(v1.0.1.9004) Support dplyr 1.0.0

man/AMR.Rd

@@ -26,6 +26,7 @@ This package can be used for:
 \item Getting SNOMED codes of a microorganism, or get its name associated with a SNOMED code
 \item Getting LOINC codes of an antibiotic, or get its name associated with a LOINC code
 \item Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI
+\item Principal component analysis for AMR
 }
 }
 \section{Read more on our website!}{

man/WHONET.Rd

@@ -4,7 +4,8 @@
 \name{WHONET}
 \alias{WHONET}
 \title{Data set with 500 isolates - WHONET example}
-\format{A \code{\link{data.frame}} with 500 observations and 53 variables:
+\format{
+A \code{\link{data.frame}} with 500 observations and 53 variables:
 \itemize{
 \item \verb{Identification number}\cr ID of the sample
 \item \verb{Specimen number}\cr ID of the specimen
@@ -32,7 +33,8 @@
 \item \code{Comment}\cr Other comments
 \item \verb{Date of data entry}\cr Date this data was entered in WHONET
 \item \code{AMP_ND10:CIP_EE}\cr 27 different antibiotics. You can lookup the abbreviatons 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()}}.
-}}
+}
+}
 \usage{
 WHONET
 }

man/antibiotics.Rd

@@ -5,7 +5,8 @@
 \alias{antibiotics}
 \alias{antivirals}
 \title{Data sets with ~550 antimicrobials}
-\format{\subsection{For the \link{antibiotics} data set: a \code{\link{data.frame}} with 452 observations and 14 variables:}{
+\format{
+\subsection{For the \link{antibiotics} data set: a \code{\link{data.frame}} with 452 observations and 14 variables:}{
 \itemize{
 \item \code{ab}\cr Antibiotic ID as used in this package (like \code{AMC}), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available
 \item \code{atc}\cr ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC, like \code{J01CR02}
@@ -36,7 +37,10 @@
 \item \code{iv_ddd}\cr Defined Daily Dose (DDD), parenteral treatment
 \item \code{iv_units}\cr Units of \code{iv_ddd}
 }
-}}
+}
+
+An object of class \code{data.frame} with 102 rows and 9 columns.
+}
 \source{
 World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology (WHOCC): \url{https://www.whocc.no/atc_ddd_index/}
 

man/example_isolates.Rd

@@ -4,7 +4,8 @@
 \name{example_isolates}
 \alias{example_isolates}
 \title{Data set with 2,000 example isolates}
-\format{A \code{\link{data.frame}} with 2,000 observations and 49 variables:
+\format{
+A \code{\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
@@ -16,7 +17,8 @@
 \item \code{patient_id}\cr ID of the patient
 \item \code{mo}\cr ID of microorganism created with \code{\link[=as.mo]{as.mo()}}, see also \link{microorganisms}
 \item \code{PEN:RIF}\cr 40 different antibiotics with class \code{\link{rsi}} (see \code{\link[=as.rsi]{as.rsi()}}); these column names occur in the \link{antibiotics} data set and can be translated with \code{\link[=ab_name]{ab_name()}}
-}}
+}
+}
 \usage{
 example_isolates
 }

man/example_isolates_unclean.Rd

@@ -4,14 +4,16 @@
 \name{example_isolates_unclean}
 \alias{example_isolates_unclean}
 \title{Data set with unclean data}
-\format{A \code{\link{data.frame}} with 3,000 observations and 8 variables:
+\format{
+A \code{\link{data.frame}} with 3,000 observations and 8 variables:
 \itemize{
 \item \code{patient_id}\cr ID of the patient
 \item \code{date}\cr date of receipt at the laboratory
 \item \code{hospital}\cr ID of the hospital, from A to C
 \item \code{bacteria}\cr info about microorganism that can be transformed with \code{\link[=as.mo]{as.mo()}}, see also \link{microorganisms}
 \item \code{AMX:GEN}\cr 4 different antibiotics that have to be transformed with \code{\link[=as.rsi]{as.rsi()}}
-}}
+}
+}
 \usage{
 example_isolates_unclean
 }

man/microorganisms.Rd

@@ -4,7 +4,8 @@
 \name{microorganisms}
 \alias{microorganisms}
 \title{Data set with ~70,000 microorganisms}
-\format{A \code{\link{data.frame}} with 69,447 observations and 17 variables:
+\format{
+A \code{\link{data.frame}} with 69,447 observations and 17 variables:
 \itemize{
 \item \code{mo}\cr ID of microorganism as used by this package
 \item \code{col_id}\cr Catalogue of Life ID
@@ -16,7 +17,8 @@
 \item \code{source}\cr Either "CoL", "DSMZ" (see Source) or "manually added"
 \item \code{prevalence}\cr Prevalence of the microorganism, see \code{\link[=as.mo]{as.mo()}}
 \item \code{snomed}\cr SNOMED code of the microorganism. Use \code{\link[=mo_snomed]{mo_snomed()}} to retrieve it quickly, see \code{\link[=mo_property]{mo_property()}}.
-}}
+}
+}
 \source{
 Catalogue of Life: Annual Checklist (public online taxonomic database), \url{http://www.catalogueoflife.org} (check included annual version with \code{\link[=catalogue_of_life_version]{catalogue_of_life_version()}}).
 

man/microorganisms.codes.Rd

@@ -4,11 +4,13 @@
 \name{microorganisms.codes}
 \alias{microorganisms.codes}
 \title{Translation table for common microorganism codes}
-\format{A \code{\link{data.frame}} with 5,450 observations and 2 variables:
+\format{
+A \code{\link{data.frame}} with 5,450 observations and 2 variables:
 \itemize{
 \item \code{code}\cr Commonly used code of a microorganism
 \item \code{mo}\cr ID of the microorganism in the \link{microorganisms} data set
-}}
+}
+}
 \usage{
 microorganisms.codes
 }

man/microorganisms.old.Rd

@@ -4,14 +4,16 @@
 \name{microorganisms.old}
 \alias{microorganisms.old}
 \title{Data set with previously accepted taxonomic names}
-\format{A \code{\link{data.frame}} with 24,246 observations and 5 variables:
+\format{
+A \code{\link{data.frame}} with 24,246 observations and 5 variables:
 \itemize{
 \item \code{col_id}\cr Catalogue of Life ID that was originally given
 \item \code{col_id_new}\cr New Catalogue of Life ID that responds to an entry in the \link{microorganisms} data set
 \item \code{fullname}\cr Old full taxonomic name of the microorganism
 \item \code{ref}\cr Author(s) and year of concerning scientific publication
 \item \code{prevalence}\cr Prevalence of the microorganism, see \code{\link[=as.mo]{as.mo()}}
-}}
+}
+}
 \source{
 Catalogue of Life: Annual Checklist (public online taxonomic database), \url{http://www.catalogueoflife.org} (check included annual version with \code{\link[=catalogue_of_life_version]{catalogue_of_life_version()}}).
 }

man/pca.Rd

@@ -59,10 +59,10 @@ The \code{\link[=pca]{pca()}} function takes a \link{data.frame} as input and pe
 
 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()}}.
 }
-\section{Experimental lifecycle}{
+\section{Maturing lifecycle}{
 
-\if{html}{\figure{lifecycle_experimental.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{experimental}. An experimental function is in the very early stages of development. The unlying code might be changing frequently as we rapidly iterate and explore variations in search of the best fit. 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 will not be included in releases we submit to CRAN, since they have not yet matured enough.
+\if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
+The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. We will strive to maintain backward compatibility, but the function needs wider usage and more extensive testing in order to optimise the unlying code.
 }
 
 \examples{

man/rsi_translation.Rd

@@ -4,7 +4,8 @@
 \name{rsi_translation}
 \alias{rsi_translation}
 \title{Data set for R/SI interpretation}
-\format{A \code{\link{data.frame}} with 13,975 observations and 9 variables:
+\format{
+A \code{\link{data.frame}} with 13,975 observations and 9 variables:
 \itemize{
 \item \code{guideline}\cr Name of the guideline
 \item \code{method}\cr Either "MIC" or "DISK"
@@ -15,7 +16,8 @@
 \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"
-}}
+}
+}
 \usage{
 rsi_translation
 }