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(v2.1.1.9079) fix for uti in as.sir()
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@ -58,7 +58,7 @@ set_ab_names(
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\arguments{
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\item{x}{any (vector of) text that can be coerced to a valid antibiotic drug code with \code{\link[=as.ab]{as.ab()}}}
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\item{language}{language of the returned text - the default is the current system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can also be set with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_locale}}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
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\item{language}{language of the returned text - the default is the current system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can also be set with the package option \code{\link[=AMR-options]{AMR_locale}}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
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\item{tolower}{a \link{logical} to indicate whether the first \link{character} of every output should be transformed to a lower case \link{character}. This will lead to e.g. "polymyxin B" and not "polymyxin b".}
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@ -20,10 +20,10 @@ With \code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}} you c
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There are two ways to circumvent this and automate the process of adding antimicrobials:
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\strong{Method 1:} Using the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_custom_ab}}, which is the preferred method. To use this method:
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\strong{Method 1:} Using the package option \code{\link[=AMR-options]{AMR_custom_ab}}, which is the preferred method. To use this method:
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\enumerate{
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\item Create a data set in the structure of the \link{antibiotics} data set (containing at the very least columns "ab" and "name") and save it with \code{\link[=saveRDS]{saveRDS()}} to a location of choice, e.g. \code{"~/my_custom_ab.rds"}, or any remote location.
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\item Set the file location to the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_custom_ab}}: \code{options(AMR_custom_ab = "~/my_custom_ab.rds")}. This can even be a remote file location, such as an https URL. Since options are not saved between \R sessions, it is best to save this option to the \code{.Rprofile} file so that it will be loaded on start-up of \R. To do this, open the \code{.Rprofile} file using e.g. \code{utils::file.edit("~/.Rprofile")}, add this text and save the file:
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\item Set the file location to the package option \code{\link[=AMR-options]{AMR_custom_ab}}: \code{options(AMR_custom_ab = "~/my_custom_ab.rds")}. This can even be a remote file location, such as an https URL. Since options are not saved between \R sessions, it is best to save this option to the \code{.Rprofile} file so that it will be loaded on start-up of \R. To do this, open the \code{.Rprofile} file using e.g. \code{utils::file.edit("~/.Rprofile")}, add this text and save the file:
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\if{html}{\out{<div class="sourceCode r">}}\preformatted{# Add custom antimicrobial codes:
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options(AMR_custom_ab = "~/my_custom_ab.rds")
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@ -22,10 +22,10 @@ This function will fill in missing taxonomy for you, if specific taxonomic colum
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There are two ways to circumvent this and automate the process of adding microorganisms:
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\strong{Method 1:} Using the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_custom_mo}}, which is the preferred method. To use this method:
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\strong{Method 1:} Using the package option \code{\link[=AMR-options]{AMR_custom_mo}}, which is the preferred method. To use this method:
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\enumerate{
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\item Create a data set in the structure of the \link{microorganisms} data set (containing at the very least column "genus") and save it with \code{\link[=saveRDS]{saveRDS()}} to a location of choice, e.g. \code{"~/my_custom_mo.rds"}, or any remote location.
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\item Set the file location to the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_custom_mo}}: \code{options(AMR_custom_mo = "~/my_custom_mo.rds")}. This can even be a remote file location, such as an https URL. Since options are not saved between \R sessions, it is best to save this option to the \code{.Rprofile} file so that it will be loaded on start-up of \R. To do this, open the \code{.Rprofile} file using e.g. \code{utils::file.edit("~/.Rprofile")}, add this text and save the file:
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\item Set the file location to the package option \code{\link[=AMR-options]{AMR_custom_mo}}: \code{options(AMR_custom_mo = "~/my_custom_mo.rds")}. This can even be a remote file location, such as an https URL. Since options are not saved between \R sessions, it is best to save this option to the \code{.Rprofile} file so that it will be loaded on start-up of \R. To do this, open the \code{.Rprofile} file using e.g. \code{utils::file.edit("~/.Rprofile")}, add this text and save the file:
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\if{html}{\out{<div class="sourceCode r">}}\preformatted{# Add custom microorganism codes:
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options(AMR_custom_mo = "~/my_custom_mo.rds")
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@ -51,7 +51,7 @@ antibiogram(
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\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: "mo", "fullname", "status", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "oxygen_tolerance", "source", "lpsn", "lpsn_parent", "lpsn_renamed_to", "mycobank", "mycobank_parent", "mycobank_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence", or "snomed". Can also be \code{NULL} to not transform the input.}
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\item{ab_transform}{a character to transform antibiotic input - must be one of the column names of the \link{antibiotics} data set (defaults to "name"): "ab", "cid", "name", "group", "atc", "atc_group1", "atc_group2", "abbreviations", "synonyms", "oral_ddd", "oral_units", "iv_ddd", "iv_units", or "loinc". Can also be \code{NULL} to not transform the input.}
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\item{ab_transform}{a character to transform antibiotic input - must be one of the column names of the \link{antibiotics} data set (defaults to \code{"name"}): "ab", "cid", "name", "group", "atc", "atc_group1", "atc_group2", "abbreviations", "synonyms", "oral_ddd", "oral_units", "iv_ddd", "iv_units", or "loinc". Can also be \code{NULL} to not transform the input.}
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\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_when]{case_when()}}. See \emph{Examples}.}
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@ -108,7 +108,7 @@ The formatting of the 'cells' of the table can be set with the argument \code{fo
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\item 5\% (N=15/300)
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}
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The default is \code{10}, which can be set globally with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_antibiogram_formatting_type}}, e.g. \code{options(AMR_antibiogram_formatting_type = 5)}.
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The default is \code{10}, which can be set globally with the package option \code{\link[=AMR-options]{AMR_antibiogram_formatting_type}}, e.g. \code{options(AMR_antibiogram_formatting_type = 5)}.
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Set \code{digits} (defaults to \code{0}) to alter the rounding of the susceptibility percentage.
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}
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@ -51,15 +51,15 @@ This excludes enterococci at default (who are in group D), use \code{Lancefield
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\item{minimum_matching_score}{a numeric value to set as the lower limit for the \link[=mo_matching_score]{MO matching score}. When left blank, this will be determined automatically based on the character length of \code{x}, its \link[=microorganisms]{taxonomic kingdom} and \link[=mo_matching_score]{human pathogenicity}.}
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\item{keep_synonyms}{a \link{logical} to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. The default is \code{FALSE}, which will return a note if old taxonomic names were processed. The default can be set with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_keep_synonyms}}, i.e. \code{options(AMR_keep_synonyms = TRUE)} or \code{options(AMR_keep_synonyms = FALSE)}.}
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\item{keep_synonyms}{a \link{logical} to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. The default is \code{FALSE}, which will return a note if old taxonomic names were processed. The default can be set with the package option \code{\link[=AMR-options]{AMR_keep_synonyms}}, i.e. \code{options(AMR_keep_synonyms = TRUE)} or \code{options(AMR_keep_synonyms = FALSE)}.}
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\item{reference_df}{a \link{data.frame} to be used for extra reference when translating \code{x} to a valid \code{\link{mo}}. See \code{\link[=set_mo_source]{set_mo_source()}} and \code{\link[=get_mo_source]{get_mo_source()}} to automate the usage of your own codes (e.g. used in your analysis or organisation).}
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\item{ignore_pattern}{a Perl-compatible \link[base:regex]{regular expression} (case-insensitive) of which all matches in \code{x} must return \code{NA}. This can be convenient to exclude known non-relevant input and can also be set with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_ignore_pattern}}, e.g. \code{options(AMR_ignore_pattern = "(not reported|contaminated flora)")}.}
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\item{ignore_pattern}{a Perl-compatible \link[base:regex]{regular expression} (case-insensitive) of which all matches in \code{x} must return \code{NA}. This can be convenient to exclude known non-relevant input and can also be set with the package option \code{\link[=AMR-options]{AMR_ignore_pattern}}, e.g. \code{options(AMR_ignore_pattern = "(not reported|contaminated flora)")}.}
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\item{cleaning_regex}{a Perl-compatible \link[base:regex]{regular expression} (case-insensitive) to clean the input of \code{x}. Every matched part in \code{x} will be removed. At default, this is the outcome of \code{\link[=mo_cleaning_regex]{mo_cleaning_regex()}}, which removes texts between brackets and texts such as "species" and "serovar". The default can be set with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_cleaning_regex}}.}
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\item{cleaning_regex}{a Perl-compatible \link[base:regex]{regular expression} (case-insensitive) to clean the input of \code{x}. Every matched part in \code{x} will be removed. At default, this is the outcome of \code{\link[=mo_cleaning_regex]{mo_cleaning_regex()}}, which removes texts between brackets and texts such as "species" and "serovar". The default can be set with the package option \code{\link[=AMR-options]{AMR_cleaning_regex}}.}
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\item{only_fungi}{a \link{logical} to indicate if only fungi must be found, making sure that e.g. misspellings always return records from the kingdom of Fungi. This can be set globally for \link[=mo_property]{all microorganism functions} with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_only_fungi}}, i.e. \code{options(AMR_only_fungi = TRUE)}.}
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\item{only_fungi}{a \link{logical} to indicate if only fungi must be found, making sure that e.g. misspellings always return records from the kingdom of Fungi. This can be set globally for \link[=mo_property]{all microorganism functions} with the package option \code{\link[=AMR-options]{AMR_only_fungi}}, i.e. \code{options(AMR_only_fungi = TRUE)}.}
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\item{language}{language to translate text like "no growth", which defaults to the system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}})}
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@ -107,7 +107,7 @@ sir_interpretation_history(clean = FALSE)
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\item{ab}{a vector (or column name) with \link{character}s that can be coerced to a valid antimicrobial drug code with \code{\link[=as.ab]{as.ab()}}}
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\item{guideline}{defaults to EUCAST 2024 (the latest implemented EUCAST guideline in the \link{clinical_breakpoints} data set), but can be set with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_guideline}}. Currently supports EUCAST (2011-2024) and CLSI (2011-2024), see \emph{Details}.}
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\item{guideline}{defaults to EUCAST 2024 (the latest implemented EUCAST guideline in the \link{clinical_breakpoints} data set), but can be set with the package option \code{\link[=AMR-options]{AMR_guideline}}. Currently supports EUCAST (2011-2024) and CLSI (2011-2024), see \emph{Details}.}
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\item{uti}{(Urinary Tract Infection) a vector (or column name) with \link{logical}s (\code{TRUE} or \code{FALSE}) to specify whether a UTI specific interpretation from the guideline should be chosen. For using \code{\link[=as.sir]{as.sir()}} on a \link{data.frame}, this can also be a column containing \link{logical}s or when left blank, the data set will be searched for a column 'specimen', and rows within this column containing 'urin' (such as 'urine', 'urina') will be regarded isolates from a UTI. See \emph{Examples}.}
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@ -117,11 +117,11 @@ sir_interpretation_history(clean = FALSE)
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\item{reference_data}{a \link{data.frame} to be used for interpretation, which defaults to the \link{clinical_breakpoints} data set. Changing this argument allows for using own interpretation guidelines. This argument must contain a data set that is equal in structure to the \link{clinical_breakpoints} data set (same column names and column types). Please note that the \code{guideline} argument will be ignored when \code{reference_data} is manually set.}
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\item{include_screening}{a \link{logical} to indicate that clinical breakpoints for screening are allowed - the default is \code{FALSE}. Can also be set with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_include_screening}}.}
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\item{include_screening}{a \link{logical} to indicate that clinical breakpoints for screening are allowed - the default is \code{FALSE}. Can also be set with the package option \code{\link[=AMR-options]{AMR_include_screening}}.}
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\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}}.}
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\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}}.}
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\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"}.}
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\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 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"}.}
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\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).}
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@ -192,7 +192,7 @@ For interpreting MIC values as well as disk diffusion diameters, currently imple
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Thus, the \code{guideline} argument must be set to e.g., \code{"EUCAST 2024"} or \code{"CLSI 2024"}. 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.
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You can set the default guideline with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_guideline}} (e.g. in your \code{.Rprofile} file), such as:
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You can set the default guideline with the package option \code{\link[=AMR-options]{AMR_guideline}} (e.g. in your \code{.Rprofile} file), such as:
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\if{html}{\out{<div class="sourceCode">}}\preformatted{ options(AMR_guideline = "CLSI")
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options(AMR_guideline = "CLSI 2018")
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@ -42,7 +42,7 @@ av_property(x, property = "name", language = get_AMR_locale(), ...)
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\arguments{
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\item{x}{any (vector of) text that can be coerced to a valid antiviral drug code with \code{\link[=as.av]{as.av()}}}
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\item{language}{language of the returned text - the default is system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can also be set with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_locale}}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
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\item{language}{language of the returned text - the default is system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can also be set with the package option \code{\link[=AMR-options]{AMR_locale}}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
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\item{tolower}{a \link{logical} to indicate whether the first \link{character} of every output should be transformed to a lower case \link{character}.}
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@ -31,7 +31,7 @@ bug_drug_combinations(x, col_mo = NULL, FUN = mo_shortname, ...)
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\item{translate_ab}{a \link{character} of length 1 containing column names of the \link{antibiotics} data set}
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\item{language}{language of the returned text - the default is the current system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can also be set with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_locale}}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
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\item{language}{language of the returned text - the default is the current system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can also be set with the package option \code{\link[=AMR-options]{AMR_locale}}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
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\item{minimum}{the minimum allowed number of available (tested) isolates. Any isolate count lower than \code{minimum} will return \code{NA} with a warning. The default number of \code{30} isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see \emph{Source}.}
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@ -29,9 +29,12 @@ clinical_breakpoints
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\description{
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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.
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Currently available breakpoint guidelines for \strong{clinical microbiology} are EUCAST 2011-2024 and CLSI 2011-2024.
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Currently available breakpoint guidelines for \strong{veterinary microbiology} are EUCAST 2021-2024 and CLSI 2019-2024.
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These breakpoints are currently implemented:
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\itemize{
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\item For \strong{clinical microbiology}: EUCAST 2011-2024 and CLSI 2011-2024;
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\item For \strong{veterinary microbiology}: EUCAST 2021-2024 and CLSI 2019-2024;
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\item For \strong{ECOFFs} (Epidemiological Cut-off Values): EUCAST 2020-2024 and CLSI 2022-2024.
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}
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Use \code{\link[=as.sir]{as.sir()}} to transform MICs or disks measurements to SIR values.
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}
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@ -40,7 +43,7 @@ Use \code{\link[=as.sir]{as.sir()}} to transform MICs or disks measurements to S
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Supported types of breakpoints are ECOFF, animal, and human. ECOFF (Epidemiological cut-off) values are used in antimicrobial susceptibility testing to differentiate between wild-type and non-wild-type strains of bacteria or fungi.
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The default is \code{"human"}, which can also be set with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_breakpoint_type}}. Use \code{\link[=as.sir]{as.sir(..., breakpoint_type = ...)}} to interpret raw data using a specific breakpoint type, e.g. \code{as.sir(..., breakpoint_type = "ECOFF")} to use ECOFFs.
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The default is \code{"human"}, which can also be set with the package option \code{\link[=AMR-options]{AMR_breakpoint_type}}. Use \code{\link[=as.sir]{as.sir(..., breakpoint_type = ...)}} to interpret raw data using a specific breakpoint type, e.g. \code{as.sir(..., breakpoint_type = "ECOFF")} to use ECOFFs.
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}
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\subsection{Imported from WHONET}{
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@ -48,7 +48,7 @@ count_df(
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\item{translate_ab}{a column name of the \link{antibiotics} data set to translate the antibiotic abbreviations to, using \code{\link[=ab_property]{ab_property()}}}
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\item{language}{language of the returned text - the default is the current system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can also be set with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_locale}}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
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\item{language}{language of the returned text - the default is the current system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can also be set with the package option \code{\link[=AMR-options]{AMR_locale}}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
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\item{combine_SI}{a \link{logical} to indicate whether all values of S and I must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant) - the default is \code{TRUE}}
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}
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@ -42,7 +42,7 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 12)
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\item{info}{a \link{logical} to indicate whether progress should be printed to the console - the default is only print while in interactive sessions}
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\item{rules}{a \link{character} vector that specifies which rules should be applied. Must be one or more of \code{"breakpoints"}, \code{"expert"}, \code{"other"}, \code{"custom"}, \code{"all"}, and defaults to \code{c("breakpoints", "expert")}. The default value can be set to another value using the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_eucastrules}}: \code{options(AMR_eucastrules = "all")}. If using \code{"custom"}, be sure to fill in argument \code{custom_rules} too. Custom rules can be created with \code{\link[=custom_eucast_rules]{custom_eucast_rules()}}.}
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\item{rules}{a \link{character} vector that specifies which rules should be applied. Must be one or more of \code{"breakpoints"}, \code{"expert"}, \code{"other"}, \code{"custom"}, \code{"all"}, and defaults to \code{c("breakpoints", "expert")}. The default value can be set to another value using the package option \code{\link[=AMR-options]{AMR_eucastrules}}: \code{options(AMR_eucastrules = "all")}. If using \code{"custom"}, be sure to fill in argument \code{custom_rules} too. Custom rules can be created with \code{\link[=custom_eucast_rules]{custom_eucast_rules()}}.}
|
||||
|
||||
\item{verbose}{a \link{logical} to turn Verbose mode on and off (default is off). In Verbose mode, the function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way. Using Verbose mode takes a lot more time.}
|
||||
|
||||
@ -96,7 +96,7 @@ Before further processing, two non-EUCAST rules about drug combinations can be a
|
||||
|
||||
Important examples include amoxicillin and amoxicillin/clavulanic acid, and trimethoprim and trimethoprim/sulfamethoxazole. Needless to say, for these rules to work, both drugs must be available in the data set.
|
||||
|
||||
Since these rules are not officially approved by EUCAST, they are not applied at default. To use these rules, include \code{"other"} to the \code{rules} argument, or use \code{eucast_rules(..., rules = "all")}. You can also set the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_eucastrules}}, i.e. run \code{options(AMR_eucastrules = "all")}.
|
||||
Since these rules are not officially approved by EUCAST, they are not applied at default. To use these rules, include \code{"other"} to the \code{rules} argument, or use \code{eucast_rules(..., rules = "all")}. You can also set the package option \code{\link[=AMR-options]{AMR_eucastrules}}, i.e. run \code{options(AMR_eucastrules = "all")}.
|
||||
}
|
||||
}
|
||||
\section{Antibiotics}{
|
||||
|
||||
@ -87,7 +87,7 @@ labels_sir_count(
|
||||
|
||||
\item{minimum}{the minimum allowed number of available (tested) isolates. Any isolate count lower than \code{minimum} will return \code{NA} with a warning. The default number of \code{30} isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see \emph{Source}.}
|
||||
|
||||
\item{language}{language of the returned text - the default is the current system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can also be set with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_locale}}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
|
||||
\item{language}{language of the returned text - the default is the current system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can also be set with the package option \code{\link[=AMR-options]{AMR_locale}}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
|
||||
|
||||
\item{nrow}{(when using \code{facet}) number of rows}
|
||||
|
||||
|
||||
@ -302,7 +302,7 @@ mo_property(
|
||||
|
||||
\item{language}{language to translate text like "no growth", which defaults to the system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}})}
|
||||
|
||||
\item{keep_synonyms}{a \link{logical} to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. The default is \code{FALSE}, which will return a note if old taxonomic names were processed. The default can be set with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_keep_synonyms}}, i.e. \code{options(AMR_keep_synonyms = TRUE)} or \code{options(AMR_keep_synonyms = FALSE)}.}
|
||||
\item{keep_synonyms}{a \link{logical} to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. The default is \code{FALSE}, which will return a note if old taxonomic names were processed. The default can be set with the package option \code{\link[=AMR-options]{AMR_keep_synonyms}}, i.e. \code{options(AMR_keep_synonyms = TRUE)} or \code{options(AMR_keep_synonyms = FALSE)}.}
|
||||
|
||||
\item{...}{other arguments passed on to \code{\link[=as.mo]{as.mo()}}, such as 'minimum_matching_score', 'ignore_pattern', and 'remove_from_input'}
|
||||
|
||||
|
||||
@ -26,7 +26,7 @@ This is \strong{the fastest way} to have your organisation (or analysis) specifi
|
||||
\details{
|
||||
The reference file can be a text file separated with commas (CSV) or tabs or pipes, an Excel file (either 'xls' or 'xlsx' format) or an \R object file (extension '.rds'). To use an Excel file, you will need to have the \code{readxl} package installed.
|
||||
|
||||
\code{\link[=set_mo_source]{set_mo_source()}} will check the file for validity: it must be a \link{data.frame}, must have a column named \code{"mo"} which contains values from \code{\link[=microorganisms]{microorganisms$mo}} or \code{\link[=microorganisms]{microorganisms$fullname}} and must have a reference column with your own defined values. If all tests pass, \code{\link[=set_mo_source]{set_mo_source()}} will read the file into \R and will ask to export it to \code{"~/mo_source.rds"}. The CRAN policy disallows packages to write to the file system, although '\emph{exceptions may be allowed in interactive sessions if the package obtains confirmation from the user}'. For this reason, this function only works in interactive sessions so that the user can \strong{specifically confirm and allow} that this file will be created. The destination of this file can be set with the \code{destination} argument and defaults to the user's home directory. It can also be set with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_mo_source}}, e.g. \code{options(AMR_mo_source = "my/location/file.rds")}.
|
||||
\code{\link[=set_mo_source]{set_mo_source()}} will check the file for validity: it must be a \link{data.frame}, must have a column named \code{"mo"} which contains values from \code{\link[=microorganisms]{microorganisms$mo}} or \code{\link[=microorganisms]{microorganisms$fullname}} and must have a reference column with your own defined values. If all tests pass, \code{\link[=set_mo_source]{set_mo_source()}} will read the file into \R and will ask to export it to \code{"~/mo_source.rds"}. The CRAN policy disallows packages to write to the file system, although '\emph{exceptions may be allowed in interactive sessions if the package obtains confirmation from the user}'. For this reason, this function only works in interactive sessions so that the user can \strong{specifically confirm and allow} that this file will be created. The destination of this file can be set with the \code{destination} argument and defaults to the user's home directory. It can also be set with the package option \code{\link[=AMR-options]{AMR_mo_source}}, e.g. \code{options(AMR_mo_source = "my/location/file.rds")}.
|
||||
|
||||
The created compressed data file \code{"mo_source.rds"} will be used at default for MO determination (function \code{\link[=as.mo]{as.mo()}} and consequently all \verb{mo_*} functions like \code{\link[=mo_genus]{mo_genus()}} and \code{\link[=mo_gramstain]{mo_gramstain()}}). The location and timestamp of the original file will be saved as an \link[base:attributes]{attribute} to the compressed data file.
|
||||
|
||||
|
||||
@ -137,13 +137,13 @@ scale_fill_mic(keep_operators = "edges", mic_range = NULL, drop = FALSE, ...)
|
||||
|
||||
\item{colours_SIR}{colours to use for filling in the bars, must be a vector of three values (in the order S, I and R). The default colours are colour-blind friendly.}
|
||||
|
||||
\item{language}{language to be used to translate 'Susceptible', 'Increased exposure'/'Intermediate' and 'Resistant' - the default is system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can be overwritten by setting the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_locale}}, e.g. \code{options(AMR_locale = "de")}, see \link{translate}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
|
||||
\item{language}{language to be used to translate 'Susceptible', 'Increased exposure'/'Intermediate' and 'Resistant' - the default is system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can be overwritten by setting the package option \code{\link[=AMR-options]{AMR_locale}}, e.g. \code{options(AMR_locale = "de")}, see \link{translate}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
|
||||
|
||||
\item{expand}{a \link{logical} to indicate whether the range on the x axis should be expanded between the lowest and highest value. For MIC values, intermediate values will be factors of 2 starting from the highest MIC value. For disk diameters, the whole diameter range will be filled.}
|
||||
|
||||
\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{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 "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{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 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.
|
||||
|
||||
@ -84,7 +84,7 @@ sir_df(
|
||||
|
||||
\item{translate_ab}{a column name of the \link{antibiotics} data set to translate the antibiotic abbreviations to, using \code{\link[=ab_property]{ab_property()}}}
|
||||
|
||||
\item{language}{language of the returned text - the default is the current system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can also be set with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_locale}}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
|
||||
\item{language}{language of the returned text - the default is the current system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can also be set with the package option \code{\link[=AMR-options]{AMR_locale}}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
|
||||
|
||||
\item{combine_SI}{a \link{logical} to indicate whether all values of S and I must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant) - the default is \code{TRUE}}
|
||||
}
|
||||
|
||||
@ -27,7 +27,7 @@ For language-dependent output of \code{AMR} functions, such as \code{\link[=mo_n
|
||||
\details{
|
||||
The currently 20 supported languages are 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), and Ukrainian (uk). All these languages have translations available for all antimicrobial drugs and colloquial microorganism names.
|
||||
|
||||
To permanently silence the once-per-session language note on a non-English operating system, you can set the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_locale}} in your \code{.Rprofile} file like this:
|
||||
To permanently silence the once-per-session language note on a non-English operating system, you can set the package option \code{\link[=AMR-options]{AMR_locale}} in your \code{.Rprofile} file like this:
|
||||
|
||||
\if{html}{\out{<div class="sourceCode r">}}\preformatted{# Open .Rprofile file
|
||||
utils::file.edit("~/.Rprofile")
|
||||
@ -43,13 +43,13 @@ Please read about adding or updating a language in \href{https://github.com/msbe
|
||||
|
||||
The system language will be used at default (as returned by \code{Sys.getenv("LANG")} or, if \code{LANG} is not set, \code{\link[=Sys.getlocale]{Sys.getlocale("LC_COLLATE")}}), if that language is supported. But the language to be used can be overwritten in two ways and will be checked in this order:
|
||||
\enumerate{
|
||||
\item Setting the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_locale}}, either by using e.g. \code{set_AMR_locale("German")} or by running e.g. \code{options(AMR_locale = "German")}.
|
||||
\item Setting the package option \code{\link[=AMR-options]{AMR_locale}}, either by using e.g. \code{set_AMR_locale("German")} or by running e.g. \code{options(AMR_locale = "German")}.
|
||||
|
||||
Note that setting an \R option only works in the same session. Save the command \code{options(AMR_locale = "(your language)")} to your \code{.Rprofile} file to apply it for every session. Run \code{utils::file.edit("~/.Rprofile")} to edit your \code{.Rprofile} file.
|
||||
\item Setting the system variable \code{LANGUAGE} or \code{LANG}, e.g. by adding \code{LANGUAGE="de_DE.utf8"} to your \code{.Renviron} file in your home directory.
|
||||
}
|
||||
|
||||
Thus, if the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_locale}} is set, the system variables \code{LANGUAGE} and \code{LANG} will be ignored.
|
||||
Thus, if the package option \code{\link[=AMR-options]{AMR_locale}} is set, the system variables \code{LANGUAGE} and \code{LANG} will be ignored.
|
||||
}
|
||||
}
|
||||
\examples{
|
||||
|
||||
Reference in New Issue
Block a user