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(v1.4.0.9041) updates based on review
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@ -23,8 +23,8 @@ This package can be used for:
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\item Determining multi-drug resistance (MDR) / multi-drug resistant organisms (MDRO)
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\item Calculating (empirical) susceptibility of both mono therapy and combination therapies
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\item Predicting future antimicrobial resistance using regression models
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\item Getting properties for any microorganism (like Gram stain, species, genus or family)
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\item Getting properties for any antibiotic (like name, code of EARS-Net/ATC/LOINC/PubChem, defined daily dose or trade name)
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\item Getting properties for any microorganism (such as Gram stain, species, genus or family)
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\item Getting properties for any antibiotic (such as name, code of EARS-Net/ATC/LOINC/PubChem, defined daily dose or trade name)
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\item Plotting antimicrobial resistance
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\item Applying EUCAST expert rules
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\item Getting SNOMED codes of a microorganism, or getting properties of a microorganism based on a SNOMED code
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@ -48,7 +48,7 @@ With \code{type = "administration"} (or abbreviations, like "admin", "adm"), all
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Without using \code{collapse}, this function will return a \link{list}. This can be convenient to use e.g. inside a \code{mutate()}):\cr
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\code{df \%>\% mutate(abx = ab_from_text(clinical_text))}
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The returned AB codes can be transformed to official names, groups, etc. with all \code{\link[=ab_property]{ab_property()}} functions like \code{\link[=ab_name]{ab_name()}} and \code{\link[=ab_group]{ab_group()}}, or by using the \code{translate_ab} parameter.
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The returned AB codes can be transformed to official names, groups, etc. with all \code{\link[=ab_property]{ab_*}} functions such as \code{\link[=ab_name]{ab_name()}} and \code{\link[=ab_group]{ab_group()}}, or by using the \code{translate_ab} parameter.
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With using \code{collapse}, this function will return a \link{character}:\cr
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\code{df \%>\% mutate(abx = ab_from_text(clinical_text, collapse = "|"))}
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@ -8,7 +8,7 @@
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\format{
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\subsection{For the \link{antibiotics} data set: a \link{data.frame} with 455 observations and 14 variables:}{
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\itemize{
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\item \code{ab}\cr Antibiotic ID as used in this package (like \code{AMC}), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available
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\item \code{ab}\cr Antibiotic ID as used in this package (such as \code{AMC}), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available
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\item \code{atc}\cr ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC, like \code{J01CR02}
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\item \code{cid}\cr Compound ID as found in PubChem
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\item \code{name}\cr Official name as used by WHONET/EARS-Net or the WHO
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@ -54,7 +54,7 @@ antibiotics
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antivirals
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}
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\description{
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Two data sets containing all antibiotics/antimycotics and antivirals. Use \code{\link[=as.ab]{as.ab()}} or one of the \code{\link[=ab_property]{ab_property()}} functions to retrieve values from the \link{antibiotics} data set. Three identifiers are included in this data set: an antibiotic ID (\code{ab}, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (\code{atc}) as defined by the WHO, and a Compound ID (\code{cid}) as found in PubChem. Other properties in this data set are derived from one or more of these codes.
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Two data sets containing all antibiotics/antimycotics and antivirals. Use \code{\link[=as.ab]{as.ab()}} or one of the \code{\link[=ab_property]{ab_*}} functions to retrieve values from the \link{antibiotics} data set. Three identifiers are included in this data set: an antibiotic ID (\code{ab}, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (\code{atc}) as defined by the WHO, and a Compound ID (\code{cid}) as found in PubChem. Other properties in this data set are derived from one or more of these codes.
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}
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\details{
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Properties that are based on an ATC code are only available when an ATC is available. These properties are: \code{atc_group1}, \code{atc_group2}, \code{oral_ddd}, \code{oral_units}, \code{iv_ddd} and \code{iv_units}.
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@ -30,13 +30,15 @@ All entries in the \link{antibiotics} data set have three different identifiers:
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All these properties will be searched for the user input. The \code{\link[=as.ab]{as.ab()}} can correct for different forms of misspelling:
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\itemize{
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\item Wrong spelling of drug names (like "tobramicin" or "gentamycin"), which corrects for most audible similarities such as f/ph, x/ks, c/z/s, t/th, etc.
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\item Wrong spelling of drug names (such as "tobramicin" or "gentamycin"), which corrects for most audible similarities such as f/ph, x/ks, c/z/s, t/th, etc.
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\item Too few or too many vowels or consonants
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\item Switching two characters (like "mreopenem", often the case in clinical data, when doctors typed too fast)
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\item Switching two characters (such as "mreopenem", often the case in clinical data, when doctors typed too fast)
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\item Digitalised paper records, leaving artefacts like 0/o/O (zero and O's), B/8, n/r, etc.
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}
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Use the \code{\link[=ab_property]{ab_property()}} functions to get properties based on the returned antibiotic ID, see Examples.
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Use the \code{\link[=ab_property]{ab_*}} functions to get properties based on the returned antibiotic ID, see Examples.
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Note: the \code{\link[=as.ab]{as.ab()}} and \code{\link[=ab_property]{ab_*}} functions may use very long regular expression to match brand names of antimicrobial agents. This may fail on some systems.
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}
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\section{Source}{
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@ -53,7 +53,7 @@ This excludes \emph{Enterococci} at default (who are in group D), use \code{Lanc
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A \link{character} \link{vector} with additional class \code{\link{mo}}
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}
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\description{
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Use this function to determine a valid microorganism ID (\code{\link{mo}}). Determination is done using intelligent rules and the complete taxonomic kingdoms Bacteria, Chromista, Protozoa, Archaea and most microbial species from the kingdom Fungi (see Source). The input can be almost anything: a full name (like \code{"Staphylococcus aureus"}), an abbreviated name (like \code{"S. aureus"}), an abbreviation known in the field (like \code{"MRSA"}), or just a genus. Please see \emph{Examples}.
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Use this function to determine a valid microorganism ID (\code{\link{mo}}). Determination is done using intelligent rules and the complete taxonomic kingdoms Bacteria, Chromista, Protozoa, Archaea and most microbial species from the kingdom Fungi (see Source). The input can be almost anything: a full name (like \code{"Staphylococcus aureus"}), an abbreviated name (such as \code{"S. aureus"}), an abbreviation known in the field (such as \code{"MRSA"}), or just a genus. Please see \emph{Examples}.
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}
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\details{
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\subsection{General info}{
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@ -220,7 +220,7 @@ mo_is_intrinsic_resistant("E. coli", "vanco") # returns TRUE
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\seealso{
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\link{microorganisms} for the \link{data.frame} that is being used to determine ID's.
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The \code{\link[=mo_property]{mo_property()}} functions (like \code{\link[=mo_genus]{mo_genus()}}, \code{\link[=mo_gramstain]{mo_gramstain()}}) to get properties based on the returned code.
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The \code{\link[=mo_property]{mo_*}} functions (such as \code{\link[=mo_genus]{mo_genus()}}, \code{\link[=mo_gramstain]{mo_gramstain()}}) to get properties based on the returned code.
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}
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\keyword{Becker}
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\keyword{Lancefield}
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@ -39,7 +39,7 @@ bug_drug_combinations(x, col_mo = NULL, FUN = mo_shortname, ...)
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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 Source.}
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\item{combine_SI}{a 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). This used to be the parameter \code{combine_IR}, but this now follows the redefinition by EUCAST about the interpretion of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. Default is \code{TRUE}.}
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\item{combine_SI}{a 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). This used to be the parameter \code{combine_IR}, but this now follows the redefinition by EUCAST about the interpretation of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. Default is \code{TRUE}.}
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\item{combine_IR}{logical to indicate whether values R and I should be summed}
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@ -19,8 +19,8 @@ This package contains the complete taxonomic tree of almost all microorganisms (
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Included are:
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\itemize{
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\item All ~55,000 (sub)species from the kingdoms of Archaea, Bacteria, Chromista and Protozoa
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\item All ~5,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Microascales, Mucorales, Onygenales, Pneumocystales, Saccharomycetales, Schizosaccharomycetales and Tremellales, as well as ~4,600 other fungal (sub)species. The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package and including everything would tremendously slow down our algorithms too. By only including the aforementioned taxonomic orders, the most relevant fungi are covered (like all species of \emph{Aspergillus}, \emph{Candida}, \emph{Cryptococcus}, \emph{Histplasma}, \emph{Pneumocystis}, \emph{Saccharomyces} and \emph{Trichophyton}).
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\item All ~2,200 (sub)species from ~50 other relevant genera from the kingdom of Animalia (like \emph{Strongyloides} and \emph{Taenia})
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\item All ~5,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Microascales, Mucorales, Onygenales, Pneumocystales, Saccharomycetales, Schizosaccharomycetales and Tremellales, as well as ~4,600 other fungal (sub)species. The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package and including everything would tremendously slow down our algorithms too. By only including the aforementioned taxonomic orders, the most relevant fungi are covered (such as all species of \emph{Aspergillus}, \emph{Candida}, \emph{Cryptococcus}, \emph{Histplasma}, \emph{Pneumocystis}, \emph{Saccharomyces} and \emph{Trichophyton}).
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\item All ~2,200 (sub)species from ~50 other relevant genera from the kingdom of Animalia (such as \emph{Strongyloides} and \emph{Taenia})
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\item All ~13,000 previously accepted names of all included (sub)species (these were taxonomically renamed)
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\item The complete taxonomic tree of all included (sub)species: from kingdom to subspecies
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\item The responsible author(s) and year of scientific publication
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@ -47,11 +47,11 @@ count_df(
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\item{data}{a \link{data.frame} containing columns with class \code{\link{rsi}} (see \code{\link[=as.rsi]{as.rsi()}})}
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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()}}. Use a value}
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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, defaults to system language (see \code{\link[=get_locale]{get_locale()}}) and can also be set with \code{getOption("AMR_locale")}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
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\item{combine_SI}{a 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). This used to be the parameter \code{combine_IR}, but this now follows the redefinition by EUCAST about the interpretion of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. Default is \code{TRUE}.}
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\item{combine_SI}{a 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). This used to be the parameter \code{combine_IR}, but this now follows the redefinition by EUCAST about the interpretation of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. Default is \code{TRUE}.}
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\item{combine_IR}{a logical to indicate whether all values of I and R must be merged into one, so the output only consists of S vs. I+R (susceptible vs. non-susceptible). This is outdated, see parameter \code{combine_SI}.}
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}
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@ -58,7 +58,7 @@ filter_first_weighted_isolate(
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\item{col_mo}{column name of the IDs of the microorganisms (see \code{\link[=as.mo]{as.mo()}}), defaults to the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
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\item{col_testcode}{column name of the test codes. Use \code{col_testcode = NULL} to \strong{not} exclude certain test codes (like test codes for screening). In that case \code{testcodes_exclude} will be ignored.}
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\item{col_testcode}{column name of the test codes. Use \code{col_testcode = NULL} to \strong{not} exclude certain test codes (such as test codes for screening). In that case \code{testcodes_exclude} will be ignored.}
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\item{col_specimen}{column name of the specimen type or group}
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@ -58,7 +58,7 @@ If \code{x} is a matrix with at least two rows and columns, it is taken as a two
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The p-value is computed from the asymptotic chi-squared distribution of the test statistic.
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In the contingency table case simulation is done by random sampling from the set of all contingency tables with given marginals, and works only if the marginals are strictly positive. Note that this is not the usual sampling situation assumed for a chi-squared test (like the \emph{G}-test) but rather that for Fisher's exact test.
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In the contingency table case simulation is done by random sampling from the set of all contingency tables with given marginals, and works only if the marginals are strictly positive. Note that this is not the usual sampling situation assumed for a chi-squared test (such as the \emph{G}-test) but rather that for Fisher's exact test.
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In the goodness-of-fit case simulation is done by random sampling from the discrete distribution specified by \code{p}, each sample being of size \code{n = sum(x)}. This simulation is done in \R and may be slow.
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\subsection{\emph{G}-test of goodness-of-fit (likelihood ratio test)}{
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@ -87,9 +87,9 @@ labels_rsi_count(
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\item{limits}{numeric vector of length two providing limits of the scale, use \code{NA} to refer to the existing minimum or maximum}
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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()}}. Use a value}
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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{combine_SI}{a 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). This used to be the parameter \code{combine_IR}, but this now follows the redefinition by EUCAST about the interpretion of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. Default is \code{TRUE}.}
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\item{combine_SI}{a 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). This used to be the parameter \code{combine_IR}, but this now follows the redefinition by EUCAST about the interpretation of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. Default is \code{TRUE}.}
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\item{combine_IR}{a logical to indicate whether all values of I and R must be merged into one, so the output only consists of S vs. I+R (susceptible vs. non-susceptible). This is outdated, see parameter \code{combine_SI}.}
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@ -26,7 +26,7 @@ anti_join_microorganisms(x, by = NULL, ...)
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\arguments{
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\item{x}{existing table to join, or character vector}
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\item{by}{a variable to join by - if left empty will search for a column with class \code{\link{mo}} (created with \code{\link[=as.mo]{as.mo()}}) or will be \code{"mo"} if that column name exists in \code{x}, could otherwise be a column name of \code{x} with values that exist in \code{microorganisms$mo} (like \code{by = "bacteria_id"}), or another column in \link{microorganisms} (but then it should be named, like \code{by = c("bacteria_id" = "fullname")})}
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\item{by}{a variable to join by - if left empty will search for a column with class \code{\link{mo}} (created with \code{\link[=as.mo]{as.mo()}}) or will be \code{"mo"} if that column name exists in \code{x}, could otherwise be a column name of \code{x} with values that exist in \code{microorganisms$mo} (such as \code{by = "bacteria_id"}), or another column in \link{microorganisms} (but then it should be named, like \code{by = c("bacteria_id" = "fullname")})}
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\item{suffix}{if there are non-joined duplicate variables in \code{x} and \code{y}, these suffixes will be added to the output to disambiguate them. Should be a character vector of length 2.}
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@ -117,7 +117,7 @@ All functions will return the most recently known taxonomic property according t
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\item \code{mo_ref("Shimwellia blattae")} will return \code{"Priest et al., 2010"} (without a message)
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}
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The short name - \code{\link[=mo_shortname]{mo_shortname()}} - almost always returns the first character of the genus and the full species, like \code{"E. coli"}. Exceptions are abbreviations of staphylococci (like \emph{"CoNS"}, Coagulase-Negative Staphylococci) and beta-haemolytic streptococci (like \emph{"GBS"}, Group B Streptococci). Please bear in mind that e.g. \emph{E. coli} could mean \emph{Escherichia coli} (kingdom of Bacteria) as well as \emph{Entamoeba coli} (kingdom of Protozoa). Returning to the full name will be done using \code{\link[=as.mo]{as.mo()}} internally, giving priority to bacteria and human pathogens, i.e. \code{"E. coli"} will be considered \emph{Escherichia coli}. In other words, \code{mo_fullname(mo_shortname("Entamoeba coli"))} returns \code{"Escherichia coli"}.
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The short name - \code{\link[=mo_shortname]{mo_shortname()}} - almost always returns the first character of the genus and the full species, like \code{"E. coli"}. Exceptions are abbreviations of staphylococci (such as \emph{"CoNS"}, Coagulase-Negative Staphylococci) and beta-haemolytic streptococci (such as \emph{"GBS"}, Group B Streptococci). Please bear in mind that e.g. \emph{E. coli} could mean \emph{Escherichia coli} (kingdom of Bacteria) as well as \emph{Entamoeba coli} (kingdom of Protozoa). Returning to the full name will be done using \code{\link[=as.mo]{as.mo()}} internally, giving priority to bacteria and human pathogens, i.e. \code{"E. coli"} will be considered \emph{Escherichia coli}. In other words, \code{mo_fullname(mo_shortname("Entamoeba coli"))} returns \code{"Escherichia coli"}.
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Since the top-level of the taxonomy is sometimes referred to as 'kingdom' and sometimes as 'domain', the functions \code{\link[=mo_kingdom]{mo_kingdom()}} and \code{\link[=mo_domain]{mo_domain()}} return the exact same results.
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@ -6,12 +6,17 @@
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\alias{get_mo_source}
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\title{User-defined reference data set for microorganisms}
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\usage{
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set_mo_source(path)
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set_mo_source(
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path,
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destination = getOption("AMR_mo_source", "~/mo_source.rds")
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)
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get_mo_source()
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get_mo_source(destination = getOption("AMR_mo_source", "~/mo_source.rds"))
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}
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\arguments{
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\item{path}{location of your reference file, see Details. Can be \code{""}, \code{NULL} or \code{FALSE} to delete the reference file.}
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\item{destination}{destination of the compressed data file, default to the user's home directory.}
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}
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\description{
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These functions can be used to predefine your own reference to be used in \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()}}.
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@ -21,11 +26,11 @@ This is \strong{the fastest way} to have your organisation (or analysis) specifi
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\details{
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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.
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\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$mo}} and must have a reference column with your own defined values. If all tests pass, \code{\link[=set_mo_source]{set_mo_source()}} will read the file into R and will ask to export it to \code{"~/.mo_source.rds"}. The CRAN policy disallows packages to write to the file system, although '\emph{exceptions may be allowed in interactive sessions if the package obtains confirmation from the user}'. For this reason, this function only works in interactive sessions so that the user can \strong{specifically confirm and allow} that this file will be created.
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\code{\link[=set_mo_source]{set_mo_source()}} will check the file for validity: it must be a \link{data.frame}, must have a column named \code{"mo"} which contains values from \code{\link[=microorganisms]{microorganisms$mo}} 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} parameter and defaults to the user's home directory. It can also be set as an \R option, using \verb{options(AMR_mo_source = "my/location/file.rds)}.
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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 of the original file will be saved as an R option with \code{options(mo_source = path)}. Its timestamp will be saved with \code{options(mo_source_datetime = ...)}.
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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 attribute to the compressed data file.
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|
||||
The function \code{\link[=get_mo_source]{get_mo_source()}} will return the data set by reading \code{"~/.mo_source.rds"} with \code{\link[=readRDS]{readRDS()}}. If the original file has changed (by checking the aforementioned options \code{mo_source} and \code{mo_source_datetime}), it will call \code{\link[=set_mo_source]{set_mo_source()}} to update the data file automatically if used in an interactive session.
|
||||
The function \code{\link[=get_mo_source]{get_mo_source()}} will return the data set by reading \code{"mo_source.rds"} with \code{\link[=readRDS]{readRDS()}}. If the original file has changed (by checking the location and timestamp of the original file), it will call \code{\link[=set_mo_source]{set_mo_source()}} to update the data file automatically if used in an interactive session.
|
||||
|
||||
Reading an Excel file (\code{.xlsx}) with only one row has a size of 8-9 kB. The compressed file created with \code{\link[=set_mo_source]{set_mo_source()}} will then have a size of 0.1 kB and can be read by \code{\link[=get_mo_source]{get_mo_source()}} in only a couple of microseconds (millionths of a second).
|
||||
}
|
||||
@ -41,13 +46,15 @@ Imagine this data on a sheet of an Excel file (mo codes were looked up in the \l
|
||||
}
|
||||
|
||||
We save it as \code{"home/me/ourcodes.xlsx"}. Now we have to set it as a source:\preformatted{set_mo_source("home/me/ourcodes.xlsx")
|
||||
#> NOTE: Created mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'
|
||||
#> (columns "Organisation XYZ" and "mo")
|
||||
#> NOTE: Created mo_source file '/Users/me/mo_source.rds' (0.3 kB) from
|
||||
#> '/Users/me/Documents/ourcodes.xlsx' (9 kB), columns
|
||||
#> "Organisation XYZ" and "mo"
|
||||
}
|
||||
|
||||
It has now created a file \code{"~/.mo_source.rds"} with the contents of our Excel file. Only the first column with foreign values and the 'mo' column will be kept when creating the RDS file.
|
||||
It has now created a file \code{"~/mo_source.rds"} with the contents of our Excel file. Only the first column with foreign values and the 'mo' column will be kept when creating the RDS file.
|
||||
|
||||
And now we can use it in our functions:\preformatted{as.mo("lab_mo_ecoli")
|
||||
#> Class <mo>
|
||||
#> [1] B_ESCHR_COLI
|
||||
|
||||
mo_genus("lab_mo_kpneumoniae")
|
||||
@ -55,6 +62,9 @@ mo_genus("lab_mo_kpneumoniae")
|
||||
|
||||
# other input values still work too
|
||||
as.mo(c("Escherichia coli", "E. coli", "lab_mo_ecoli"))
|
||||
#> NOTE: Translation to one microorganism was guessed with uncertainty.
|
||||
#> Use mo_uncertainties() to review it.
|
||||
#> Class <mo>
|
||||
#> [1] B_ESCHR_COLI B_ESCHR_COLI B_ESCHR_COLI
|
||||
}
|
||||
|
||||
@ -68,8 +78,10 @@ If we edit the Excel file by, let's say, adding row 4 like this:\preformatted{
|
||||
}
|
||||
|
||||
...any new usage of an MO function in this package will update your data file:\preformatted{as.mo("lab_mo_ecoli")
|
||||
#> NOTE: Updated mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'
|
||||
#> (columns "Organisation XYZ" and "mo")
|
||||
#> NOTE: Updated mo_source file '/Users/me/mo_source.rds' (0.3 kB) from
|
||||
#> '/Users/me/Documents/ourcodes.xlsx' (9 kB), columns
|
||||
#> "Organisation XYZ" and "mo"
|
||||
#> Class <mo>
|
||||
#> [1] B_ESCHR_COLI
|
||||
|
||||
mo_genus("lab_Staph_aureus")
|
||||
@ -77,10 +89,10 @@ mo_genus("lab_Staph_aureus")
|
||||
}
|
||||
|
||||
To delete the reference data file, just use \code{""}, \code{NULL} or \code{FALSE} as input for \code{\link[=set_mo_source]{set_mo_source()}}:\preformatted{set_mo_source(NULL)
|
||||
# Removed mo_source file '~/.mo_source.rds'.
|
||||
#> Removed mo_source file '/Users/me/mo_source.rds'
|
||||
}
|
||||
|
||||
If the original Excel file is moved or deleted, the mo_source file will be removed upon the next use of \code{\link[=as.mo]{as.mo()}}. If the mo_source file is manually deleted (i.e. without using \code{\link[=set_mo_source]{set_mo_source()}}), the references to the mo_source file will be removed upon the next use of \code{\link[=as.mo]{as.mo()}}.
|
||||
If the original Excel file is moved or deleted, the mo_source file will be removed upon the next use of \code{\link[=as.mo]{as.mo()}}.
|
||||
}
|
||||
|
||||
\section{Stable lifecycle}{
|
||||
|
||||
@ -62,11 +62,11 @@ rsi_df(
|
||||
|
||||
\item{data}{a \link{data.frame} containing columns with class \code{\link{rsi}} (see \code{\link[=as.rsi]{as.rsi()}})}
|
||||
|
||||
\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()}}. Use a value}
|
||||
\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, defaults to system language (see \code{\link[=get_locale]{get_locale()}}) and can also be set with \code{getOption("AMR_locale")}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
|
||||
|
||||
\item{combine_SI}{a 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). This used to be the parameter \code{combine_IR}, but this now follows the redefinition by EUCAST about the interpretion of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. Default is \code{TRUE}.}
|
||||
\item{combine_SI}{a 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). This used to be the parameter \code{combine_IR}, but this now follows the redefinition by EUCAST about the interpretation of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. Default is \code{TRUE}.}
|
||||
|
||||
\item{combine_IR}{a logical to indicate whether all values of I and R must be merged into one, so the output only consists of S vs. I+R (susceptible vs. non-susceptible). This is outdated, see parameter \code{combine_SI}.}
|
||||
}
|
||||
|
||||
@ -63,7 +63,7 @@ ggplot_rsi_predict(
|
||||
|
||||
\item{model}{the statistical model of choice. This could be a generalised linear regression model with binomial distribution (i.e. using `glm(..., family = binomial)``, assuming that a period of zero resistance was followed by a period of increasing resistance leading slowly to more and more resistance. See Details for all valid options.}
|
||||
|
||||
\item{I_as_S}{a logical to indicate whether values \code{I} should be treated as \code{S} (will otherwise be treated as \code{R}). The default, \code{TRUE}, follows the redefinition by EUCAST about the interpretion of I (increased exposure) in 2019, see section \emph{Interpretation of S, I and R} below.}
|
||||
\item{I_as_S}{a logical to indicate whether values \code{"I"} should be treated as \code{"S"} (will otherwise be treated as \code{"R"}). The default, \code{TRUE}, follows the redefinition by EUCAST about the interpretation of I (increased exposure) in 2019, see section \emph{Interpretation of S, I and R} below.}
|
||||
|
||||
\item{preserve_measurements}{a logical to indicate whether predictions of years that are actually available in the data should be overwritten by the original data. The standard errors of those years will be \code{NA}.}
|
||||
|
||||
|
||||
@ -11,7 +11,7 @@ get_locale()
|
||||
For language-dependent output of AMR functions, like \code{\link[=mo_name]{mo_name()}}, \code{\link[=mo_gramstain]{mo_gramstain()}}, \code{\link[=mo_type]{mo_type()}} and \code{\link[=ab_name]{ab_name()}}.
|
||||
}
|
||||
\details{
|
||||
Strings will be translated to foreign languages if they are defined in a local translation file. Additions to this file can be suggested at our repository. The file can be found here: \url{https://github.com/msberends/AMR/blob/master/data-raw/translations.tsv}. This file will be read by all functions where a translated output can be desired, like all \code{\link[=mo_property]{mo_property()}} functions (\code{\link[=mo_name]{mo_name()}}, \code{\link[=mo_gramstain]{mo_gramstain()}}, \code{\link[=mo_type]{mo_type()}}, etc.) and \code{\link[=ab_property]{ab_property()}} functions (\code{\link[=ab_name]{ab_name()}}, \code{\link[=ab_group]{ab_group()}} etc.).
|
||||
Strings will be translated to foreign languages if they are defined in a local translation file. Additions to this file can be suggested at our repository. The file can be found here: \url{https://github.com/msberends/AMR/blob/master/data-raw/translations.tsv}. This file will be read by all functions where a translated output can be desired, like all \code{\link[=mo_property]{mo_*}} functions (such as \code{\link[=mo_name]{mo_name()}}, \code{\link[=mo_gramstain]{mo_gramstain()}}, \code{\link[=mo_type]{mo_type()}}, etc.) and \code{\link[=ab_property]{ab_*}} functions (such as \code{\link[=ab_name]{ab_name()}}, \code{\link[=ab_group]{ab_group()}}, etc.).
|
||||
|
||||
Currently supported languages are: Dutch, English, French, German, Italian, Portuguese, Spanish. Please note that currently not all these languages have translations available for all antimicrobial agents and colloquial microorganism names.
|
||||
|
||||
|
||||
Reference in New Issue
Block a user