vignettes/datasets.Rmd
datasets.Rmd
(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.)
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, Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change.
antibiotics
antimicrobials
rsi
sir
resistance_predict()
tidymodels
as.sir()
breakpoint_type = "animal"
host
ab
mo
uti
as.sir(..., ab = "column1", mo = "column2", uti = "column3")
>32
32
as.mic(">32") == as.mic(32)
FALSE
as.mic(">32") > as.mic(32)
TRUE
sort()
<0.001
0.001
>0.001
is.mic()
data.frame
eucast_rules()
overwrite
NA
.xpt
This changelog only contains changes from AMR v3.0 (March 2025) and later.
text to analyse
Text to analyse
type of property to search for, either "drug", "dose" or "administration", see Examples
"drug"
"dose"
"administration"
Type of property to search for, either "drug", "dose" or "administration", see Examples
a character to pass on to paste(, collapse = ...) to only return one character per element of text, see Examples
paste(, collapse = ...)
text
A character to pass on to paste(, collapse = ...) to only return one character per element of text, see Examples
if type = "drug": a column name of the antimicrobials data set to translate the antibiotic abbreviations to, using ab_property(). The default is FALSE. Using TRUE is equal to using "name".
type = "drug"
ab_property()
If type = "drug": a column name of the antimicrobials data set to translate the antibiotic abbreviations to, using ab_property(). The default is FALSE. Using TRUE is equal to using "name".
a logical to indicate whether the input must be extensively searched for misspelling and other faulty input values. Setting this to TRUE will take considerably more time than when using FALSE. At default, it will turn TRUE when all input elements contain a maximum of three words.
A logical to indicate whether the input must be extensively searched for misspelling and other faulty input values. Setting this to TRUE will take considerably more time than when using FALSE. At default, it will turn TRUE when all input elements contain a maximum of three words.
a logical to indicate whether a progress bar should be printed - the default is TRUE only in interactive mode
A logical to indicate whether a progress bar should be printed - the default is TRUE only in interactive mode
arguments passed on to as.ab()
as.ab()
Arguments passed on to as.ab()
any (vector of) text that can be coerced to a valid antibiotic drug code with as.ab()
Any (vector of) text that can be coerced to a valid antibiotic drug code with as.ab()
language of the returned text - the default is the current system language (see get_AMR_locale()) and can also be set with the package option AMR_locale. Use language = NULL or language = "" to prevent translation.
get_AMR_locale()
AMR_locale
language = NULL
language = ""
Language of the returned text - the default is the current system language (see get_AMR_locale()) and can also be set with the package option AMR_locale. Use language = NULL or language = "" to prevent translation.
a logical to indicate whether the first character of every output should be transformed to a lower case character. This will lead to e.g. "polymyxin B" and not "polymyxin b".
A logical to indicate whether the first character of every output should be transformed to a lower case character. This will lead to e.g. "polymyxin B" and not "polymyxin b".
in case of set_ab_names() and data is a data.frame: columns to select (supports tidy selection such as column1:column4), otherwise other arguments passed on to as.ab()
set_ab_names()
data
column1:column4
In case of set_ab_names() and data is a data.frame: columns to select (supports tidy selection such as column1:column4), otherwise other arguments passed on to as.ab()
a logical to indicate whether only the first ATC code must be returned, with giving preference to J0-codes (i.e., the antimicrobial drug group)
A logical to indicate whether only the first ATC code must be returned, with giving preference to J0-codes (i.e., the antimicrobial drug group)
way of administration, either "oral" or "iv"
"oral"
"iv"
Way of administration, either "oral" or "iv"
browse the URL using utils::browseURL()
utils::browseURL()
Browse the URL using utils::browseURL()
one of the column names of one of the antimicrobials data set: vector_or(colnames(antimicrobials), sort = FALSE).
vector_or(colnames(antimicrobials), sort = FALSE)
One of the column names of one of the antimicrobials data set: vector_or(colnames(antimicrobials), sort = FALSE).
a data.frame of which the columns need to be renamed, or a character vector of column names
A data.frame of which the columns need to be renamed, or a character vector of column names
a logical to indicate whether the names should be in so-called snake case: in lower case and all spaces/slashes replaced with an underscore (_)
_
A logical to indicate whether the names should be in so-called snake case: in lower case and all spaces/slashes replaced with an underscore (_)
a data.frame resembling the antimicrobials data set, at least containing columns "ab" and "name"
A data.frame resembling the antimicrobials data set, at least containing columns "ab" and "name"
a data.frame resembling the microorganisms data set, at least containing column "genus" (case-insensitive)
A data.frame resembling the microorganisms data set, at least containing column "genus" (case-insensitive)
date(s), character (vectors) will be coerced with as.POSIXlt()
as.POSIXlt()
Date(s), character (vectors) will be coerced with as.POSIXlt()
reference date(s) (default is today), character (vectors) will be coerced with as.POSIXlt()
Reference date(s) (default is today), character (vectors) will be coerced with as.POSIXlt()
a logical to indicate whether age calculation should be exact, i.e. with decimals. It divides the number of days of year-to-date (YTD) of x by the number of days in the year of reference (either 365 or 366).
x
reference
A logical to indicate whether age calculation should be exact, i.e. with decimals. It divides the number of days of year-to-date (YTD) of x by the number of days in the year of reference (either 365 or 366).
a logical to indicate whether missing values should be removed
A logical to indicate whether missing values should be removed
arguments passed on to as.POSIXlt(), such as origin
origin
Arguments passed on to as.POSIXlt(), such as origin