(v1.4.0.9032) auto-data guessing for functions

man/first_isolate.Rd

@@ -50,7 +50,7 @@ filter_first_weighted_isolate(
 )
 }
 \arguments{
-\item{x}{a \link{data.frame} containing isolates.}
+\item{x}{a \link{data.frame} containing isolates. Can be omitted when used inside \code{dplyr} verbs, such as \code{filter()}, \code{mutate()} and \code{summarise()}.}
 
 \item{col_date}{column name of the result date (or date that is was received on the lab), defaults to the first column with a date class}
 
@@ -93,6 +93,8 @@ A \code{\link{logical}} vector
 Determine first (weighted) isolates of all microorganisms of every patient per episode and (if needed) per specimen type. To determine patient episodes not necessarily based on microorganisms, use \code{\link[=is_new_episode]{is_new_episode()}} that also supports grouping with the \code{dplyr} package.
 }
 \details{
+These functions are context-aware when used inside \code{dplyr} verbs, such as \code{filter()}, \code{mutate()} and \code{summarise()}. This means that then the \code{x} parameter can be omitted, please see \emph{Examples}.
+
 The \code{\link[=first_isolate]{first_isolate()}} function is a wrapper around the \code{\link[=is_new_episode]{is_new_episode()}} function, but more efficient for data sets containing microorganism codes or names.
 
 All isolates with a microbial ID of \code{NA} will be excluded as first isolate.
@@ -107,7 +109,7 @@ The functions \code{\link[=filter_first_isolate]{filter_first_isolate()}} and \c
 
 The function \code{\link[=filter_first_isolate]{filter_first_isolate()}} is essentially equal to either:\preformatted{  x[first_isolate(x, ...), ]
   
-  x \%>\% filter(first_isolate(x, ...))
+  x \%>\% filter(first_isolate(...))
 }
 
 The function \code{\link[=filter_first_weighted_isolate]{filter_first_weighted_isolate()}} is essentially equal to:\preformatted{  x \%>\%
@@ -161,6 +163,8 @@ if (require("dplyr")) {
     filter(first_isolate == TRUE)
  
   # short-hand versions:
+  example_isolates \%>\%
+    filter(first_isolate())
   example_isolates \%>\%
     filter_first_isolate()
     

man/is_new_episode.Rd

@@ -41,7 +41,7 @@ On our website \url{https://msberends.github.io/AMR/} you can find \href{https:/
 
 is_new_episode(example_isolates$date)
 is_new_episode(example_isolates$date, episode_days = 60)
-
+#' \donttest{
 if (require("dplyr")) {
   # is_new_episode() can also be used in dplyr verbs to determine patient
   # episodes based on any (combination of) grouping variables:
@@ -78,3 +78,4 @@ if (require("dplyr")) {
     mutate(flag_episode = is_new_episode(date))
 }
 }
+}

man/key_antibiotics.Rd

@@ -40,7 +40,7 @@ key_antibiotics_equal(
 )
 }
 \arguments{
-\item{x}{a data.frame with antibiotics columns, like \code{AMX} or \code{amox}}
+\item{x}{a \link{data.frame} with antibiotics columns, like \code{AMX} or \code{amox}. Can be omitted when used inside \code{dplyr} verbs, such as \code{filter()}, \code{mutate()} and \code{summarise()}.}
 
 \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()}}.}
 
@@ -65,9 +65,11 @@ key_antibiotics_equal(
 \item{info}{print progress}
 }
 \description{
-These function can be used to determine first isolates (see \code{\link[=first_isolate]{first_isolate()}}). Using key antibiotics to determine first isolates is more reliable than without key antibiotics. These selected isolates will then be called first \emph{weighted} isolates.
+These function can be used to determine first isolates (see \code{\link[=first_isolate]{first_isolate()}}). Using key antibiotics to determine first isolates is more reliable than without key antibiotics. These selected isolates can then be called first \emph{weighted} isolates.
 }
 \details{
+The \code{\link[=key_antibiotics]{key_antibiotics()}} function is context-aware when used inside \code{dplyr} verbs, such as \code{filter()}, \code{mutate()} and \code{summarise()}. This means that then the \code{x} parameter can be omitted, please see \emph{Examples}.
+
 The function \code{\link[=key_antibiotics]{key_antibiotics()}} returns a character vector with 12 antibiotic results for every isolate. These isolates can then be compared using \code{\link[=key_antibiotics_equal]{key_antibiotics_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_antibiotics]{key_antibiotics()}} and ignored by \code{\link[=key_antibiotics_equal]{key_antibiotics_equal()}}.
 
 The \code{\link[=first_isolate]{first_isolate()}} function only uses this function on the same microbial species from the same patient. Using this, e.g. an MRSA will be included after a susceptible \emph{S. aureus} (MSSA) is found within the same patient episode. Without key antibiotic comparison it would not. See \code{\link[=first_isolate]{first_isolate()}} for more info.
@@ -136,30 +138,30 @@ On our website \url{https://msberends.github.io/AMR/} you can find \href{https:/
 # `example_isolates` is a dataset available in the AMR package.
 # See ?example_isolates.
 
-# output of the `key_antibiotics` function could be like this:
+# output of the `key_antibiotics()` function could be like this:
 strainA <- "SSSRR.S.R..S"
 strainB <- "SSSIRSSSRSSS"
 
-# can those strings can be compared with:
+# those strings can be compared with:
 key_antibiotics_equal(strainA, strainB)
 # TRUE, because I is ignored (as well as missing values)
 
 key_antibiotics_equal(strainA, strainB, ignore_I = FALSE)
-# FALSE, because I is not ignored and so the 4th value differs
+# FALSE, because I is not ignored and so the 4th character differs
 
 \donttest{
 if (require("dplyr")) {
   # set key antibiotics to a new variable
   my_patients <- example_isolates \%>\%
-    mutate(keyab = key_antibiotics(.)) \%>\%
+    mutate(keyab = key_antibiotics()) \%>\% # no need to define `x`
     mutate(
       # now calculate first isolates
-      first_regular = first_isolate(., col_keyantibiotics = FALSE),
+      first_regular = first_isolate(col_keyantibiotics = FALSE),
       # and first WEIGHTED isolates
-      first_weighted = first_isolate(., col_keyantibiotics = "keyab")
+      first_weighted = first_isolate(col_keyantibiotics = "keyab")
     )
  
-  # Check the difference, in this data set it results in 7\% more isolates:
+  # Check the difference, in this data set it results in a lot more isolates:
   sum(my_patients$first_regular, na.rm = TRUE)
   sum(my_patients$first_weighted, na.rm = TRUE)
 }

man/mdro.Rd

@@ -40,7 +40,7 @@ mdr_cmi2012(x, guideline = "CMI2012", ...)
 eucast_exceptional_phenotypes(x, guideline = "EUCAST", ...)
 }
 \arguments{
-\item{x}{data with antibiotic columns, such as \code{amox}, \code{AMX} and \code{AMC}}
+\item{x}{a \link{data.frame} with antibiotics columns, like \code{AMX} or \code{amox}. Can be omitted when used inside \code{dplyr} verbs, such as \code{filter()}, \code{mutate()} and \code{summarise()}.}
 
 \item{guideline}{a specific guideline to follow. When left empty, the publication by Magiorakos \emph{et al.} (2012, Clinical Microbiology and Infection) will be followed, please see \emph{Details}.}
 
@@ -72,21 +72,29 @@ Ordered \link{factor} with levels \code{Negative} < \verb{Positive, unconfirmed}
 Determine which isolates are multidrug-resistant organisms (MDRO) according to international and national guidelines.
 }
 \details{
+These functions are context-aware when used inside \code{dplyr} verbs, such as \code{filter()}, \code{mutate()} and \code{summarise()}. This means that then the \code{x} parameter can be omitted, please see \emph{Examples}.
+
 For the \code{pct_required_classes} argument, values above 1 will be divided by 100. This is to support both fractions (\code{0.75} or \code{3/4}) and percentages (\code{75}).
 
 Currently supported guidelines are (case-insensitive):
 \itemize{
-\item \code{guideline = "CMI2012"}\cr
+\item \code{guideline = "CMI2012"} (default)
+
 Magiorakos AP, Srinivasan A \emph{et al.} "Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance." Clinical Microbiology and Infection (2012) (\href{https://www.clinicalmicrobiologyandinfection.com/article/S1198-743X(14)61632-3/fulltext}{link})
-\item \code{guideline = "EUCAST3.2"} (or simply \code{guideline = "EUCAST"})\cr
+\item \code{guideline = "EUCAST3.2"} (or simply \code{guideline = "EUCAST"})
+
 The European international guideline - EUCAST Expert Rules Version 3.2 "Intrinsic Resistance and Unusual Phenotypes" (\href{https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf}{link})
-\item \code{guideline = "EUCAST3.1"}\cr
+\item \code{guideline = "EUCAST3.1"}
+
 The European international guideline - EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (\href{https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}{link})
-\item \code{guideline = "TB"}\cr
+\item \code{guideline = "TB"}
+
 The international guideline for multi-drug resistant tuberculosis - World Health Organization "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis" (\href{https://www.who.int/tb/publications/pmdt_companionhandbook/en/}{link})
-\item \code{guideline = "MRGN"}\cr
+\item \code{guideline = "MRGN"}
+
 The German national guideline - Mueller et al. (2015) Antimicrobial Resistance and Infection Control 4:7. DOI: 10.1186/s13756-015-0047-6
-\item \code{guideline = "BRMO"}\cr
+\item \code{guideline = "BRMO"}
+
 The Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu "WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) (ZKH)" (\href{https://www.rivm.nl/wip-richtlijn-brmo-bijzonder-resistente-micro-organismen-zkh}{link})
 }
 
@@ -140,10 +148,12 @@ if (require("dplyr")) {
     mdro() \%>\%
     table()
   
+  # no need to define `x` when used inside dplyr verbs:
   example_isolates \%>\%
-    mutate(EUCAST = eucast_exceptional_phenotypes(.),
-           BRMO = brmo(.),
-           MRGN = mrgn(.))
+    mutate(MDRO = mdro(),
+           EUCAST = eucast_exceptional_phenotypes(),
+           BRMO = brmo(),
+           MRGN = mrgn())
 }
 }
 }

man/resistance_predict.Rd

@@ -47,7 +47,7 @@ ggplot_rsi_predict(
 )
 }
 \arguments{
-\item{x}{a \link{data.frame} containing isolates.}
+\item{x}{a \link{data.frame} containing isolates. Can be omitted when used inside \code{dplyr} verbs, such as \code{filter()}, \code{mutate()} and \code{summarise()}.}
 
 \item{col_ab}{column name of \code{x} containing antimicrobial interpretations (\code{"R"}, \code{"I"} and \code{"S"})}