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(v1.8.1.9011) update prevalence of some genera
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@ -35,7 +35,9 @@ This transforms vectors to a new class \code{\link{mic}}, which treats the input
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\details{
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To interpret MIC values as RSI values, use \code{\link[=as.rsi]{as.rsi()}} on MIC values. It supports guidelines from EUCAST (2011-2022) and CLSI (2011-2022).
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This class for MIC values is a quite a special data type: formally it is an ordered \link{factor} with valid MIC values as \link{factor} levels (to make sure only valid MIC values are retained), but for any mathematical operation it acts as decimal numbers:\preformatted{x <- random_mic(10)
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This class for MIC values is a quite a special data type: formally it is an ordered \link{factor} with valid MIC values as \link{factor} levels (to make sure only valid MIC values are retained), but for any mathematical operation it acts as decimal numbers:
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\if{html}{\out{<div class="sourceCode">}}\preformatted{x <- random_mic(10)
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x
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#> Class <mic>
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#> [1] 16 1 8 8 64 >=128 0.0625 32 32 16
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@ -48,9 +50,11 @@ x[1] * 2
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median(x)
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#> [1] 26
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}
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}\if{html}{\out{</div>}}
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This makes it possible to maintain operators that often come with MIC values, such ">=" and "<=", even when filtering using \link{numeric} values in data analysis, e.g.:\preformatted{x[x > 4]
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This makes it possible to maintain operators that often come with MIC values, such ">=" and "<=", even when filtering using \link{numeric} values in data analysis, e.g.:
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\if{html}{\out{<div class="sourceCode">}}\preformatted{x[x > 4]
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#> Class <mic>
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#> [1] 16 8 8 64 >=128 32 32 16
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@ -63,7 +67,7 @@ subset(df, x > 4) # or with dplyr: df \%>\% filter(x > 4)
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#> 8 32 A
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#> 9 32 A
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#> 10 16 A
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}
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}\if{html}{\out{</div>}}
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The following \link[=groupGeneric]{generic functions} are implemented for the MIC class: \code{!}, \code{!=}, \code{\%\%}, \code{\%/\%}, \code{&}, \code{*}, \code{+}, \code{-}, \code{/}, \code{<}, \code{<=}, \code{==}, \code{>}, \code{>=}, \code{^}, \code{|}, \code{\link[=abs]{abs()}}, \code{\link[=acos]{acos()}}, \code{\link[=acosh]{acosh()}}, \code{\link[=all]{all()}}, \code{\link[=any]{any()}}, \code{\link[=asin]{asin()}}, \code{\link[=asinh]{asinh()}}, \code{\link[=atan]{atan()}}, \code{\link[=atanh]{atanh()}}, \code{\link[=ceiling]{ceiling()}}, \code{\link[=cos]{cos()}}, \code{\link[=cosh]{cosh()}}, \code{\link[=cospi]{cospi()}}, \code{\link[=cummax]{cummax()}}, \code{\link[=cummin]{cummin()}}, \code{\link[=cumprod]{cumprod()}}, \code{\link[=cumsum]{cumsum()}}, \code{\link[=digamma]{digamma()}}, \code{\link[=exp]{exp()}}, \code{\link[=expm1]{expm1()}}, \code{\link[=floor]{floor()}}, \code{\link[=gamma]{gamma()}}, \code{\link[=lgamma]{lgamma()}}, \code{\link[=log]{log()}}, \code{\link[=log1p]{log1p()}}, \code{\link[=log2]{log2()}}, \code{\link[=log10]{log10()}}, \code{\link[=max]{max()}}, \code{\link[=mean]{mean()}}, \code{\link[=min]{min()}}, \code{\link[=prod]{prod()}}, \code{\link[=range]{range()}}, \code{\link[=round]{round()}}, \code{\link[=sign]{sign()}}, \code{\link[=signif]{signif()}}, \code{\link[=sin]{sin()}}, \code{\link[=sinh]{sinh()}}, \code{\link[=sinpi]{sinpi()}}, \code{\link[=sqrt]{sqrt()}}, \code{\link[=sum]{sum()}}, \code{\link[=tan]{tan()}}, \code{\link[=tanh]{tanh()}}, \code{\link[=tanpi]{tanpi()}}, \code{\link[=trigamma]{trigamma()}} and \code{\link[=trunc]{trunc()}}. Some functions of the \code{stats} package are also implemented: \code{\link[=median]{median()}}, \code{\link[=quantile]{quantile()}}, \code{\link[=mad]{mad()}}, \code{\link[=IQR]{IQR()}}, \code{\link[=fivenum]{fivenum()}}. Also, \code{\link[=boxplot.stats]{boxplot.stats()}} is supported. Since \code{\link[=sd]{sd()}} and \code{\link[=var]{var()}} are non-generic functions, these could not be extended. Use \code{\link[=mad]{mad()}} as an alternative, or use e.g. \code{sd(as.numeric(x))} where \code{x} is your vector of MIC values.
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@ -61,7 +61,9 @@ Use this function to determine a valid microorganism code (\code{\link{mo}}). De
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\details{
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\subsection{General Info}{
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A microorganism (MO) code from this package (class: \code{\link{mo}}) is human readable and typically looks like these examples:\preformatted{ Code Full name
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A microorganism (MO) code from this package (class: \code{\link{mo}}) is human readable and typically looks like these examples:
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\if{html}{\out{<div class="sourceCode">}}\preformatted{ Code Full name
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--------------- --------------------------------------
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B_KLBSL Klebsiella
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B_KLBSL_PNMN Klebsiella pneumoniae
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@ -73,7 +75,7 @@ A microorganism (MO) code from this package (class: \code{\link{mo}}) is human r
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| \\----> genus, a 5-7 letter acronym
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\\----> taxonomic kingdom: A (Archaea), AN (Animalia), B (Bacteria),
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C (Chromista), F (Fungi), P (Protozoa)
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}
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}\if{html}{\out{</div>}}
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Values that cannot be coerced will be considered 'unknown' and will get the MO code \code{UNKNOWN}.
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@ -94,16 +94,20 @@ The \code{\link[=as.rsi]{as.rsi()}} function works in four ways:
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\item For \strong{cleaning raw / untransformed data}. The data will be cleaned to only contain values S, I and R and will try its best to determine this with some intelligence. For example, mixed values with R/SI interpretations and MIC values such as \code{"<0.25; S"} will be coerced to \code{"S"}. Combined interpretations for multiple test methods (as seen in laboratory records) such as \code{"S; S"} will be coerced to \code{"S"}, but a value like \code{"S; I"} will return \code{NA} with a warning that the input is unclear.
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\item For \strong{interpreting minimum inhibitory concentration (MIC) values} according to EUCAST or CLSI. You must clean your MIC values first using \code{\link[=as.mic]{as.mic()}}, that also gives your columns the new data class \code{\link{mic}}. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the \code{mo} argument.
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\itemize{
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\item Using \code{dplyr}, R/SI interpretation can be done very easily with either:\preformatted{your_data \%>\% mutate_if(is.mic, as.rsi) # until dplyr 1.0.0
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\item Using \code{dplyr}, R/SI interpretation can be done very easily with either:
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\if{html}{\out{<div class="sourceCode">}}\preformatted{your_data \%>\% mutate_if(is.mic, as.rsi) # until dplyr 1.0.0
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your_data \%>\% mutate(across(where(is.mic), as.rsi)) # since dplyr 1.0.0
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}
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}\if{html}{\out{</div>}}
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\item Operators like "<=" will be stripped before interpretation. When using \code{conserve_capped_values = TRUE}, an MIC value of e.g. ">2" will always return "R", even if the breakpoint according to the chosen guideline is ">=4". This is to prevent that capped values from raw laboratory data would not be treated conservatively. The default behaviour (\code{conserve_capped_values = FALSE}) considers ">2" to be lower than ">=4" and might in this case return "S" or "I".
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}
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\item For \strong{interpreting disk diffusion diameters} according to EUCAST or CLSI. You must clean your disk zones first using \code{\link[=as.disk]{as.disk()}}, that also gives your columns the new data class \code{\link{disk}}. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the \code{mo} argument.
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\itemize{
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\item Using \code{dplyr}, R/SI interpretation can be done very easily with either:\preformatted{your_data \%>\% mutate_if(is.disk, as.rsi) # until dplyr 1.0.0
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\item Using \code{dplyr}, R/SI interpretation can be done very easily with either:
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\if{html}{\out{<div class="sourceCode">}}\preformatted{your_data \%>\% mutate_if(is.disk, as.rsi) # until dplyr 1.0.0
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your_data \%>\% mutate(across(where(is.disk), as.rsi)) # since dplyr 1.0.0
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}
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}\if{html}{\out{</div>}}
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}
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\item For \strong{interpreting a complete data set}, with automatic determination of MIC values, disk diffusion diameters, microorganism names or codes, and antimicrobial test results. This is done very simply by running \code{as.rsi(your_data)}.
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}
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18
man/count.Rd
18
man/count.Rd
@ -97,7 +97,9 @@ This AMR package honours this (new) insight. Use \code{\link[=susceptibility]{su
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\section{Combination Therapy}{
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When using more than one variable for \code{...} (= combination therapy), use \code{only_all_tested} to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Drug A and Drug B, about how \code{\link[=susceptibility]{susceptibility()}} works to calculate the \%SI:\preformatted{--------------------------------------------------------------------
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When using more than one variable for \code{...} (= combination therapy), use \code{only_all_tested} to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Drug A and Drug B, about how \code{\link[=susceptibility]{susceptibility()}} works to calculate the \%SI:
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\if{html}{\out{<div class="sourceCode">}}\preformatted{--------------------------------------------------------------------
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only_all_tested = FALSE only_all_tested = TRUE
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----------------------- -----------------------
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Drug A Drug B include as include as include as include as
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@ -113,15 +115,19 @@ When using more than one variable for \code{...} (= combination therapy), use \c
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R <NA> - - - -
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<NA> <NA> - - - -
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--------------------------------------------------------------------
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}
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}\if{html}{\out{</div>}}
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Please note that, in combination therapies, for \code{only_all_tested = TRUE} applies that:\preformatted{ count_S() + count_I() + count_R() = count_all()
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Please note that, in combination therapies, for \code{only_all_tested = TRUE} applies that:
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\if{html}{\out{<div class="sourceCode">}}\preformatted{ count_S() + count_I() + count_R() = count_all()
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proportion_S() + proportion_I() + proportion_R() = 1
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}
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}\if{html}{\out{</div>}}
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and that, in combination therapies, for \code{only_all_tested = FALSE} applies that:\preformatted{ count_S() + count_I() + count_R() >= count_all()
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and that, in combination therapies, for \code{only_all_tested = FALSE} applies that:
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\if{html}{\out{<div class="sourceCode">}}\preformatted{ count_S() + count_I() + count_R() >= count_all()
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proportion_S() + proportion_I() + proportion_R() >= 1
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}
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}\if{html}{\out{</div>}}
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Using \code{only_all_tested} has no impact when only using one antibiotic as input.
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}
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@ -22,11 +22,15 @@ Some organisations have their own adoption of EUCAST rules. This function can be
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\subsection{Basics}{
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If you are familiar with the \code{\link[dplyr:case_when]{case_when()}} function of the \code{dplyr} package, you will recognise the input method to set your own rules. Rules must be set using what \R considers to be the 'formula notation'. The rule itself is written \emph{before} the tilde (\code{~}) and the consequence of the rule is written \emph{after} the tilde:\preformatted{x <- custom_eucast_rules(TZP == "S" ~ aminopenicillins == "S",
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TZP == "R" ~ aminopenicillins == "R")
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}
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If you are familiar with the \code{\link[dplyr:case_when]{case_when()}} function of the \code{dplyr} package, you will recognise the input method to set your own rules. Rules must be set using what \R considers to be the 'formula notation'. The rule itself is written \emph{before} the tilde (\code{~}) and the consequence of the rule is written \emph{after} the tilde:
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These are two custom EUCAST rules: if TZP (piperacillin/tazobactam) is "S", all aminopenicillins (ampicillin and amoxicillin) must be made "S", and if TZP is "R", aminopenicillins must be made "R". These rules can also be printed to the console, so it is immediately clear how they work:\preformatted{x
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\if{html}{\out{<div class="sourceCode">}}\preformatted{x <- custom_eucast_rules(TZP == "S" ~ aminopenicillins == "S",
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TZP == "R" ~ aminopenicillins == "R")
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}\if{html}{\out{</div>}}
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These are two custom EUCAST rules: if TZP (piperacillin/tazobactam) is "S", all aminopenicillins (ampicillin and amoxicillin) must be made "S", and if TZP is "R", aminopenicillins must be made "R". These rules can also be printed to the console, so it is immediately clear how they work:
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\if{html}{\out{<div class="sourceCode">}}\preformatted{x
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#> A set of custom EUCAST rules:
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#>
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#> 1. If TZP is S then set to S:
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@ -34,9 +38,11 @@ These are two custom EUCAST rules: if TZP (piperacillin/tazobactam) is "S", all
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#>
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#> 2. If TZP is R then set to R:
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#> amoxicillin (AMX), ampicillin (AMP)
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}
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}\if{html}{\out{</div>}}
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The rules (the part \emph{before} the tilde, in above example \code{TZP == "S"} and \code{TZP == "R"}) must be evaluable in your data set: it should be able to run as a filter in your data set without errors. This means for the above example that the column \code{TZP} must exist. We will create a sample data set and test the rules set:\preformatted{df <- data.frame(mo = c("E. coli", "K. pneumoniae"),
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The rules (the part \emph{before} the tilde, in above example \code{TZP == "S"} and \code{TZP == "R"}) must be evaluable in your data set: it should be able to run as a filter in your data set without errors. This means for the above example that the column \code{TZP} must exist. We will create a sample data set and test the rules set:
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\if{html}{\out{<div class="sourceCode">}}\preformatted{df <- data.frame(mo = c("E. coli", "K. pneumoniae"),
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TZP = "R",
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amox = "",
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AMP = "")
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@ -49,54 +55,28 @@ eucast_rules(df, rules = "custom", custom_rules = x)
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#> mo TZP amox AMP
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#> 1 E. coli R R R
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#> 2 K. pneumoniae R R R
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}
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}\if{html}{\out{</div>}}
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}
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\subsection{Using taxonomic properties in rules}{
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There is one exception in variables used for the rules: all column names of the \link{microorganisms} data set can also be used, but do not have to exist in the data set. These column names are: \code{mo}, \code{fullname}, \code{kingdom}, \code{phylum}, \code{class}, \code{order}, \code{family}, \code{genus}, \code{species}, \code{subspecies}, \code{rank}, \code{ref}, \code{species_id}, \code{source}, \code{prevalence} and \code{snomed}. Thus, this next example will work as well, despite the fact that the \code{df} data set does not contain a column \code{genus}:\preformatted{y <- custom_eucast_rules(TZP == "S" & genus == "Klebsiella" ~ aminopenicillins == "S",
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There is one exception in variables used for the rules: all column names of the \link{microorganisms} data set can also be used, but do not have to exist in the data set. These column names are: \verb{r vector_and(colnames(microorganisms), quote = "``", sort = FALSE)}. Thus, this next example will work as well, despite the fact that the \code{df} data set does not contain a column \code{genus}:
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\if{html}{\out{<div class="sourceCode">}}\preformatted{y <- custom_eucast_rules(TZP == "S" & genus == "Klebsiella" ~ aminopenicillins == "S",
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TZP == "R" & genus == "Klebsiella" ~ aminopenicillins == "R")
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eucast_rules(df, rules = "custom", custom_rules = y)
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#> mo TZP amox AMP
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#> 1 E. coli R
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#> 2 K. pneumoniae R R R
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}
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}\if{html}{\out{</div>}}
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}
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\subsection{Usage of antibiotic group names}{
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It is possible to define antibiotic groups instead of single antibiotics for the rule consequence, the part \emph{after} the tilde. In above examples, the antibiotic group \code{aminopenicillins} is used to include ampicillin and amoxicillin. The following groups are allowed (case-insensitive). Within parentheses are the agents that will be matched when running the rule.
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\itemize{
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\item \code{aminoglycosides}\cr(amikacin, amikacin/fosfomycin, amphotericin B-high, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin and tobramycin-high)
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\item \code{aminopenicillins}\cr(amoxicillin and ampicillin)
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\item \code{antifungals}\cr(5-fluorocytosine, amphotericin B, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, fosfluconazole, griseofulvin, hachimycin, ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole, manogepix, micafungin, miconazole, nystatin, pimaricin, posaconazole, rezafungin, ribociclib, sulconazole, terbinafine, terconazole and voriconazole)
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\item \code{antimycobacterials}\cr(4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, morinamide, p-aminosalicylic acid, pretomanid, prothionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, simvastatin/fenofibrate, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone/isoniazid, tiocarlide and viomycin)
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\item \code{betalactams}\cr(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, avibactam, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, biapenem, carbenicillin, carindacillin, cefacetrile, cefaclor, cefadroxil, cefaloridine, cefamandole, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/nacubactam, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor, ceftolozane/tazobactam, ceftriaxone, cefuroxime, cefuroxime axetil, cephalexin, cephalothin, cephapirin, cephradine, ciclacillin, clometocillin, cloxacillin, dicloxacillin, doripenem, epicillin, ertapenem, flucloxacillin, hetacillin, imipenem, imipenem/EDTA, imipenem/relebactam, latamoxef, lenampicillin, loracarbef, mecillinam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, metampicillin, methicillin, mezlocillin, mezlocillin/sulbactam, nacubactam, nafcillin, oxacillin, panipenem, penamecillin, penicillin/novobiocin, penicillin/sulbactam, phenethicillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, razupenem, ritipenem, ritipenem acoxil, sarmoxicillin, sulbactam, sulbenicillin, sultamicillin, talampicillin, tazobactam, tebipenem, temocillin, ticarcillin and ticarcillin/clavulanic acid)
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\item \code{carbapenems}\cr(biapenem, doripenem, ertapenem, imipenem, imipenem/EDTA, imipenem/relebactam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, panipenem, razupenem, ritipenem, ritipenem acoxil and tebipenem)
|
||||
\item \code{cephalosporins}\cr(cefacetrile, cefaclor, cefadroxil, cefaloridine, cefamandole, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor, ceftolozane/tazobactam, ceftriaxone, cefuroxime, cefuroxime axetil, cephalexin, cephalothin, cephapirin, cephradine, latamoxef and loracarbef)
|
||||
\item \code{cephalosporins_1st}\cr(cefacetrile, cefadroxil, cefaloridine, cefatrizine, cefazedone, cefazolin, cefroxadine, ceftezole, cephalexin, cephalothin, cephapirin and cephradine)
|
||||
\item \code{cephalosporins_2nd}\cr(cefaclor, cefamandole, cefmetazole, cefonicid, ceforanide, cefotetan, cefotiam, cefoxitin, cefoxitin screening, cefprozil, cefuroxime, cefuroxime axetil and loracarbef)
|
||||
\item \code{cephalosporins_3rd}\cr(cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefetamet, cefetamet pivoxil, cefixime, cefmenoxime, cefodizime, cefoperazone, cefoperazone/sulbactam, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotiam hexetil, cefovecin, cefpimizole, cefpiramide, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefsulodin, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftriaxone and latamoxef)
|
||||
\item \code{cephalosporins_4th}\cr(cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetecol, cefoselis, cefozopran, cefpirome and cefquinome)
|
||||
\item \code{cephalosporins_5th}\cr(ceftaroline, ceftaroline/avibactam, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor and ceftolozane/tazobactam)
|
||||
\item \code{cephalosporins_except_caz}\cr(cefacetrile, cefaclor, cefadroxil, cefaloridine, cefamandole, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor, ceftolozane/tazobactam, ceftriaxone, cefuroxime, cefuroxime axetil, cephalexin, cephalothin, cephapirin, cephradine, latamoxef and loracarbef)
|
||||
\item \code{fluoroquinolones}\cr(besifloxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nifuroquine, norfloxacin, ofloxacin, orbifloxacin, pazufloxacin, pefloxacin, pradofloxacin, premafloxacin, prulifloxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin and trovafloxacin)
|
||||
\item \code{glycopeptides}\cr(avoparcin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin and vancomycin-macromethod)
|
||||
\item \code{glycopeptides_except_lipo}\cr(avoparcin, norvancomycin, ramoplanin, teicoplanin, teicoplanin-macromethod, vancomycin and vancomycin-macromethod)
|
||||
\item \code{lincosamides}\cr(acetylmidecamycin, acetylspiramycin, clindamycin, gamithromycin, kitasamycin, lincomycin, meleumycin, nafithromycin, pirlimycin, primycin, solithromycin, tildipirosin, tilmicosin, tulathromycin, tylosin and tylvalosin)
|
||||
\item \code{lipoglycopeptides}\cr(dalbavancin, oritavancin and telavancin)
|
||||
\item \code{macrolides}\cr(acetylmidecamycin, acetylspiramycin, azithromycin, clarithromycin, dirithromycin, erythromycin, flurithromycin, gamithromycin, josamycin, kitasamycin, meleumycin, midecamycin, miocamycin, nafithromycin, oleandomycin, pirlimycin, primycin, rokitamycin, roxithromycin, solithromycin, spiramycin, telithromycin, tildipirosin, tilmicosin, troleandomycin, tulathromycin, tylosin and tylvalosin)
|
||||
\item \code{oxazolidinones}\cr(cadazolid, cycloserine, linezolid, tedizolid and thiacetazone)
|
||||
\item \code{penicillins}\cr(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, avibactam, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, carbenicillin, carindacillin, cefepime/nacubactam, ciclacillin, clometocillin, cloxacillin, dicloxacillin, epicillin, flucloxacillin, hetacillin, lenampicillin, mecillinam, metampicillin, methicillin, mezlocillin, mezlocillin/sulbactam, nacubactam, nafcillin, oxacillin, penamecillin, penicillin/novobiocin, penicillin/sulbactam, phenethicillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, sarmoxicillin, sulbactam, sulbenicillin, sultamicillin, talampicillin, tazobactam, temocillin, ticarcillin and ticarcillin/clavulanic acid)
|
||||
\item \code{polymyxins}\cr(colistin, polymyxin B and polymyxin B/polysorbate 80)
|
||||
\item \code{quinolones}\cr(besifloxacin, cinoxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, flumequine, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nalidixic acid, nifuroquine, nitroxoline, norfloxacin, ofloxacin, orbifloxacin, oxolinic acid, pazufloxacin, pefloxacin, pipemidic acid, piromidic acid, pradofloxacin, premafloxacin, prulifloxacin, rosoxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin and trovafloxacin)
|
||||
\item \code{streptogramins}\cr(pristinamycin and quinupristin/dalfopristin)
|
||||
\item \code{tetracyclines}\cr(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, tetracycline and tigecycline)
|
||||
\item \code{tetracyclines_except_tgc}\cr(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline and tetracycline)
|
||||
\item \code{trimethoprims}\cr(brodimoprim, sulfadiazine, sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole, sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, sulfathiourea, trimethoprim and trimethoprim/sulfamethoxazole)
|
||||
\item \code{ureidopenicillins}\cr(azlocillin, mezlocillin, piperacillin and piperacillin/tazobactam)
|
||||
}
|
||||
|
||||
\verb{r paste0(" * ", sapply(DEFINED_AB_GROUPS, function(x) paste0("``", tolower(gsub("^AB_", "", x)), "``\\\\cr(", vector_and(ab_name(eval(parse(text = x), envir = asNamespace("AMR")), language = NULL, tolower = TRUE), quotes = FALSE), ")"), USE.NAMES = FALSE), "\\n", collapse = "")}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
@ -76,11 +76,13 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
|
||||
The file containing all EUCAST rules is located here: \url{https://github.com/msberends/AMR/blob/main/data-raw/eucast_rules.tsv}. \strong{Note:} Old taxonomic names are replaced with the current taxonomy where applicable. For example, \emph{Ochrobactrum anthropi} was renamed to \emph{Brucella anthropi} in 2020; the original EUCAST rules v3.1 and v3.2 did not yet contain this new taxonomic name. The file used as input for this \code{AMR} package contains the taxonomy updated until \link[=catalogue_of_life]{5 October 2021}.
|
||||
\subsection{Custom Rules}{
|
||||
|
||||
Custom rules can be created using \code{\link[=custom_eucast_rules]{custom_eucast_rules()}}, e.g.:\preformatted{x <- custom_eucast_rules(AMC == "R" & genus == "Klebsiella" ~ aminopenicillins == "R",
|
||||
Custom rules can be created using \code{\link[=custom_eucast_rules]{custom_eucast_rules()}}, e.g.:
|
||||
|
||||
\if{html}{\out{<div class="sourceCode">}}\preformatted{x <- custom_eucast_rules(AMC == "R" & genus == "Klebsiella" ~ aminopenicillins == "R",
|
||||
AMC == "I" & genus == "Klebsiella" ~ aminopenicillins == "I")
|
||||
|
||||
eucast_rules(example_isolates, rules = "custom", custom_rules = x)
|
||||
}
|
||||
}\if{html}{\out{</div>}}
|
||||
}
|
||||
|
||||
\subsection{'Other' Rules}{
|
||||
|
||||
@ -89,8 +89,10 @@ The \emph{G}-test uses the log of the ratio of two likelihoods as the test stati
|
||||
|
||||
\eqn{G = 2 * sum(x * log(x / E))}
|
||||
|
||||
where \code{E} are the expected values. Since this is chi-square distributed, the p value can be calculated in \R with:\preformatted{p <- stats::pchisq(G, df, lower.tail = FALSE)
|
||||
}
|
||||
where \code{E} are the expected values. Since this is chi-square distributed, the p value can be calculated in \R with:
|
||||
|
||||
\if{html}{\out{<div class="sourceCode">}}\preformatted{p <- stats::pchisq(G, df, lower.tail = FALSE)
|
||||
}\if{html}{\out{</div>}}
|
||||
|
||||
where \code{df} are the degrees of freedom.
|
||||
|
||||
|
||||
24
man/mdro.Rd
24
man/mdro.Rd
@ -122,35 +122,43 @@ Please suggest your own (country-specific) guidelines by letting us know: \url{h
|
||||
|
||||
Custom guidelines can be set with the \code{\link[=custom_mdro_guideline]{custom_mdro_guideline()}} function. This is of great importance if you have custom rules to determine MDROs in your hospital, e.g., rules that are dependent on ward, state of contact isolation or other variables in your data.
|
||||
|
||||
If you are familiar with the \code{\link[dplyr:case_when]{case_when()}} function of the \code{dplyr} package, you will recognise the input method to set your own rules. Rules must be set using what \R considers to be the 'formula notation'. The rule is written \emph{before} the tilde (\code{~}) and the consequence of the rule is written \emph{after} the tilde:\preformatted{custom <- custom_mdro_guideline(CIP == "R" & age > 60 ~ "Elderly Type A",
|
||||
If you are familiar with the \code{\link[dplyr:case_when]{case_when()}} function of the \code{dplyr} package, you will recognise the input method to set your own rules. Rules must be set using what \R considers to be the 'formula notation'. The rule is written \emph{before} the tilde (\code{~}) and the consequence of the rule is written \emph{after} the tilde:
|
||||
|
||||
\if{html}{\out{<div class="sourceCode">}}\preformatted{custom <- custom_mdro_guideline(CIP == "R" & age > 60 ~ "Elderly Type A",
|
||||
ERY == "R" & age > 60 ~ "Elderly Type B")
|
||||
}
|
||||
}\if{html}{\out{</div>}}
|
||||
|
||||
If a row/an isolate matches the first rule, the value after the first \code{~} (in this case \emph{'Elderly Type A'}) will be set as MDRO value. Otherwise, the second rule will be tried and so on. The number of rules is unlimited.
|
||||
|
||||
You can print the rules set in the console for an overview. Colours will help reading it if your console supports colours.\preformatted{custom
|
||||
You can print the rules set in the console for an overview. Colours will help reading it if your console supports colours.
|
||||
|
||||
\if{html}{\out{<div class="sourceCode">}}\preformatted{custom
|
||||
#> A set of custom MDRO rules:
|
||||
#> 1. CIP is "R" and age is higher than 60 -> Elderly Type A
|
||||
#> 2. ERY is "R" and age is higher than 60 -> Elderly Type B
|
||||
#> 3. Otherwise -> Negative
|
||||
#>
|
||||
#> Unmatched rows will return NA.
|
||||
}
|
||||
}\if{html}{\out{</div>}}
|
||||
|
||||
The outcome of the function can be used for the \code{guideline} argument in the \code{\link[=mdro]{mdro()}} function:\preformatted{x <- mdro(example_isolates,
|
||||
The outcome of the function can be used for the \code{guideline} argument in the \code{\link[=mdro]{mdro()}} function:
|
||||
|
||||
\if{html}{\out{<div class="sourceCode">}}\preformatted{x <- mdro(example_isolates,
|
||||
guideline = custom)
|
||||
table(x)
|
||||
#> Negative Elderly Type A Elderly Type B
|
||||
#> 1070 198 732
|
||||
}
|
||||
}\if{html}{\out{</div>}}
|
||||
|
||||
Rules can also be combined with other custom rules by using \code{\link[=c]{c()}}:\preformatted{x <- mdro(example_isolates,
|
||||
Rules can also be combined with other custom rules by using \code{\link[=c]{c()}}:
|
||||
|
||||
\if{html}{\out{<div class="sourceCode">}}\preformatted{x <- mdro(example_isolates,
|
||||
guideline = c(custom,
|
||||
custom_mdro_guideline(ERY == "R" & age > 50 ~ "Elderly Type C")))
|
||||
table(x)
|
||||
#> Negative Elderly Type A Elderly Type B Elderly Type C
|
||||
#> 961 198 732 109
|
||||
}
|
||||
}\if{html}{\out{</div>}}
|
||||
|
||||
The rules set (the \code{custom} object in this case) could be exported to a shared file location using \code{\link[=saveRDS]{saveRDS()}} if you collaborate with multiple users. The custom rules set could then be imported using \code{\link[=readRDS]{readRDS()}}.
|
||||
}
|
||||
|
||||
@ -37,23 +37,29 @@ Reading an Excel file (\code{.xlsx}) with only one row has a size of 8-9 kB. The
|
||||
\section{How to Setup}{
|
||||
|
||||
|
||||
Imagine this data on a sheet of an Excel file. The first column contains the organisation specific codes, the second column contains valid taxonomic names:\preformatted{ | A | B |
|
||||
Imagine this data on a sheet of an Excel file. The first column contains the organisation specific codes, the second column contains valid taxonomic names:
|
||||
|
||||
\if{html}{\out{<div class="sourceCode">}}\preformatted{ | A | B |
|
||||
--|--------------------|-----------------------|
|
||||
1 | Organisation XYZ | mo |
|
||||
2 | lab_mo_ecoli | Escherichia coli |
|
||||
3 | lab_mo_kpneumoniae | Klebsiella pneumoniae |
|
||||
4 | | |
|
||||
}
|
||||
}\if{html}{\out{</div>}}
|
||||
|
||||
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")
|
||||
We save it as \code{"home/me/ourcodes.xlsx"}. Now we have to set it as a source:
|
||||
|
||||
\if{html}{\out{<div class="sourceCode">}}\preformatted{set_mo_source("home/me/ourcodes.xlsx")
|
||||
#> 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"
|
||||
}
|
||||
}\if{html}{\out{</div>}}
|
||||
|
||||
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")
|
||||
And now we can use it in our functions:
|
||||
|
||||
\if{html}{\out{<div class="sourceCode">}}\preformatted{as.mo("lab_mo_ecoli")
|
||||
#> Class <mo>
|
||||
#> [1] B_ESCHR_COLI
|
||||
|
||||
@ -66,18 +72,22 @@ as.mo(c("Escherichia coli", "E. coli", "lab_mo_ecoli"))
|
||||
#> Use mo_uncertainties() to review it.
|
||||
#> Class <mo>
|
||||
#> [1] B_ESCHR_COLI B_ESCHR_COLI B_ESCHR_COLI
|
||||
}
|
||||
}\if{html}{\out{</div>}}
|
||||
|
||||
If we edit the Excel file by, let's say, adding row 4 like this:\preformatted{ | A | B |
|
||||
If we edit the Excel file by, let's say, adding row 4 like this:
|
||||
|
||||
\if{html}{\out{<div class="sourceCode">}}\preformatted{ | A | B |
|
||||
--|--------------------|-----------------------|
|
||||
1 | Organisation XYZ | mo |
|
||||
2 | lab_mo_ecoli | Escherichia coli |
|
||||
3 | lab_mo_kpneumoniae | Klebsiella pneumoniae |
|
||||
4 | lab_Staph_aureus | Staphylococcus aureus |
|
||||
5 | | |
|
||||
}
|
||||
}\if{html}{\out{</div>}}
|
||||
|
||||
...any new usage of an MO function in this package will update your data file:\preformatted{as.mo("lab_mo_ecoli")
|
||||
...any new usage of an MO function in this package will update your data file:
|
||||
|
||||
\if{html}{\out{<div class="sourceCode">}}\preformatted{as.mo("lab_mo_ecoli")
|
||||
#> 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"
|
||||
@ -86,11 +96,13 @@ If we edit the Excel file by, let's say, adding row 4 like this:\preformatted{
|
||||
|
||||
mo_genus("lab_Staph_aureus")
|
||||
#> [1] "Staphylococcus"
|
||||
}
|
||||
}\if{html}{\out{</div>}}
|
||||
|
||||
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)
|
||||
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()}}:
|
||||
|
||||
\if{html}{\out{<div class="sourceCode">}}\preformatted{set_mo_source(NULL)
|
||||
#> Removed mo_source file '/Users/me/mo_source.rds'
|
||||
}
|
||||
}\if{html}{\out{</div>}}
|
||||
|
||||
If the original file (in the previous case an Excel file) is moved or deleted, the \code{mo_source.rds} file will be removed upon the next use of \code{\link[=as.mo]{as.mo()}} or any \code{\link[=mo_property]{mo_*}} function.
|
||||
}
|
||||
|
||||
@ -89,7 +89,9 @@ The function \code{\link[=proportion_df]{proportion_df()}} takes any variable fr
|
||||
}
|
||||
\section{Combination Therapy}{
|
||||
|
||||
When using more than one variable for \code{...} (= combination therapy), use \code{only_all_tested} to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Drug A and Drug B, about how \code{\link[=susceptibility]{susceptibility()}} works to calculate the \%SI:\preformatted{--------------------------------------------------------------------
|
||||
When using more than one variable for \code{...} (= combination therapy), use \code{only_all_tested} to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Drug A and Drug B, about how \code{\link[=susceptibility]{susceptibility()}} works to calculate the \%SI:
|
||||
|
||||
\if{html}{\out{<div class="sourceCode">}}\preformatted{--------------------------------------------------------------------
|
||||
only_all_tested = FALSE only_all_tested = TRUE
|
||||
----------------------- -----------------------
|
||||
Drug A Drug B include as include as include as include as
|
||||
@ -105,15 +107,19 @@ When using more than one variable for \code{...} (= combination therapy), use \c
|
||||
R <NA> - - - -
|
||||
<NA> <NA> - - - -
|
||||
--------------------------------------------------------------------
|
||||
}
|
||||
}\if{html}{\out{</div>}}
|
||||
|
||||
Please note that, in combination therapies, for \code{only_all_tested = TRUE} applies that:\preformatted{ count_S() + count_I() + count_R() = count_all()
|
||||
Please note that, in combination therapies, for \code{only_all_tested = TRUE} applies that:
|
||||
|
||||
\if{html}{\out{<div class="sourceCode">}}\preformatted{ count_S() + count_I() + count_R() = count_all()
|
||||
proportion_S() + proportion_I() + proportion_R() = 1
|
||||
}
|
||||
}\if{html}{\out{</div>}}
|
||||
|
||||
and that, in combination therapies, for \code{only_all_tested = FALSE} applies that:\preformatted{ count_S() + count_I() + count_R() >= count_all()
|
||||
and that, in combination therapies, for \code{only_all_tested = FALSE} applies that:
|
||||
|
||||
\if{html}{\out{<div class="sourceCode">}}\preformatted{ count_S() + count_I() + count_R() >= count_all()
|
||||
proportion_S() + proportion_I() + proportion_R() >= 1
|
||||
}
|
||||
}\if{html}{\out{</div>}}
|
||||
|
||||
Using \code{only_all_tested} has no impact when only using one antibiotic as input.
|
||||
}
|
||||
|
||||
@ -27,8 +27,12 @@ rsi_translation
|
||||
Data set containing reference data to interpret MIC and disk diffusion to R/SI values, according to international guidelines. Currently implemented guidelines are EUCAST (2011-2022) and CLSI (2011-2022). Use \code{\link[=as.rsi]{as.rsi()}} to transform MICs or disks measurements to R/SI values.
|
||||
}
|
||||
\details{
|
||||
Overview of the data set:\if{html}{\out{<div class="sourceCode r">}}\preformatted{head(rsi_translation)
|
||||
}\if{html}{\out{</div>}}\preformatted{## guideline method site mo rank_index ab ref_tbl disk_dose
|
||||
Overview of the data set:
|
||||
|
||||
\if{html}{\out{<div class="sourceCode r">}}\preformatted{head(rsi_translation)
|
||||
}\if{html}{\out{</div>}}
|
||||
|
||||
\if{html}{\out{<div class="sourceCode">}}\preformatted{## guideline method site mo rank_index ab ref_tbl disk_dose
|
||||
## 1 EUCAST 2022 MIC <NA> F_ASPRG_MGTS 2 AMB Aspergillus <NA>
|
||||
## 2 EUCAST 2022 MIC <NA> F_ASPRG_NIGR 2 AMB Aspergillus <NA>
|
||||
## 3 EUCAST 2022 MIC <NA> F_CANDD 3 AMB Candida <NA>
|
||||
@ -42,7 +46,7 @@ Overview of the data set:\if{html}{\out{<div class="sourceCode r">}}\preformatte
|
||||
## 4 1 1 FALSE
|
||||
## 5 1 1 FALSE
|
||||
## 6 1 1 FALSE
|
||||
}
|
||||
}\if{html}{\out{</div>}}
|
||||
|
||||
The repository of this \code{AMR} package contains a file comprising this exact data set: \url{https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt}. This file \strong{allows for machine reading EUCAST and CLSI guidelines}, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. The file is updated automatically and the \code{mo} and \code{ab} columns have been transformed to contain the full official names instead of codes.
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user