P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2026-05-31 19:41:51 +02:00
Code Releases Activity

fix add_missing

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2026-04-21 20:48:43 +02:00
parent cd23422a5f
commit c2b9af94ff
38 changed files with 1165 additions and 972 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
man/AMR-options.Rd
View File

@@ -12,7 +12,7 @@ This is an overview of all the package-specific options you can set in the \code
\itemize{
\item \code{AMR_antibiogram_formatting_type} \cr A \link{numeric} (1-22) to use in \code{\link[=antibiogram]{antibiogram()}}, to indicate which formatting type to use.
\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 {.val ECOFF}, {.val animal}, or {.val human}.
\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 \code{"ECOFF"}, \code{"animal"}, or \code{"human"}.
\item \code{AMR_capped_mic_handling} \cr A \link{character} to use in \code{\link[=as.sir]{as.sir()}}, to indicate how capped MIC values (\code{<}, \code{<=}, \code{>}, \code{>=}) should be interpreted. Must be one of \code{"none"}, \code{"conservative"}, \code{"standard"}, or \code{"lenient"} - the default is \code{"conservative"}.
\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()}}.

2
man/ab_property.Rd
View File

@@ -67,7 +67,7 @@ set_ab_names(data, ..., property = "name", language = get_AMR_locale(),
\item{open}{Browse the URL using \code{\link[utils:browseURL]{utils::browseURL()}}.}
\item{property}{One of the column names of one of the \link{antimicrobials} data set: \code{vector_or(colnames(antimicrobials), sort = FALSE)}.}
\item{property}{One of the column names of one of the \link{antimicrobials} data set: \code{"ab"}, \code{"cid"}, \code{"name"}, \code{"group"}, \code{"atc"}, \code{"atc_group1"}, \code{"atc_group2"}, \code{"abbreviations"}, \code{"synonyms"}, \code{"oral_ddd"}, \code{"oral_units"}, \code{"iv_ddd"}, \code{"iv_units"}, or \code{"loinc"}.}
\item{data}{A \link{data.frame} of which the columns need to be renamed, or a \link{character} vector of column names.}

4
man/antibiogram.Rd
View File

@@ -68,9 +68,9 @@ retrieve_wisca_parameters(wisca_model, ...)
}
}}
\item{mo_transform}{A character to transform microorganism input - must be \code{"name"}, \code{"shortname"} (default), \code{"gramstain"}, or one of the column names of the \link{microorganisms} data set: {.val mo}, {.val fullname}, {.val status}, {.val kingdom}, {.val phylum}, {.val class}, {.val order}, {.val family}, {.val genus}, {.val species}, {.val subspecies}, {.val rank}, {.val ref}, {.val oxygen_tolerance}, {.val source}, {.val lpsn}, {.val lpsn_parent}, {.val lpsn_renamed_to}, {.val mycobank}, {.val mycobank_parent}, {.val mycobank_renamed_to}, {.val gbif}, {.val gbif_parent}, {.val gbif_renamed_to}, {.val prevalence}, or {.val snomed}. Can also be \code{NULL} to not transform the input or \code{NA} to consider all microorganisms 'unknown'.}
\item{mo_transform}{A character to transform microorganism input - must be \code{"name"}, \code{"shortname"} (default), \code{"gramstain"}, or one of the column names of the \link{microorganisms} data set: \code{"mo"}, \code{"fullname"}, \code{"status"}, \code{"kingdom"}, \code{"phylum"}, \code{"class"}, \code{"order"}, \code{"family"}, \code{"genus"}, \code{"species"}, \code{"subspecies"}, \code{"rank"}, \code{"ref"}, \code{"oxygen_tolerance"}, \code{"source"}, \code{"lpsn"}, \code{"lpsn_parent"}, \code{"lpsn_renamed_to"}, \code{"mycobank"}, \code{"mycobank_parent"}, \code{"mycobank_renamed_to"}, \code{"gbif"}, \code{"gbif_parent"}, \code{"gbif_renamed_to"}, \code{"prevalence"}, or \code{"snomed"}. Can also be \code{NULL} to not transform the input or \code{NA} to consider all microorganisms 'unknown'.}
\item{ab_transform}{A character to transform antimicrobial input - must be one of the column names of the \link{antimicrobials} data set (defaults to \code{"name"}): {.val ab}, {.val cid}, {.val name}, {.val group}, {.val atc}, {.val atc_group1}, {.val atc_group2}, {.val abbreviations}, {.val synonyms}, {.val oral_ddd}, {.val oral_units}, {.val iv_ddd}, {.val iv_units}, or {.val loinc}. Can also be \code{NULL} to not transform the input.}
\item{ab_transform}{A character to transform antimicrobial input - must be one of the column names of the \link{antimicrobials} data set (defaults to \code{"name"}): \code{"ab"}, \code{"cid"}, \code{"name"}, \code{"group"}, \code{"atc"}, \code{"atc_group1"}, \code{"atc_group2"}, \code{"abbreviations"}, \code{"synonyms"}, \code{"oral_ddd"}, \code{"oral_units"}, \code{"iv_ddd"}, \code{"iv_units"}, or \code{"loinc"}. Can also be \code{NULL} to not transform the input.}
\item{syndromic_group}{A column name of \code{x}, or values calculated to split rows of \code{x}, e.g. by using \code{\link[=ifelse]{ifelse()}} or \code{\link[dplyr:case-and-replace-when]{case_when()}}. See \emph{Examples}.}

2
man/antimicrobial_selectors.Rd
View File

@@ -157,7 +157,7 @@ not_intrinsic_resistant(only_sir_columns = FALSE, col_mo = NULL,
\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()}}.}
\item{version_expected_phenotypes}{The version number to use for the EUCAST Expected Phenotypes. Can be {.val 1.2}.}
\item{version_expected_phenotypes}{The version number to use for the EUCAST Expected Phenotypes. Can be \code{"1.2"}.}
}
\value{
When used inside selecting or filtering, this returns a \link{character} vector of column names, with additional class \code{"amr_selector"}. When used individually, this returns an \link[=as.ab]{'ab' vector} with all possible antimicrobials that the function would be able to select or filter.

2
man/as.sir.Rd
View File

@@ -138,7 +138,7 @@ The default \code{"conservative"} setting ensures cautious handling of uncertain
\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 package option \code{\link[=AMR-options]{AMR_include_PKPD}}.}
\item{breakpoint_type}{The type of breakpoints to use, either {.val ECOFF}, {.val animal}, or {.val human}. ECOFF stands for Epidemiological Cut-Off values. The default is \code{"human"}, which can also be set with the 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{breakpoint_type}{The type of breakpoints to use, either \code{"ECOFF"}, \code{"animal"}, or \code{"human"}. ECOFF stands for Epidemiological Cut-Off values. The default is \code{"human"}, which can also be set with the 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 28 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).}

2
man/av_property.Rd
View File

@@ -52,7 +52,7 @@ av_property(x, property = "name", language = get_AMR_locale(), ...)
\item{open}{Browse the URL using \code{\link[utils:browseURL]{utils::browseURL()}}.}
\item{property}{One of the column names of one of the \link{antivirals} data set: \code{vector_or(colnames(antivirals), sort = FALSE)}.}
\item{property}{One of the column names of one of the \link{antivirals} data set: \code{"av"}, \code{"name"}, \code{"atc"}, \code{"cid"}, \code{"atc_group"}, \code{"synonyms"}, \code{"oral_ddd"}, \code{"oral_units"}, \code{"iv_ddd"}, \code{"iv_units"}, or \code{"loinc"}.}
}
\value{
\itemize{

6
man/interpretive_rules.Rd
View File

@@ -54,9 +54,9 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 15)
\item{version_breakpoints}{The version number to use for the EUCAST Clinical Breakpoints guideline. Can be \code{"16.0"}, \code{"15.0"}, \code{"14.0"}, \code{"13.1"}, \code{"12.0"}, \code{"11.0"}, or \code{"10.0"}.}
\item{version_expected_phenotypes}{The version number to use for the EUCAST Expected Phenotypes. Can be {.val 1.2}.}
\item{version_expected_phenotypes}{The version number to use for the EUCAST Expected Phenotypes. Can be \code{"1.2"}.}
\item{version_expertrules}{The version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be {.val 3.3}, {.val 3.2}, or {.val 3.1}.}
\item{version_expertrules}{The version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be \code{"3.3"}, \code{"3.2"}, or \code{"3.1"}.}
\item{ampc_cephalosporin_resistance}{(only applies when \code{rules} contains \code{"expert"} or \code{"all"}) a \link{character} value that should be applied to cefotaxime, ceftriaxone and ceftazidime for AmpC de-repressed cephalosporin-resistant mutants - the default is \code{NA}. Currently only works when \code{version_expertrules} is \code{3.2} and higher; these versions of '\emph{EUCAST Expert Rules on Enterobacterales}' state that results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these three drugs. A value of \code{NA} (the default) for this argument will remove results for these three drugs, while e.g. a value of \code{"R"} will make the results for these drugs resistant. Use \code{NULL} or \code{FALSE} to not alter results for these three drugs of AmpC de-repressed cephalosporin-resistant mutants. Using \code{TRUE} is equal to using \code{"R"}. \cr For \emph{EUCAST Expert Rules} v3.2, this rule applies to: \emph{Citrobacter braakii}, \emph{Citrobacter freundii}, \emph{Citrobacter gillenii}, \emph{Citrobacter murliniae}, \emph{Citrobacter rodenticum}, \emph{Citrobacter sedlakii}, \emph{Citrobacter werkmanii}, \emph{Citrobacter youngae}, \emph{Enterobacter}, \emph{Hafnia alvei}, \emph{Klebsiella aerogenes}, \emph{Morganella morganii}, \emph{Providencia}, and \emph{Serratia}.}
@@ -72,7 +72,7 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 15)
\item{ab}{Any (vector of) text that can be coerced to a valid antimicrobial drug code with \code{\link[=as.ab]{as.ab()}}.}
\item{administration}{Route of administration, either {.val }, {.val im}, {.val iv}, {.val oral}, or NA.}
\item{administration}{Route of administration, either \code{""}, \code{"im"}, \code{"iv"}, \code{"oral"}, or NA.}
}
\value{
The input of \code{x}, possibly with edited values of antimicrobials. Or, if \code{verbose = TRUE}, a \link{data.frame} with all original and new values of the affected bug-drug combinations.

2
man/mo_property.Rd
View File

@@ -165,7 +165,7 @@ The default is \code{FALSE}, which will return a note if outdated taxonomic name
\item{open}{Browse the URL using \code{\link[utils:browseURL]{browseURL()}}.}
\item{property}{One of the column names of the \link{microorganisms} data set: {.val mo}, {.val fullname}, {.val status}, {.val kingdom}, {.val phylum}, {.val class}, {.val order}, {.val family}, {.val genus}, {.val species}, {.val subspecies}, {.val rank}, {.val ref}, {.val oxygen_tolerance}, {.val source}, {.val lpsn}, {.val lpsn_parent}, {.val lpsn_renamed_to}, {.val mycobank}, {.val mycobank_parent}, {.val mycobank_renamed_to}, {.val gbif}, {.val gbif_parent}, {.val gbif_renamed_to}, {.val prevalence}, or {.val snomed}, or must be \code{"shortname"}.}
\item{property}{One of the column names of the \link{microorganisms} data set: \code{"mo"}, \code{"fullname"}, \code{"status"}, \code{"kingdom"}, \code{"phylum"}, \code{"class"}, \code{"order"}, \code{"family"}, \code{"genus"}, \code{"species"}, \code{"subspecies"}, \code{"rank"}, \code{"ref"}, \code{"oxygen_tolerance"}, \code{"source"}, \code{"lpsn"}, \code{"lpsn_parent"}, \code{"lpsn_renamed_to"}, \code{"mycobank"}, \code{"mycobank_parent"}, \code{"mycobank_renamed_to"}, \code{"gbif"}, \code{"gbif_parent"}, \code{"gbif_renamed_to"}, \code{"prevalence"}, or \code{"snomed"}, or must be \code{"shortname"}.}
}
\value{
\itemize{

2
man/plot.Rd
View File

@@ -137,7 +137,7 @@ labels_sir_count(position = NULL, x = "antibiotic",
\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 package option \code{\link[=AMR-options]{AMR_include_PKPD}}.}
\item{breakpoint_type}{The type of breakpoints to use, either {.val ECOFF}, {.val animal}, or {.val human}. ECOFF stands for Epidemiological Cut-Off values. The default is \code{"human"}, which can also be set with the 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{breakpoint_type}{The type of breakpoints to use, either \code{"ECOFF"}, \code{"animal"}, or \code{"human"}. ECOFF stands for Epidemiological Cut-Off values. The default is \code{"human"}, which can also be set with the 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{facet}{Variable to split plots by, either \code{"interpretation"} (default) or \code{"antibiotic"} or a grouping variable.}

2
man/top_n_microorganisms.Rd
View File

@@ -12,7 +12,7 @@ top_n_microorganisms(x, n, property = "species", n_for_each = NULL,
\item{n}{An integer specifying the maximum number of unique values of the \code{property} to include in the output.}
\item{property}{A character string indicating the microorganism property to use for filtering. Must be one of the column names of the \link{microorganisms} data set: {.val mo}, {.val fullname}, {.val status}, {.val kingdom}, {.val phylum}, {.val class}, {.val order}, {.val family}, {.val genus}, {.val species}, {.val subspecies}, {.val rank}, {.val ref}, {.val oxygen_tolerance}, {.val source}, {.val lpsn}, {.val lpsn_parent}, {.val lpsn_renamed_to}, {.val mycobank}, {.val mycobank_parent}, {.val mycobank_renamed_to}, {.val gbif}, {.val gbif_parent}, {.val gbif_renamed_to}, {.val prevalence}, or {.val snomed}. If \code{NULL}, the raw values from \code{col_mo} will be used without transformation. When using \code{"species"} (default) or \code{"subpecies"}, the genus will be added to make sure each (sub)species still belongs to the right genus.}
\item{property}{A character string indicating the microorganism property to use for filtering. Must be one of the column names of the \link{microorganisms} data set: \code{"mo"}, \code{"fullname"}, \code{"status"}, \code{"kingdom"}, \code{"phylum"}, \code{"class"}, \code{"order"}, \code{"family"}, \code{"genus"}, \code{"species"}, \code{"subspecies"}, \code{"rank"}, \code{"ref"}, \code{"oxygen_tolerance"}, \code{"source"}, \code{"lpsn"}, \code{"lpsn_parent"}, \code{"lpsn_renamed_to"}, \code{"mycobank"}, \code{"mycobank_parent"}, \code{"mycobank_renamed_to"}, \code{"gbif"}, \code{"gbif_parent"}, \code{"gbif_renamed_to"}, \code{"prevalence"}, or \code{"snomed"}. If \code{NULL}, the raw values from \code{col_mo} will be used without transformation. When using \code{"species"} (default) or \code{"subpecies"}, the genus will be added to make sure each (sub)species still belongs to the right genus.}
\item{n_for_each}{An optional integer specifying the maximum number of rows to retain for each value of the selected property. If \code{NULL}, all rows within the top \emph{n} groups will be included.}