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(v1.6.0.9021) join functions update

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dr. M.S. (Matthijs) Berends
2021-05-12 18:15:03 +02:00
parent 3319fbae58
commit 29dbfa2f49
119 changed files with 973 additions and 1040 deletions
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6
man/WHONET.Rd
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@ -17,8 +17,8 @@ A \link{data.frame} with 500 observations and 53 variables:
\item \code{Sex}\cr Fictitious gender of patient
\item \code{Age}\cr Fictitious age of patient
\item \verb{Age category}\cr Age group, can also be looked up using \code{\link[=age_groups]{age_groups()}}
\item \verb{Date of admission}\cr Date of hospital admission
\item \verb{Specimen date}\cr Date when specimen was received at laboratory
\item \verb{Date of admission}\cr \link{Date} of hospital admission
\item \verb{Specimen date}\cr \link{Date} when specimen was received at laboratory
\item \verb{Specimen type}\cr Specimen type or group
\item \verb{Specimen type (Numeric)}\cr Translation of \code{"Specimen type"}
\item \code{Reason}\cr Reason of request with Differential Diagnosis
@ -31,7 +31,7 @@ A \link{data.frame} with 500 observations and 53 variables:
\item \verb{MRSA screening test}\cr Microorganism is possible MRSA?
\item \verb{Inducible clindamycin resistance}\cr Clindamycin can be induced?
\item \code{Comment}\cr Other comments
\item \verb{Date of data entry}\cr Date this data was entered in WHONET
\item \verb{Date of data entry}\cr \link{Date} this data was entered in WHONET
\item \code{AMP_ND10:CIP_EE}\cr 28 different antibiotics. You can lookup the abbreviations in the \link{antibiotics} data set, or use e.g. \code{\link[=ab_name]{ab_name("AMP")}} to get the official name immediately. Before analysis, you should transform this to a valid antibiotic class, using \code{\link[=as.rsi]{as.rsi()}}.
}
}

8
man/ab_from_text.Rd
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@ -19,13 +19,13 @@ ab_from_text(
\item{type}{type of property to search for, either \code{"drug"}, \code{"dose"} or \code{"administration"}, see \emph{Examples}}
\item{collapse}{character to pass on to \code{paste(, collapse = ...)} to only return one character per element of \code{text}, see \emph{Examples}}
\item{collapse}{a \link{character} to pass on to \code{paste(, collapse = ...)} to only return one \link{character} per element of \code{text}, see \emph{Examples}}
\item{translate_ab}{if \code{type = "drug"}: a column name of the \link{antibiotics} data set to translate the antibiotic abbreviations to, using \code{\link[=ab_property]{ab_property()}}. Defaults to \code{FALSE}. Using \code{TRUE} is equal to using "name".}
\item{thorough_search}{logical to indicate whether the input must be extensively searched for misspelling and other faulty input values. Setting this to \code{TRUE} will take considerably more time than when using \code{FALSE}. At default, it will turn \code{TRUE} when all input elements contain a maximum of three words.}
\item{thorough_search}{a \link{logical} to indicate whether the input must be extensively searched for misspelling and other faulty input values. Setting this to \code{TRUE} will take considerably more time than when using \code{FALSE}. At default, it will turn \code{TRUE} when all input elements contain a maximum of three words.}
\item{info}{logical to indicate whether a progress bar should be printed, defaults to \code{TRUE} only in interactive mode}
\item{info}{a \link{logical} to indicate whether a progress bar should be printed, defaults to \code{TRUE} only in interactive mode}
\item{...}{arguments passed on to \code{\link[=as.ab]{as.ab()}}}
}
@ -41,7 +41,7 @@ This function is also internally used by \code{\link[=as.ab]{as.ab()}}, although
At default, the function will search for antimicrobial drug names. All text elements will be searched for official names, ATC codes and brand names. As it uses \code{\link[=as.ab]{as.ab()}} internally, it will correct for misspelling.
With \code{type = "dose"} (or similar, like "dosing", "doses"), all text elements will be searched for numeric values that are higher than 100 and do not resemble years. The output will be numeric. It supports any unit (g, mg, IE, etc.) and multiple values in one clinical text, see \emph{Examples}.
With \code{type = "dose"} (or similar, like "dosing", "doses"), all text elements will be searched for \link{numeric} values that are higher than 100 and do not resemble years. The output will be \link{numeric}. It supports any unit (g, mg, IE, etc.) and multiple values in one clinical text, see \emph{Examples}.
With \code{type = "administration"} (or abbreviations, like "admin", "adm"), all text elements will be searched for a form of drug administration. It supports the following forms (including common abbreviations): buccal, implant, inhalation, instillation, intravenous, nasal, oral, parenteral, rectal, sublingual, transdermal and vaginal. Abbreviations for oral (such as 'po', 'per os') will become "oral", all values for intravenous (such as 'iv', 'intraven') will become "iv". It supports multiple values in one clinical text, see \emph{Examples}.
}

4
man/ab_property.Rd
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@ -48,13 +48,13 @@ ab_property(x, property = "name", language = get_locale(), ...)
\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{tolower}{logical to indicate whether the first character of every output should be transformed to a lower case character. This will lead to e.g. "polymyxin B" and not "polymyxin b".}
\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".}
\item{...}{other arguments passed on to \code{\link[=as.ab]{as.ab()}}}
\item{administration}{way of administration, either \code{"oral"} or \code{"iv"}}
\item{units}{a logical to indicate whether the units instead of the DDDs itself must be returned, see \emph{Examples}}
\item{units}{a \link{logical} to indicate whether the units instead of the DDDs itself must be returned, see \emph{Examples}}
\item{open}{browse the URL using \code{\link[utils:browseURL]{utils::browseURL()}}}

4
man/age.Rd
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@ -11,9 +11,9 @@ age(x, reference = Sys.Date(), exact = FALSE, na.rm = FALSE, ...)
\item{reference}{reference date(s) (defaults to today), will be coerced with \code{\link[=as.POSIXlt]{as.POSIXlt()}}}
\item{exact}{a logical to indicate whether age calculation should be exact, i.e. with decimals. It divides the number of days of \href{https://en.wikipedia.org/wiki/Year-to-date}{year-to-date} (YTD) of \code{x} by the number of days in the year of \code{reference} (either 365 or 366).}
\item{exact}{a \link{logical} to indicate whether age calculation should be exact, i.e. with decimals. It divides the number of days of \href{https://en.wikipedia.org/wiki/Year-to-date}{year-to-date} (YTD) of \code{x} by the number of days in the year of \code{reference} (either 365 or 366).}
\item{na.rm}{a logical to indicate whether missing values should be removed}
\item{na.rm}{a \link{logical} to indicate whether missing values should be removed}
\item{...}{arguments passed on to \code{\link[=as.POSIXlt]{as.POSIXlt()}}, such as \code{origin}}
}

2
man/age_groups.Rd
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@ -22,7 +22,7 @@ Split ages into age groups defined by the \code{split} argument. This allows for
\details{
To split ages, the input for the \code{split_at} argument can be:
\itemize{
\item A numeric vector. A value of e.g. \code{c(10, 20)} will split \code{x} on 0-9, 10-19 and 20+. A value of only \code{50} will split \code{x} on 0-49 and 50+.
\item A \link{numeric} vector. A value of e.g. \code{c(10, 20)} will split \code{x} on 0-9, 10-19 and 20+. A value of only \code{50} will split \code{x} on 0-49 and 50+.
The default is to split on young children (0-11), youth (12-24), young adults (25-54), middle-aged adults (55-74) and elderly (75+).
\item A character:
\itemize{

2
man/antibiotic_class_selectors.Rd
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@ -52,7 +52,7 @@ tetracyclines(only_rsi_columns = FALSE)
\arguments{
\item{ab_class}{an antimicrobial class, like \code{"carbapenems"}. The columns \code{group}, \code{atc_group1} and \code{atc_group2} of the \link{antibiotics} data set will be searched (case-insensitive) for this value.}
\item{only_rsi_columns}{a logical to indicate whether only columns of class \verb{<rsi>} must be selected (defaults to \code{FALSE}), see \code{\link[=as.rsi]{as.rsi()}}}
\item{only_rsi_columns}{a \link{logical} to indicate whether only columns of class \verb{<rsi>} must be selected (defaults to \code{FALSE}), see \code{\link[=as.rsi]{as.rsi()}}}
}
\description{
These functions help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. \strong{\Sexpr{ifelse(as.double(R.Version()$major) + (as.double(R.Version()$minor) / 10) < 3.2, paste0("NOTE: THESE FUNCTIONS DO NOT WORK ON YOUR CURRENT R VERSION. These functions require R version 3.2 or later - you have ", R.version.string, "."), "")}}

4
man/as.ab.Rd
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@ -11,9 +11,9 @@ as.ab(x, flag_multiple_results = TRUE, info = interactive(), ...)
is.ab(x)
}
\arguments{
\item{x}{character vector to determine to antibiotic ID}
\item{x}{a \link{character} vector to determine to antibiotic ID}
\item{flag_multiple_results}{logical to indicate whether a note should be printed to the console that probably more than one antibiotic code or name can be retrieved from a single input value.}
\item{flag_multiple_results}{a \link{logical} to indicate whether a note should be printed to the console that probably more than one antibiotic code or name can be retrieved from a single input value.}
\item{info}{a \link{logical} to indicate whether a progress bar should be printed, defaults to \code{TRUE} only in interactive mode}

2
man/as.disk.Rd
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@ -13,7 +13,7 @@ is.disk(x)
\arguments{
\item{x}{vector}
\item{na.rm}{a logical indicating whether missing values should be removed}
\item{na.rm}{a \link{logical} indicating whether missing values should be removed}
}
\value{
An \link{integer} with additional class \code{\link{disk}}

12
man/as.mic.Rd
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@ -11,12 +11,12 @@ as.mic(x, na.rm = FALSE)
is.mic(x)
}
\arguments{
\item{x}{character or numeric vector}
\item{x}{a \link{character} or \link{numeric} vector}
\item{na.rm}{a logical indicating whether missing values should be removed}
\item{na.rm}{a \link{logical} indicating whether missing values should be removed}
}
\value{
Ordered \link{factor} with additional class \code{\link{mic}}, that in mathematical operations acts as decimal numbers. Bare in mind that the outcome of any mathematical operation on MICs will return a numeric value.
Ordered \link{factor} with additional class \code{\link{mic}}, that in mathematical operations acts as decimal numbers. Bare in mind that the outcome of any mathematical operation on MICs will return a \link{numeric} value.
}
\description{
This ransforms vectors to a new class \code{\link{mic}}, which treats the input as decimal numbers, while maintaining operators (such as ">=") and only allowing valid MIC values known to the field of (medical) microbiology.
@ -24,7 +24,7 @@ This ransforms vectors to a new class \code{\link{mic}}, which treats the input
\details{
To interpret MIC values as RSI values, use \code{\link[=as.rsi]{as.rsi()}} on MIC values. It supports guidelines from EUCAST and CLSI.
This class for MIC values is a quite a special data type: formally it is an ordered factor with valid MIC values as 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)
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)
x
#> Class <mic>
#> [1] 16 1 8 8 64 >=128 0.0625 32 32 16
@ -39,7 +39,7 @@ median(x)
#> [1] 26
}
This makes it possible to maintain operators that often come with MIC values, such ">=" and "<=", even when filtering using numeric values in data analysis, e.g.:\preformatted{x[x > 4]
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]
#> Class <mic>
#> [1] 16 8 8 64 >=128 32 32 16
@ -76,7 +76,7 @@ is.mic(mic_data)
# this can also coerce combined MIC/RSI values:
as.mic("<=0.002; S") # will return <=0.002
# mathematical processing treats MICs as numeric values
# mathematical processing treats MICs as [numeric] values
fivenum(mic_data)
quantile(mic_data)
all(mic_data < 512)

6
man/as.mo.Rd
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@ -30,13 +30,13 @@ mo_uncertainties()
mo_renamed()
}
\arguments{
\item{x}{a character vector or a \link{data.frame} with one or two columns}
\item{x}{a \link{character} vector or a \link{data.frame} with one or two columns}
\item{Becker}{a logical to indicate whether staphylococci should be categorised into coagulase-negative staphylococci ("CoNS") and coagulase-positive staphylococci ("CoPS") instead of their own species, according to Karsten Becker \emph{et al.} (1,2,3).
\item{Becker}{a \link{logical} to indicate whether staphylococci should be categorised into coagulase-negative staphylococci ("CoNS") and coagulase-positive staphylococci ("CoPS") instead of their own species, according to Karsten Becker \emph{et al.} (1,2,3).
This excludes \emph{Staphylococcus aureus} at default, use \code{Becker = "all"} to also categorise \emph{S. aureus} as "CoPS".}
\item{Lancefield}{a logical to indicate whether beta-haemolytic \emph{Streptococci} should be categorised into Lancefield groups instead of their own species, according to Rebecca C. Lancefield (4). These \emph{Streptococci} will be categorised in their first group, e.g. \emph{Streptococcus dysgalactiae} will be group C, although officially it was also categorised into groups G and L.
\item{Lancefield}{a \link{logical} to indicate whether beta-haemolytic \emph{Streptococci} should be categorised into Lancefield groups instead of their own species, according to Rebecca C. Lancefield (4). These \emph{Streptococci} will be categorised in their first group, e.g. \emph{Streptococcus dysgalactiae} will be group C, although officially it was also categorised into groups G and L.
This excludes \emph{Enterococci} at default (who are in group D), use \code{Lancefield = "all"} to also categorise all \emph{Enterococci} as group D.}

28
man/as.rsi.Rd
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@ -51,33 +51,33 @@ is.rsi.eligible(x, threshold = 0.05)
)
}
\arguments{
\item{x}{vector of values (for class \code{\link{mic}}: an MIC value in mg/L, for class \code{\link{disk}}: a disk diffusion radius in millimetres)}
\item{x}{vector of values (for class \code{\link{mic}}: MIC values in mg/L, for class \code{\link{disk}}: a disk diffusion radius in millimetres)}
\item{...}{for using on a \link{data.frame}: names of columns to apply \code{\link[=as.rsi]{as.rsi()}} on (supports tidy selection like \code{AMX:VAN}). Otherwise: arguments passed on to methods.}
\item{threshold}{maximum fraction of invalid antimicrobial interpretations of \code{x}, see \emph{Examples}}
\item{mo}{any (vector of) text that can be coerced to a valid microorganism code with \code{\link[=as.mo]{as.mo()}}, can be left empty to determine it automatically}
\item{mo}{any (vector of) text that can be coerced to valid microorganism codes with \code{\link[=as.mo]{as.mo()}}, can be left empty to determine it automatically}
\item{ab}{any (vector of) text that can be coerced to a valid antimicrobial code with \code{\link[=as.ab]{as.ab()}}}
\item{guideline}{defaults to the latest included EUCAST guideline, see \emph{Details} for all options}
\item{uti}{(Urinary Tract Infection) A vector 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.rsi]{as.rsi()}} 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 'specimen' and rows containing 'urin' (such as 'urine', 'urina') in that column will be regarded isolates from a UTI. See \emph{Examples}.}
\item{uti}{(Urinary Tract Infection) A vector 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.rsi]{as.rsi()}} 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}.}
\item{conserve_capped_values}{a logical to indicate that MIC values starting with \code{">"} (but not \code{">="}) must always return "R" , and that MIC values starting with \code{"<"} (but not \code{"<="}) must always return "S"}
\item{conserve_capped_values}{a \link{logical} to indicate that MIC values starting with \code{">"} (but not \code{">="}) must always return "R" , and that MIC values starting with \code{"<"} (but not \code{"<="}) must always return "S"}
\item{add_intrinsic_resistance}{\emph{(only useful when using a EUCAST guideline)} a logical to indicate whether intrinsic antibiotic resistance must also be considered for applicable bug-drug combinations, meaning that e.g. ampicillin will always return "R" in \emph{Klebsiella} species. Determination is based on the \link{intrinsic_resistant} data set, that itself is based on \href{https://www.eucast.org/expert_rules_and_intrinsic_resistance/}{'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.2} (2020).}
\item{add_intrinsic_resistance}{\emph{(only useful when using a EUCAST guideline)} a \link{logical} to indicate whether intrinsic antibiotic resistance must also be considered for applicable bug-drug combinations, meaning that e.g. ampicillin will always return "R" in \emph{Klebsiella} species. Determination is based on the \link{intrinsic_resistant} data set, that itself is based on \href{https://www.eucast.org/expert_rules_and_intrinsic_resistance/}{'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.2} (2020).}
\item{reference_data}{a \link{data.frame} to be used for interpretation, which defaults to the \link{rsi_translation} 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{rsi_translation} 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.}
\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()}}.}
}
\value{
Ordered factor with new class \verb{<rsi>}
Ordered \link{factor} with new class \verb{<rsi>}
}
\description{
Interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class \code{\link{rsi}}, which is an ordered factor with levels \verb{S < I < R}. Values that cannot be interpreted will be returned as \code{NA} with a warning.
Interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class \code{\link{rsi}}, which is an ordered \link{factor} with levels \verb{S < I < R}.
}
\details{
\subsection{How it Works}{
@ -87,15 +87,15 @@ The \code{\link[=as.rsi]{as.rsi()}} function works in four ways:
\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.
\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.
\itemize{
\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
your_data \%>\% mutate(across((is.mic), as.rsi)) # since dplyr 1.0.0
\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
your_data \%>\% mutate(across(where(is.mic), as.rsi)) # since dplyr 1.0.0
}
\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".
}
\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.
\itemize{
\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
your_data \%>\% mutate(across((is.disk), as.rsi)) # since dplyr 1.0.0
\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
your_data \%>\% mutate(across(where(is.disk), as.rsi)) # since dplyr 1.0.0
}
}
\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(data)}.
@ -104,7 +104,7 @@ your_data \%>\% mutate(across((is.disk), as.rsi)) # since dplyr 1.0.0
\subsection{Supported Guidelines}{
For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the \code{guideline} argument are: "EUCAST 2021", "EUCAST 2020", "EUCAST 2019", "EUCAST 2018", "EUCAST 2017", "EUCAST 2016", "EUCAST 2015", "EUCAST 2014", "EUCAST 2013", "EUCAST 2012", "EUCAST 2011", "CLSI 2019", "CLSI 2018", "CLSI 2017", "CLSI 2016", "CLSI 2015", "CLSI 2014", "CLSI 2013", "CLSI 2012", "CLSI 2011" and "CLSI 2010".
For interpreting MIC values as well as disk diffusion diameters, currently supported guidelines to be used as input for the \code{guideline} argument are: "EUCAST 2021", "EUCAST 2020", "EUCAST 2019", "EUCAST 2018", "EUCAST 2017", "EUCAST 2016", "EUCAST 2015", "EUCAST 2014", "EUCAST 2013", "EUCAST 2012", "EUCAST 2011", "CLSI 2019", "CLSI 2018", "CLSI 2017", "CLSI 2016", "CLSI 2015", "CLSI 2014", "CLSI 2013", "CLSI 2012", "CLSI 2011" and "CLSI 2010".
Simply using \code{"CLSI"} or \code{"EUCAST"} as input will automatically select the latest version of that guideline. You can set your own data set using the \code{reference_data} argument. The \code{guideline} argument will then be ignored.
}
@ -121,9 +121,9 @@ The repository of this package \href{https://github.com/msberends/AMR/blob/maste
\subsection{Other}{
The function \code{\link[=is.rsi]{is.rsi()}} detects if the input contains class \verb{<rsi>}. If the input is a data.frame, it iterates over all columns and returns a logical vector.
The function \code{\link[=is.rsi]{is.rsi()}} detects if the input contains class \verb{<rsi>}. If the input is a \link{data.frame}, it iterates over all columns and returns a \link{logical} vector.
The function \code{\link[=is.rsi.eligible]{is.rsi.eligible()}} returns \code{TRUE} when a columns contains at most 5\% invalid antimicrobial interpretations (not S and/or I and/or R), and \code{FALSE} otherwise. The threshold of 5\% can be set with the \code{threshold} argument. If the input is a data.frame, it iterates over all columns and returns a logical vector.
The function \code{\link[=is.rsi.eligible]{is.rsi.eligible()}} returns \code{TRUE} when a columns contains at most 5\% invalid antimicrobial interpretations (not S and/or I and/or R), and \code{FALSE} otherwise. The threshold of 5\% can be set with the \code{threshold} argument. If the input is a \link{data.frame}, it iterates over all columns and returns a \link{logical} vector.
}
}
\section{Interpretation of R and S/I}{

2
man/atc_online.Rd
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@ -22,7 +22,7 @@ atc_online_groups(atc_code, ...)
atc_online_ddd(atc_code, ...)
}
\arguments{
\item{atc_code}{a character or character vector with ATC code(s) of antibiotic(s)}
\item{atc_code}{a \link{character} or \link{character} vector with ATC code(s) of antibiotic(s)}
\item{property}{property of an ATC code. Valid values are \code{"ATC"}, \code{"Name"}, \code{"DDD"}, \code{"U"} (\code{"unit"}), \code{"Adm.R"}, \code{"Note"} and \code{groups}. For this last option, all hierarchical groups of an ATC code will be returned, see \emph{Examples}.}

12
man/bug_drug_combinations.Rd
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@ -29,23 +29,23 @@ bug_drug_combinations(x, col_mo = NULL, FUN = mo_shortname, ...)
\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()}}.}
\item{FUN}{function to call on the \code{mo} column to transform the microorganism IDs, defaults to \code{\link[=mo_shortname]{mo_shortname()}}}
\item{FUN}{the function to call on the \code{mo} column to transform the microorganism IDs, defaults to \code{\link[=mo_shortname]{mo_shortname()}}}
\item{...}{arguments passed on to \code{FUN}}
\item{translate_ab}{character of length 1 containing column names of the \link{antibiotics} data set}
\item{translate_ab}{a \link{character} of length 1 containing column names of the \link{antibiotics} data set}
\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{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{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 argument \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_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). This used to be the argument \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}{logical to indicate whether values R and I should be summed}
\item{combine_IR}{a \link{logical} to indicate whether values R and I should be summed}
\item{add_ab_group}{logical to indicate where the group of the antimicrobials must be included as a first column}
\item{add_ab_group}{a \link{logical} to indicate where the group of the antimicrobials must be included as a first column}
\item{remove_intrinsic_resistant}{logical to indicate that rows and columns with 100\% resistance for all tested antimicrobials must be removed from the table}
\item{remove_intrinsic_resistant}{\link{logical} to indicate that rows and columns with 100\% resistance for all tested antimicrobials must be removed from the table}
\item{decimal.mark}{the character to be used to indicate the numeric
decimal point.}

6
man/count.Rd
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@ -43,7 +43,7 @@ count_df(
\arguments{
\item{...}{one or more vectors (or columns) with antibiotic interpretations. They will be transformed internally with \code{\link[=as.rsi]{as.rsi()}} if needed.}
\item{only_all_tested}{(for combination therapies, i.e. using more than one variable for \code{...}): a logical to indicate that isolates must be tested for all antibiotics, see section \emph{Combination Therapy} below}
\item{only_all_tested}{(for combination therapies, i.e. using more than one variable for \code{...}): a \link{logical} to indicate that isolates must be tested for all antibiotics, see section \emph{Combination Therapy} below}
\item{data}{a \link{data.frame} containing columns with class \code{\link{rsi}} (see \code{\link[=as.rsi]{as.rsi()}})}
@ -51,9 +51,9 @@ count_df(
\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 argument \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_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). This used to be the argument \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 argument \code{combine_SI}.}
\item{combine_IR}{a \link{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 argument \code{combine_SI}.}
}
\value{
An \link{integer}

8
man/eucast_rules.Rd
View File

@ -38,9 +38,9 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 11)
\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()}}.}
\item{info}{a logical to indicate whether progress should be printed to the console, defaults to only print while in interactive sessions}
\item{info}{a \link{logical} to indicate whether progress should be printed to the console, defaults to only print while in interactive sessions}
\item{rules}{a 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, e.g. using \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{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, e.g. using \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.}
@ -48,9 +48,9 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 11)
\item{version_expertrules}{the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be either "3.2" or "3.1".}
\item{ampc_cephalosporin_resistance}{a character value that should be applied to cefotaxime, ceftriaxone and ceftazidime for AmpC de-repressed cephalosporin-resistant mutants, defaults to \code{NA}. Currently only works when \code{version_expertrules} is \code{3.2}; '\emph{EUCAST Expert Rules v3.2 on Enterobacterales}' states that results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these three agents. A value of \code{NA} (the default) for this argument will remove results for these three agents, while e.g. a value of \code{"R"} will make the results for these agents resistant. Use \code{NULL} or \code{FALSE} to not alter results for these three agents of AmpC de-repressed cephalosporin-resistant mutants. Using \code{TRUE} is equal to using \code{"R"}. \cr For \emph{EUCAST Expert Rules} v3.2, this rule applies to: \emph{Citrobacter braakii}, \emph{Citrobacter freundii}, \emph{Citrobacter gillenii}, \emph{Citrobacter murliniae}, \emph{Citrobacter rodenticum}, \emph{Citrobacter sedlakii}, \emph{Citrobacter werkmanii}, \emph{Citrobacter youngae}, \emph{Enterobacter}, \emph{Hafnia alvei}, \emph{Klebsiella aerogenes}, \emph{Morganella morganii}, \emph{Providencia} and \emph{Serratia}.}
\item{ampc_cephalosporin_resistance}{a \link{character} value that should be applied to cefotaxime, ceftriaxone and ceftazidime for AmpC de-repressed cephalosporin-resistant mutants, defaults to \code{NA}. Currently only works when \code{version_expertrules} is \code{3.2}; '\emph{EUCAST Expert Rules v3.2 on Enterobacterales}' states that results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these three agents. A value of \code{NA} (the default) for this argument will remove results for these three agents, while e.g. a value of \code{"R"} will make the results for these agents resistant. Use \code{NULL} or \code{FALSE} to not alter results for these three agents of AmpC de-repressed cephalosporin-resistant mutants. Using \code{TRUE} is equal to using \code{"R"}. \cr For \emph{EUCAST Expert Rules} v3.2, this rule applies to: \emph{Citrobacter braakii}, \emph{Citrobacter freundii}, \emph{Citrobacter gillenii}, \emph{Citrobacter murliniae}, \emph{Citrobacter rodenticum}, \emph{Citrobacter sedlakii}, \emph{Citrobacter werkmanii}, \emph{Citrobacter youngae}, \emph{Enterobacter}, \emph{Hafnia alvei}, \emph{Klebsiella aerogenes}, \emph{Morganella morganii}, \emph{Providencia} and \emph{Serratia}.}
\item{only_rsi_columns}{a logical to indicate whether only antibiotic columns must be detected that were transformed to class \verb{<rsi>} (see \code{\link[=as.rsi]{as.rsi()}}) on beforehand (defaults to \code{FALSE})}
\item{only_rsi_columns}{a \link{logical} to indicate whether only antibiotic columns must be detected that were transformed to class \verb{<rsi>} (see \code{\link[=as.rsi]{as.rsi()}}) on beforehand (defaults to \code{FALSE})}
\item{custom_rules}{custom rules to apply, created with \code{\link[=custom_eucast_rules]{custom_eucast_rules()}}}

6
man/example_isolates.Rd
View File

@ -9,9 +9,9 @@ A \link{data.frame} with 2,000 observations and 49 variables:
\itemize{
\item \code{date}\cr date of receipt at the laboratory
\item \code{hospital_id}\cr ID of the hospital, from A to D
\item \code{ward_icu}\cr logical to determine if ward is an intensive care unit
\item \code{ward_clinical}\cr logical to determine if ward is a regular clinical ward
\item \code{ward_outpatient}\cr logical to determine if ward is an outpatient clinic
\item \code{ward_icu}\cr \link{logical} to determine if ward is an intensive care unit
\item \code{ward_clinical}\cr \link{logical} to determine if ward is a regular clinical ward
\item \code{ward_outpatient}\cr \link{logical} to determine if ward is an outpatient clinic
\item \code{age}\cr age of the patient
\item \code{gender}\cr gender of the patient
\item \code{patient_id}\cr ID of the patient

2
man/filter_ab_class.Rd
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@ -148,7 +148,7 @@ filter_tetracyclines(
\item{scope}{the scope to check which variables to check, can be \code{"any"} (default) or \code{"all"}}
\item{only_rsi_columns}{a logical to indicate whether only columns must be included that were transformed to class \verb{<rsi>} (see \code{\link[=as.rsi]{as.rsi()}}) on beforehand (defaults to \code{FALSE})}
\item{only_rsi_columns}{a \link{logical} to indicate whether only columns must be included that were transformed to class \verb{<rsi>} (see \code{\link[=as.rsi]{as.rsi()}}) on beforehand (defaults to \code{FALSE})}
\item{...}{arguments passed on to \code{\link[=filter_ab_class]{filter_ab_class()}}}
}

10
man/first_isolate.Rd
View File

@ -64,9 +64,9 @@ filter_first_isolate(
\item{episode_days}{episode in days after which a genus/species combination will be determined as 'first isolate' again. The default of 365 days is based on the guideline by CLSI, see \emph{Source}.}
\item{testcodes_exclude}{character vector with test codes that should be excluded (case-insensitive)}
\item{testcodes_exclude}{a \link{character} vector with test codes that should be excluded (case-insensitive)}
\item{icu_exclude}{logical to indicate whether ICU isolates should be excluded (rows with value \code{TRUE} in the column set with \code{col_icu})}
\item{icu_exclude}{a \link{logical} to indicate whether ICU isolates should be excluded (rows with value \code{TRUE} in the column set with \code{col_icu})}
\item{specimen_group}{value in the column set with \code{col_specimen} to filter on}
@ -74,15 +74,15 @@ filter_first_isolate(
\item{method}{the method to apply, either \code{"phenotype-based"}, \code{"episode-based"}, \code{"patient-based"} or \code{"isolate-based"} (can be abbreviated), see \emph{Details}. The default is \code{"phenotype-based"} if antimicrobial test results are present in the data, and \code{"episode-based"} otherwise.}
\item{ignore_I}{logical to indicate whether antibiotic interpretations with \code{"I"} will be ignored when \code{type = "keyantimicrobials"}, see \emph{Details}}
\item{ignore_I}{\link{logical} to indicate whether antibiotic interpretations with \code{"I"} will be ignored when \code{type = "keyantimicrobials"}, see \emph{Details}}
\item{points_threshold}{minimum number of points to require before differences in the antibiogram will lead to inclusion of an isolate when \code{type = "points"}, see \emph{Details}}
\item{info}{a \link{logical} to indicate info should be printed, defaults to \code{TRUE} only in interactive mode}
\item{include_unknown}{logical to indicate whether 'unknown' microorganisms should be included too, i.e. microbial code \code{"UNKNOWN"}, which defaults to \code{FALSE}. For WHONET users, this means that all records with organism code \code{"con"} (\emph{contamination}) will be excluded at default. Isolates with a microbial ID of \code{NA} will always be excluded as first isolate.}
\item{include_unknown}{a \link{logical} to indicate whether 'unknown' microorganisms should be included too, i.e. microbial code \code{"UNKNOWN"}, which defaults to \code{FALSE}. For WHONET users, this means that all records with organism code \code{"con"} (\emph{contamination}) will be excluded at default. Isolates with a microbial ID of \code{NA} will always be excluded as first isolate.}
\item{include_untested_rsi}{logical to indicate whether also rows without antibiotic results are still eligible for becoming a first isolate. Use \code{include_untested_rsi = FALSE} to always return \code{FALSE} for such rows. This checks the data set for columns of class \verb{<rsi>} and consequently requires transforming columns with antibiotic results using \code{\link[=as.rsi]{as.rsi()}} first.}
\item{include_untested_rsi}{a \link{logical} to indicate whether also rows without antibiotic results are still eligible for becoming a first isolate. Use \code{include_untested_rsi = FALSE} to always return \code{FALSE} for such rows. This checks the data set for columns of class \verb{<rsi>} and consequently requires transforming columns with antibiotic results using \code{\link[=as.rsi]{as.rsi()}} first.}
\item{...}{arguments passed on to \code{\link[=first_isolate]{first_isolate()}} when using \code{\link[=filter_first_isolate]{filter_first_isolate()}}, otherwise arguments passed on to \code{\link[=key_antimicrobials]{key_antimicrobials()}} (such as \code{universal}, \code{gram_negative}, \code{gram_positive})}
}

4
man/g.test.Rd
View File

@ -52,9 +52,9 @@ A list with class \code{"htest"} containing the following
\code{\link[=g.test]{g.test()}} performs chi-squared contingency table tests and goodness-of-fit tests, just like \code{\link[=chisq.test]{chisq.test()}} but is more reliable (1). A \emph{G}-test can be used to see whether the number of observations in each category fits a theoretical expectation (called a \strong{\emph{G}-test of goodness-of-fit}), or to see whether the proportions of one variable are different for different values of the other variable (called a \strong{\emph{G}-test of independence}).
}
\details{
If \code{x} is a matrix with one row or column, or if \code{x} is a vector and \code{y} is not given, then a \emph{goodness-of-fit test} is performed (\code{x} is treated as a one-dimensional contingency table). The entries of \code{x} must be non-negative integers. In this case, the hypothesis tested is whether the population probabilities equal those in \code{p}, or are all equal if \code{p} is not given.
If \code{x} is a \link{matrix} with one row or column, or if \code{x} is a vector and \code{y} is not given, then a \emph{goodness-of-fit test} is performed (\code{x} is treated as a one-dimensional contingency table). The entries of \code{x} must be non-negative integers. In this case, the hypothesis tested is whether the population probabilities equal those in \code{p}, or are all equal if \code{p} is not given.
If \code{x} is a matrix with at least two rows and columns, it is taken as a two-dimensional contingency table: the entries of \code{x} must be non-negative integers. Otherwise, \code{x} and \code{y} must be vectors or factors of the same length; cases with missing values are removed, the objects are coerced to factors, and the contingency table is computed from these. Then Pearson's chi-squared test is performed of the null hypothesis that the joint distribution of the cell counts in a 2-dimensional contingency table is the product of the row and column marginals.
If \code{x} is a \link{matrix} with at least two rows and columns, it is taken as a two-dimensional contingency table: the entries of \code{x} must be non-negative integers. Otherwise, \code{x} and \code{y} must be vectors or factors of the same length; cases with missing values are removed, the objects are coerced to factors, and the contingency table is computed from these. Then Pearson's chi-squared test is performed of the null hypothesis that the joint distribution of the cell counts in a 2-dimensional contingency table is the product of the row and column marginals.
The p-value is computed from the asymptotic chi-squared distribution of the test statistic.

6
man/ggplot_pca.Rd
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@ -74,7 +74,7 @@ ggplot_pca(
\item{groups}{an optional vector of groups for the labels, with the same length as \code{labels}. If set, the points and labels will be coloured according to these groups. When using the \code{\link[=pca]{pca()}} function as input for \code{x}, this will be determined automatically based on the attribute \code{non_numeric_cols}, see \code{\link[=pca]{pca()}}.}
\item{ellipse}{a logical to indicate whether a normal data ellipse should be drawn for each group (set with \code{groups})}
\item{ellipse}{a \link{logical} to indicate whether a normal data ellipse should be drawn for each group (set with \code{groups})}
\item{ellipse_prob}{statistical size of the ellipse in normal probability}
@ -86,7 +86,7 @@ ggplot_pca(
\item{points_alpha}{the alpha (transparency) of the points}
\item{arrows}{a logical to indicate whether arrows should be drawn}
\item{arrows}{a \link{logical} to indicate whether arrows should be drawn}
\item{arrows_colour}{the colour of the arrow and their text}
@ -94,7 +94,7 @@ ggplot_pca(
\item{arrows_textsize}{the size of the text at the end of the arrows}
\item{arrows_textangled}{a logical whether the text at the end of the arrows should be angled}
\item{arrows_textangled}{a \link{logical} whether the text at the end of the arrows should be angled}
\item{arrows_alpha}{the alpha (transparency) of the arrows and their text}

8
man/ggplot_rsi.Rd
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@ -80,15 +80,15 @@ labels_rsi_count(
\item{facet}{variable to split plots by, either \code{"interpretation"} (default) or \code{"antibiotic"} or a grouping variable}
\item{breaks}{numeric vector of positions}
\item{breaks}{a \link{numeric} vector of positions}
\item{limits}{numeric vector of length two providing limits of the scale, use \code{NA} to refer to the existing minimum or maximum}
\item{limits}{a \link{numeric} vector of length two providing limits of the scale, use \code{NA} to refer to the existing minimum or maximum}
\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{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 argument \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_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). This used to be the argument \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 argument \code{combine_SI}.}
\item{combine_IR}{a \link{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 argument \code{combine_SI}.}
\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}.}

4
man/guess_ab_col.Rd
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@ -16,9 +16,9 @@ guess_ab_col(
\item{search_string}{a text to search \code{x} for, will be checked with \code{\link[=as.ab]{as.ab()}} if this value is not a column in \code{x}}
\item{verbose}{a logical to indicate whether additional info should be printed}
\item{verbose}{a \link{logical} to indicate whether additional info should be printed}
\item{only_rsi_columns}{a logical to indicate whether only antibiotic columns must be detected that were transformed to class \verb{<rsi>} (see \code{\link[=as.rsi]{as.rsi()}}) on beforehand (defaults to \code{FALSE})}
\item{only_rsi_columns}{a \link{logical} to indicate whether only antibiotic columns must be detected that were transformed to class \verb{<rsi>} (see \code{\link[=as.rsi]{as.rsi()}}) on beforehand (defaults to \code{FALSE})}
}
\value{
A column name of \code{x}, or \code{NULL} when no result is found.

11
man/italicise_taxonomy.Rd
View File

@ -10,7 +10,7 @@ italicise_taxonomy(string, type = c("markdown", "ansi"))
italicize_taxonomy(string, type = c("markdown", "ansi"))
}
\arguments{
\item{string}{a character (vector)}
\item{string}{a \link{character} (vector)}
\item{type}{type of conversion of the taxonomic names, either "markdown" or "ansi", see \emph{Details}}
}
@ -40,4 +40,13 @@ italicise_taxonomy("An overview of Staphylococcus aureus isolates")
italicise_taxonomy("An overview of S. aureus isolates")
cat(italicise_taxonomy("An overview of S. aureus isolates", type = "ansi"))
# since ggplot2 supports no markdown (yet), use
# italicise_taxonomy() and the `ggtext` pkg for titles:
if (require("ggplot2") && require("ggtext")) {
ggplot(example_isolates$AMC,
title = italicise_taxonomy("Amoxi/clav in E. coli")) +
theme(plot.title = ggtext::element_markdown())
}
}

13
man/join.Rd
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@ -24,21 +24,24 @@ semi_join_microorganisms(x, by = NULL, ...)
anti_join_microorganisms(x, by = NULL, ...)
}
\arguments{
\item{x}{existing table to join, or character vector}
\item{x}{existing data set to join, or \link{character} vector. In case of a \link{character} vector, the resulting \link{data.frame} will contain a column 'x' with these values.}
\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")})}
\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.}
\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 \link{character} vector of length 2.}
\item{...}{ignored, only in place to allow future extensions}
}
\value{
a \link{data.frame}
}
\description{
Join the data set \link{microorganisms} easily to an existing table or character vector.
Join the data set \link{microorganisms} easily to an existing data set or to a \link{character} vector.
}
\details{
\strong{Note:} As opposed to the \code{join()} functions of \code{dplyr}, \link{character} vectors are supported and at default existing columns will get a suffix \code{"2"} and the newly joined columns will not get a suffix.
If the \code{dplyr} package is installed, their join functions will be used. Otherwise, the much slower \code{\link[=merge]{merge()}} function from base R will be used.
If the \code{dplyr} package is installed, their join functions will be used. Otherwise, the much slower \code{\link[=merge]{merge()}} and \code{\link[=interaction]{interaction()}} functions from base R will be used.
}
\section{Stable Lifecycle}{
@ -55,7 +58,7 @@ On our website \url{https://msberends.github.io/AMR/} you can find \href{https:/
\examples{
left_join_microorganisms(as.mo("K. pneumoniae"))
left_join_microorganisms("B_KLBSL_PNE")
left_join_microorganisms("B_KLBSL_PNMN")
\donttest{
if (require("dplyr")) {

10
man/key_antimicrobials.Rd
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@ -45,15 +45,15 @@ antimicrobials_equal(
\item{antifungal}{names of antifungal agents for \strong{fungi}, case-insensitive. Set to \code{NULL} to ignore. See \emph{Details} for the default agents.}
\item{only_rsi_columns}{a logical to indicate whether only columns must be included that were transformed to class \verb{<rsi>} (see \code{\link[=as.rsi]{as.rsi()}}) on beforehand (defaults to \code{FALSE})}
\item{only_rsi_columns}{a \link{logical} to indicate whether only columns must be included that were transformed to class \verb{<rsi>} (see \code{\link[=as.rsi]{as.rsi()}}) on beforehand (defaults to \code{FALSE})}
\item{...}{ignored, only in place to allow future extensions}
\item{y, z}{character vectors to compare}
\item{y, z}{\link{character} vectors to compare}
\item{type}{type to determine weighed isolates; can be \code{"keyantimicrobials"} or \code{"points"}, see \emph{Details}}
\item{ignore_I}{logical to indicate whether antibiotic interpretations with \code{"I"} will be ignored when \code{type = "keyantimicrobials"}, see \emph{Details}}
\item{ignore_I}{\link{logical} to indicate whether antibiotic interpretations with \code{"I"} will be ignored when \code{type = "keyantimicrobials"}, see \emph{Details}}
\item{points_threshold}{minimum number of points to require before differences in the antibiogram will lead to inclusion of an isolate when \code{type = "points"}, see \emph{Details}}
}
@ -63,7 +63,7 @@ These functions can be used to determine first weighted isolates by considering
\details{
The \code{\link[=key_antimicrobials]{key_antimicrobials()}} and \code{\link[=all_antimicrobials]{all_antimicrobials()}} functions are context-aware. This means that then the \code{x} argument can be left blank, see \emph{Examples}.
The function \code{\link[=key_antimicrobials]{key_antimicrobials()}} returns a character vector with 12 antimicrobial results for every isolate. The function \code{\link[=all_antimicrobials]{all_antimicrobials()}} returns a character vector with all antimicrobial results for every isolate. These vectors can then be compared using \code{\link[=antimicrobials_equal]{antimicrobials_equal()}}, to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (\code{"."}) by \code{\link[=key_antimicrobials]{key_antimicrobials()}} and ignored by \code{\link[=antimicrobials_equal]{antimicrobials_equal()}}.
The function \code{\link[=key_antimicrobials]{key_antimicrobials()}} returns a \link{character} vector with 12 antimicrobial results for every isolate. The function \code{\link[=all_antimicrobials]{all_antimicrobials()}} returns a \link{character} vector with all antimicrobial results for every isolate. These vectors can then be compared using \code{\link[=antimicrobials_equal]{antimicrobials_equal()}}, to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (\code{"."}) by \code{\link[=key_antimicrobials]{key_antimicrobials()}} and ignored by \code{\link[=antimicrobials_equal]{antimicrobials_equal()}}.
Please see the \code{\link[=first_isolate]{first_isolate()}} function how these important functions enable the 'phenotype-based' method for determination of first isolates.
@ -133,7 +133,7 @@ antimicrobials_equal(strainA, strainB, type = "keyantimicrobials")
# TRUE, because I is ignored (as well as missing values)
antimicrobials_equal(strainA, strainB, type = "keyantimicrobials", ignore_I = FALSE)
# FALSE, because I is not ignored and so the 4th character differs
# FALSE, because I is not ignored and so the 4th [character] differs
\donttest{
if (require("dplyr")) {

4
man/kurtosis.Rd
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@ -18,9 +18,9 @@ kurtosis(x, na.rm = FALSE, excess = FALSE)
\arguments{
\item{x}{a vector of values, a \link{matrix} or a \link{data.frame}}
\item{na.rm}{a logical to indicate whether \code{NA} values should be stripped before the computation proceeds}
\item{na.rm}{a \link{logical} to indicate whether \code{NA} values should be stripped before the computation proceeds}
\item{excess}{a logical to indicate whether the \emph{excess kurtosis} should be returned, defined as the kurtosis minus 3.}
\item{excess}{a \link{logical} to indicate whether the \emph{excess kurtosis} should be returned, defined as the kurtosis minus 3.}
}
\description{
Kurtosis is a measure of the "tailedness" of the probability distribution of a real-valued random variable. A normal distribution has a kurtosis of 3 and a excess kurtosis of 0.

4
man/like.Rd
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@ -22,9 +22,9 @@ x \%like_case\% pattern
x \%unlike_case\% pattern
}
\arguments{
\item{x}{a character vector where matches are sought, or an object which can be coerced by \code{\link[=as.character]{as.character()}} to a character vector.}
\item{x}{a \link{character} vector where matches are sought, or an object which can be coerced by \code{\link[=as.character]{as.character()}} to a \link{character} vector.}
\item{pattern}{a character vector containing regular expressions (or a \link{character} string for \code{fixed = TRUE}) to be matched in the given character vector. Coerced by \code{\link[=as.character]{as.character()}} to a character string if possible.}
\item{pattern}{a \link{character} vector containing regular expressions (or a \link{character} string for \code{fixed = TRUE}) to be matched in the given \link{character} vector. Coerced by \code{\link[=as.character]{as.character()}} to a \link{character} string if possible.}
\item{ignore.case}{if \code{FALSE}, the pattern matching is \emph{case sensitive} and if \code{TRUE}, case is ignored during matching.}
}

8
man/mdro.Rd
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@ -16,7 +16,7 @@
\alias{eucast_exceptional_phenotypes}
\title{Determine Multidrug-Resistant Organisms (MDRO)}
\source{
See the supported guidelines above for the list of publications used for this function.
See the supported guidelines above for the \link{list} of publications used for this function.
}
\usage{
mdro(
@ -50,15 +50,15 @@ eucast_exceptional_phenotypes(x = NULL, only_rsi_columns = FALSE, ...)
\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()}}.}
\item{info}{a logical to indicate whether progress should be printed to the console, defaults to only print while in interactive sessions}
\item{info}{a \link{logical} to indicate whether progress should be printed to the console, defaults to only print while in interactive sessions}
\item{pct_required_classes}{minimal required percentage of antimicrobial classes that must be available per isolate, rounded down. For example, with the default guideline, 17 antimicrobial classes must be available for \emph{S. aureus}. Setting this \code{pct_required_classes} argument to \code{0.5} (default) means that for every \emph{S. aureus} isolate at least 8 different classes must be available. Any lower number of available classes will return \code{NA} for that isolate.}
\item{combine_SI}{a \link{logical} to indicate whether all values of S and I must be merged into one, so resistance is only considered when isolates are R, not I. As this is the default behaviour of the \code{\link[=mdro]{mdro()}} function, it follows the redefinition by EUCAST about the interpretation of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. When using \code{combine_SI = FALSE}, resistance is considered when isolates are R or I.}
\item{verbose}{a logical to turn Verbose mode on and off (default is off). In Verbose mode, the function does not return the MDRO results, but instead returns a data set in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.}
\item{verbose}{a \link{logical} to turn Verbose mode on and off (default is off). In Verbose mode, the function does not return the MDRO results, but instead returns a data set in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.}
\item{only_rsi_columns}{a logical to indicate whether only antibiotic columns must be detected that were transformed to class \verb{<rsi>} (see \code{\link[=as.rsi]{as.rsi()}}) on beforehand (defaults to \code{FALSE})}
\item{only_rsi_columns}{a \link{logical} to indicate whether only antibiotic columns must be detected that were transformed to class \verb{<rsi>} (see \code{\link[=as.rsi]{as.rsi()}}) on beforehand (defaults to \code{FALSE})}
\item{...}{in case of \code{\link[=custom_mdro_guideline]{custom_mdro_guideline()}}: a set of rules, see section \emph{Using Custom Guidelines} below. Otherwise: column name of an antibiotic, see section \emph{Antibiotics} below.}

2
man/mo_property.Rd
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@ -88,7 +88,7 @@ mo_url(x, open = FALSE, language = get_locale(), ...)
mo_property(x, property = "fullname", language = get_locale(), ...)
}
\arguments{
\item{x}{any character (vector) that can be coerced to a valid microorganism code with \code{\link[=as.mo]{as.mo()}}. Can be left blank for auto-guessing the column containing microorganism codes if used in a data set, see \emph{Examples}.}
\item{x}{any \link{character} (vector) that can be coerced to a valid microorganism code with \code{\link[=as.mo]{as.mo()}}. Can be left blank for auto-guessing the column containing microorganism codes if used in a data set, see \emph{Examples}.}
\item{language}{language of the returned text, defaults to system language (see \code{\link[=get_locale]{get_locale()}}) and can be overwritten by setting the option \code{AMR_locale}, e.g. \code{options(AMR_locale = "de")}, see \link{translate}. Also used to translate text like "no growth". Use \code{language = NULL} or \code{language = ""} to prevent translation.}

4
man/pca.Rd
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@ -15,7 +15,7 @@ pca(
)
}
\arguments{
\item{x}{a \link{data.frame} containing numeric columns}
\item{x}{a \link{data.frame} containing \link{numeric} columns}
\item{...}{columns of \code{x} to be selected for PCA, can be unquoted since it supports quasiquotation.}
@ -57,7 +57,7 @@ Performs a principal component analysis (PCA) based on a data set with automatic
\details{
The \code{\link[=pca]{pca()}} function takes a \link{data.frame} as input and performs the actual PCA with the \R function \code{\link[=prcomp]{prcomp()}}.
The result of the \code{\link[=pca]{pca()}} function is a \link{prcomp} object, with an additional attribute \code{non_numeric_cols} which is a vector with the column names of all columns that do not contain numeric values. These are probably the groups and labels, and will be used by \code{\link[=ggplot_pca]{ggplot_pca()}}.
The result of the \code{\link[=pca]{pca()}} function is a \link{prcomp} object, with an additional attribute \code{non_numeric_cols} which is a vector with the column names of all columns that do not contain \link{numeric} values. These are probably the groups and labels, and will be used by \code{\link[=ggplot_pca]{ggplot_pca()}}.
}
\section{Stable Lifecycle}{

2
man/plot.Rd
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@ -104,7 +104,7 @@
\item{language}{language to be used to translate 'Susceptible', 'Increased exposure'/'Intermediate' and 'Resistant', defaults to system language (see \code{\link[=get_locale]{get_locale()}}) and can be overwritten by setting the option \code{AMR_locale}, e.g. \code{options(AMR_locale = "de")}, see \link{translate}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
\item{expand}{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{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{...}{arguments passed on to \code{\link[=as.rsi]{as.rsi()}}}

10
man/proportion.Rd
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@ -56,9 +56,9 @@ rsi_df(
\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{as_percent}{a logical to indicate whether the output must be returned as a hundred fold with \% sign (a character). A value of \code{0.123456} will then be returned as \code{"12.3\%"}.}
\item{as_percent}{a \link{logical} to indicate whether the output must be returned as a hundred fold with \% sign (a character). A value of \code{0.123456} will then be returned as \code{"12.3\%"}.}
\item{only_all_tested}{(for combination therapies, i.e. using more than one variable for \code{...}): a logical to indicate that isolates must be tested for all antibiotics, see section \emph{Combination Therapy} below}
\item{only_all_tested}{(for combination therapies, i.e. using more than one variable for \code{...}): a \link{logical} to indicate that isolates must be tested for all antibiotics, see section \emph{Combination Therapy} below}
\item{data}{a \link{data.frame} containing columns with class \code{\link{rsi}} (see \code{\link[=as.rsi]{as.rsi()}})}
@ -66,9 +66,9 @@ rsi_df(
\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 argument \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_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). This used to be the argument \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 argument \code{combine_SI}.}
\item{combine_IR}{a \link{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 argument \code{combine_SI}.}
}
\value{
A \link{double} or, when \code{as_percent = TRUE}, a \link{character}.
@ -81,7 +81,7 @@ These functions can be used to calculate the (co-)resistance or susceptibility o
\details{
The function \code{\link[=resistance]{resistance()}} is equal to the function \code{\link[=proportion_R]{proportion_R()}}. The function \code{\link[=susceptibility]{susceptibility()}} is equal to the function \code{\link[=proportion_SI]{proportion_SI()}}.
\strong{Remember that you should filter your table to let it contain only first isolates!} This is needed to exclude duplicates and to reduce selection bias. Use \code{\link[=first_isolate]{first_isolate()}} to determine them in your data set.
\strong{Remember that you should filter your data to let it contain only first isolates!} This is needed to exclude duplicates and to reduce selection bias. Use \code{\link[=first_isolate]{first_isolate()}} to determine them in your data set.
These functions are not meant to count isolates, but to calculate the proportion of resistance/susceptibility. Use the \code{\link[=count]{count()}} functions to count isolates. The function \code{\link[=susceptibility]{susceptibility()}} is essentially equal to \code{count_susceptible() / count_all()}. \emph{Low counts can influence the outcome - the \code{proportion} functions may camouflage this, since they only return the proportion (albeit being dependent on the \code{minimum} argument).}

4
man/random.Rd
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@ -16,9 +16,9 @@ random_rsi(size, prob_RSI = c(0.33, 0.33, 0.33), ...)
\arguments{
\item{size}{desired size of the returned vector}
\item{mo}{any character that can be coerced to a valid microorganism code with \code{\link[=as.mo]{as.mo()}}}
\item{mo}{any \link{character} that can be coerced to a valid microorganism code with \code{\link[=as.mo]{as.mo()}}}
\item{ab}{any character that can be coerced to a valid antimicrobial agent code with \code{\link[=as.ab]{as.ab()}}}
\item{ab}{any \link{character} that can be coerced to a valid antimicrobial agent code with \code{\link[=as.ab]{as.ab()}}}
\item{...}{ignored, only in place to allow future extensions}

8
man/resistance_predict.Rd
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@ -63,17 +63,17 @@ 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 \emph{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 interpretation of I (increased exposure) in 2019, see section \emph{Interpretation of S, I and R} below.}
\item{I_as_S}{a \link{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}.}
\item{preserve_measurements}{a \link{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}.}
\item{info}{a logical to indicate whether textual analysis should be printed with the name and \code{\link[=summary]{summary()}} of the statistical model.}
\item{info}{a \link{logical} to indicate whether textual analysis should be printed with the name and \code{\link[=summary]{summary()}} of the statistical model.}
\item{...}{arguments passed on to functions}
\item{main}{title of the plot}
\item{ribbon}{a logical to indicate whether a ribbon should be shown (default) or error bars}
\item{ribbon}{a \link{logical} to indicate whether a ribbon should be shown (default) or error bars}
}
\value{
A \link{data.frame} with extra class \code{\link{resistance_predict}} with columns:

2
man/rsi_translation.Rd
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@ -16,7 +16,7 @@ A \link{data.frame} with 20,486 observations and 10 variables:
\item \code{disk_dose}\cr Dose of the used disk diffusion method
\item \code{breakpoint_S}\cr Lowest MIC value or highest number of millimetres that leads to "S"
\item \code{breakpoint_R}\cr Highest MIC value or lowest number of millimetres that leads to "R"
\item \code{uti}\cr A logical value (\code{TRUE}/\code{FALSE}) to indicate whether the rule applies to a urinary tract infection (UTI)
\item \code{uti}\cr A \link{logical} value (\code{TRUE}/\code{FALSE}) to indicate whether the rule applies to a urinary tract infection (UTI)
}
}
\usage{

2
man/skewness.Rd
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@ -18,7 +18,7 @@ skewness(x, na.rm = FALSE)
\arguments{
\item{x}{a vector of values, a \link{matrix} or a \link{data.frame}}
\item{na.rm}{a logical value indicating whether \code{NA} values should be stripped before the computation proceeds}
\item{na.rm}{a \link{logical} value indicating whether \code{NA} values should be stripped before the computation proceeds}
}
\description{
Skewness is a measure of the asymmetry of the probability distribution of a real-valued random variable about its mean.