckera}, \emph{Kodamaea}, \emph{Leishmania}, \emph{Lichtheimia}, \emph{Lodderomyces}, \emph{Malassezia}, \emph{Malbranchea}, \emph{Metagonimus}, \emph{Meyerozyma}, \emph{Microsporidium}, \emph{Microsporum}, \emph{Millerozyma}, \emph{Mortierella}, \emph{Mucor}, \emph{Mycocentrospora}, \emph{Necator}, \emph{Nectria}, \emph{Ochroconis}, \emph{Oesophagostomum}, \emph{Oidiodendron}, \emph{Opisthorchis}, \emph{Paecilomyces}, \emph{Pediculus}, \emph{Penicillium}, \emph{Phlebotomus}, \emph{Phoma}, \emph{Pichia}, \emph{Piedraia}, \emph{Pithomyces}, \emph{Pityrosporum}, \emph{Pneumocystis}, \emph{Pseudallescheria}, \emph{Pseudoterranova}, \emph{Pulex}, \emph{Rhizomucor}, \emph{Rhizopus}, \emph{Rhodotorula}, \emph{Saccharomyces}, \emph{Saprochaete}, \emph{Sarcoptes}, \emph{Scedosporium}, \emph{Scolecobasidium}, \emph{Scopulariopsis}, \emph{Scytalidium}, \emph{Spirometra}, \emph{Sporobolomyces}, \emph{Sporotrichum}, \emph{Stachybotrys}, \emph{Strongyloides}, \emph{Syngamus}, \emph{Taenia}, \emph{Talaromyces}, \emph{Toxocara}, \emph{Trichinella}, \emph{Trichobilharzia}, \emph{Trichoderma}, \emph{Trichomonas}, \emph{Trichophyton}, \emph{Trichosporon}, \emph{Trichostrongylus}, \emph{Trichuris}, \emph{Tritirachium}, \emph{Trombicula}, \emph{Trypanosoma}, \emph{Tunga}, \emph{Verticillium}, or \emph{Wuchereria};
\item All other records have \code{prevalence = 2.0} in the \link{microorganisms} data set.
}

2
man/mo_property.Rd
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@ -354,7 +354,7 @@ This function uses \code{\link[=as.mo]{as.mo()}} internally, which uses an advan
\item Lancefield RC (1933). \strong{A serological differentiation of human and other groups of hemolytic streptococci.} \emph{J Exp Med.} 57(4): 571-95; \doi{10.1084/jem.57.4.571}
\item Berends MS \emph{et al.} (2022). \strong{Trends in Occurrence and Phenotypic Resistance of Coagulase-Negative Staphylococci (CoNS) Found in Human Blood in the Northern Netherlands between 2013 and 2019/} \emph{Micro.rganisms} 10(9), 1801; \doi{10.3390/microorganisms10091801}
\item Parte, AC \emph{et al.} (2020). \strong{List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ.} International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; \doi{10.1099/ijsem.0.004332}. Accessed from \url{https://lpsn.dsmz.de} on December 11th, 2022.
\item GBIF Secretariat (2022). GBIF Backbone Taxonomy. Checklist dataset \doi{10.15468/39omei}. Accessed from \url{https://www.gbif.org} on December 11th, 2022.
\item GBIF Secretariat (2023). GBIF Backbone Taxonomy. Checklist dataset \doi{10.15468/39omei}. Accessed from \url{https://www.gbif.org} on January 8th, 2024.
\item Reimer, LC \emph{et al.} (2022). \strong{\emph{BacDive} in 2022: the knowledge base for standardized bacterial and archaeal data.} Nucleic Acids Res., 50(D1):D741-D74; \doi{10.1093/nar/gkab961}. Accessed from \url{https://bacdive.dsmz.de} on May 12th, 2023.
\item Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value Set Name 'Microorganism', OID 2.16.840.1.114222.4.11.1009 (v12). URL: \url{https://phinvads.cdc.gov}
\item Bartlett A \emph{et al.} (2022). \strong{A comprehensive list of bacterial pathogens infecting humans} \emph{Microbiology} 168:001269; \doi{10.1099/mic.0.001269}

4
man/plot.Rd
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@ -117,7 +117,7 @@ scale_fill_mic(keep_operators = "edges", mic_range = NULL, drop = FALSE, ...)
\arguments{
\item{keep_operators}{a \link{character} specifying how to handle operators (such as \code{>} and \code{<=}) in the input. Accepts one of three values: \code{"all"} (or \code{TRUE}) to keep all operators, \code{"none"} (or \code{FALSE}) to remove all operators, or \code{"edges"} to keep operators only at both ends of the range.}
\item{mic_range}{a manual range to plot the MIC values, e.g., \code{mic_range = c(0.001, 32)}. Use \code{NA} to set no limit on one side, e.g., \code{mic_range = c(NA, 32)}.}
\item{mic_range}{a manual range to limit the MIC values, e.g., \code{mic_range = c(0.001, 32)}. Use \code{NA} to set no limit on one side, e.g., \code{mic_range = c(NA, 32)}.}
\item{drop}{a \link{logical} to remove intermediate MIC values, defaults to \code{FALSE}}
@ -143,7 +143,7 @@ scale_fill_mic(keep_operators = "edges", mic_range = NULL, drop = FALSE, ...)
\item{include_PKPD}{a \link{logical} to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is \code{TRUE}. Can also be set with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_include_PKPD}}.}
\item{breakpoint_type}{the type of breakpoints to use, either "ECOFF", "animal", or "human". ECOFF stands for Epidemiological Cut-Off values. The default is \code{"human"}, which can also be set with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_breakpoint_type}}.}
\item{breakpoint_type}{the type of breakpoints to use, either "ECOFF", "animal", or "human". ECOFF stands for Epidemiological Cut-Off values. The default is \code{"human"}, which can also be set with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_breakpoint_type}}. If \code{host} is set to values of veterinary species, this will automatically be set to \code{"animal"}.}
}
\value{
The \code{autoplot()} functions return a \code{\link[ggplot2:ggplot]{ggplot}} model that is extendible with any \code{ggplot2} function.