(v1.6.0.9000) custom EUCAST rules

man/custom_eucast_rules.Rd

@@ -0,0 +1,43 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/custom_eucast_rules.R
+\name{custom_eucast_rules}
+\alias{custom_eucast_rules}
+\title{Create Custom EUCAST Rules}
+\usage{
+custom_eucast_rules(...)
+}
+\arguments{
+\item{...}{rules in formula notation, see \emph{Examples}}
+}
+\description{
+Create Custom EUCAST Rules
+}
+\details{
+This documentation page will be updated shortly. \strong{This function is experimental.}
+}
+\section{How it works}{
+
+..
+
+It is also possible to define antibiotic groups instead of single antibiotics. The following groups are allowed (case-insensitive): \code{aminoglycosides}, \code{aminopenicillins}, \code{betalactams}, \code{carbapenems}, \code{cephalosporins}, \code{cephalosporins_1st}, \code{cephalosporins_2nd}, \code{cephalosporins_3rd}, \code{cephalosporins_except_caz}, \code{fluoroquinolones}, \code{glycopeptides}, \code{glycopeptides_except_lipo}, \code{lincosamides}, \code{lipoglycopeptides}, \code{macrolides}, \code{oxazolidinones}, \code{penicillins}, \code{polymyxins}, \code{streptogramins}, \code{tetracyclines}, \code{tetracyclines_except_tgc} and \code{ureidopenicillins}.
+}
+
+\section{Experimental Lifecycle}{
+
+\if{html}{\figure{lifecycle_experimental.svg}{options: style=margin-bottom:5px} \cr}
+The \link[=lifecycle]{lifecycle} of this function is \strong{experimental}. An experimental function is in early stages of development. The unlying code might be changing frequently. Experimental functions might be removed without deprecation, so you are generally best off waiting until a function is more mature before you use it in production code. Experimental functions are only available in development versions of this \code{AMR} package and will thus not be included in releases that are submitted to CRAN, since such functions have not yet matured enough.
+}
+
+\examples{
+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,
+             info = FALSE)
+             
+# combine rule sets
+x2 <- c(x,
+        custom_eucast_rules(TZP == "R" ~ carbapenems == "R"))
+x2
+}

man/eucast_rules.Rd

@@ -27,6 +27,7 @@ eucast_rules(
   version_expertrules = 3.2,
   ampc_cephalosporin_resistance = NA,
   only_rsi_columns = FALSE,
+  custom_rules = NULL,
   ...
 )
 
@@ -39,7 +40,7 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 11)
 
 \item{info}{a 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{"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")}.}
+\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{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.}
 
@@ -51,6 +52,8 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 11)
 
 \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{custom_rules}{custom rules to apply, created with \code{\link[=custom_eucast_rules]{custom_eucast_rules()}}}
+
 \item{...}{column name of an antibiotic, see section \emph{Antibiotics} below}
 
 \item{ab}{any (vector of) text that can be coerced to a valid antibiotic code with \code{\link[=as.ab]{as.ab()}}}
@@ -70,6 +73,15 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
 \strong{Note:} When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance.
 
 The file containing all EUCAST rules is located here: \url{https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv}.
+\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",
+                         AMC == "I" & genus == "Klebsiella" ~ aminopenicillins == "I")
+
+eucast_rules(example_isolates, rules = "custom", custom_rules = x)
+}
+}
+
 \subsection{'Other' Rules}{
 
 Before further processing, two non-EUCAST rules about drug combinations can be applied to improve the efficacy of the EUCAST rules, and the reliability of your data (analysis). These rules are:

man/like.Rd

@@ -4,9 +4,9 @@
 \alias{like}
 \alias{\%like\%}
 \alias{\%like_case\%}
-\title{Pattern Matching with Keyboard Shortcut}
+\title{Vectorised Pattern Matching with Keyboard Shortcut}
 \source{
-Idea from the \href{https://github.com/Rdatatable/data.table/blob/master/R/like.R}{\code{like} function from the \code{data.table} package}
+Idea from the \href{https://github.com/Rdatatable/data.table/blob/ec1259af1bf13fc0c96a1d3f9e84d55d8106a9a4/R/like.R}{\code{like} function from the \code{data.table} package}
 }
 \usage{
 like(x, pattern, ignore.case = TRUE)
@@ -23,7 +23,7 @@ x \%like_case\% pattern
 \item{ignore.case}{if \code{FALSE}, the pattern matching is \emph{case sensitive} and if \code{TRUE}, case is ignored during matching.}
 }
 \value{
-A \code{\link{logical}} vector
+A \link{logical} vector
 }
 \description{
 Convenient wrapper around \code{\link[=grepl]{grepl()}} to match a pattern: \code{x \%like\% pattern}. It always returns a \code{\link{logical}} vector and is always case-insensitive (use \code{x \%like_case\% pattern} for case-sensitive matching). Also, \code{pattern} can be as long as \code{x} to compare items of each index in both vectors, or they both can have the same length to iterate over all cases.
@@ -34,7 +34,7 @@ The \verb{\%like\%} function:
 \item Is case-insensitive (use \verb{\%like_case\%} for case-sensitive matching)
 \item Supports multiple patterns
 \item Checks if \code{pattern} is a regular expression and sets \code{fixed = TRUE} if not, to greatly improve speed
-\item Always uses compatibility with Perl
+\item Always uses compatibility with Perl unless \code{fixed = TRUE}, to greatly improve speed
 }
 
 Using RStudio? The text \verb{\%like\%} can also be directly inserted in your code from the Addins menu and can have its own Keyboard Shortcut like \code{Ctrl+Shift+L} or \code{Cmd+Shift+L} (see \code{Tools} > \verb{Modify Keyboard Shortcuts...}).
@@ -75,7 +75,7 @@ a \%like\% b[1]
 \donttest{
 if (require("dplyr")) {
   example_isolates \%>\%
-    filter(mo_name(mo) \%like\% "^ent")
+    filter(mo_name() \%like\% "^ent")
 }
 }
 }

man/mdro.Rd

@@ -134,10 +134,19 @@ You can print the rules set in the console for an overview. Colours will help re
 #> Unmatched rows will return NA.
 }
 
-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, guideline = custom)
+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,
+          guideline = custom)
 table(x)
-#> Elderly Type A Elderly Type B       Negative 
-#>             43            891           1066 
+#>       Negative Elderly Type A Elderly Type B
+#>           1070            198            732
+}
+
+Rules can also be combined with other custom rules by using \code{\link[=c]{c()}}:\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
 }
 
 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()}}.

man/plot.Rd

@@ -83,6 +83,7 @@
   xlab = "Antimicrobial Interpretation",
   ylab = "Frequency",
   colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
+  language = get_locale(),
   ...
 )
 }