AMR/man/join.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/join_microorganisms.R
\name{join}
\alias{join}
\alias{inner_join_microorganisms}
\alias{inner_join}
\alias{left_join_microorganisms}
\alias{right_join_microorganisms}
\alias{full_join_microorganisms}
\alias{semi_join_microorganisms}
\alias{anti_join_microorganisms}
\title{Join \link{microorganisms} to a Data Set}
\usage{
inner_join_microorganisms(x, by = NULL, suffix = c("2", ""), ...)

left_join_microorganisms(x, by = NULL, suffix = c("2", ""), ...)

right_join_microorganisms(x, by = NULL, suffix = c("2", ""), ...)

full_join_microorganisms(x, by = NULL, suffix = c("2", ""), ...)

semi_join_microorganisms(x, by = NULL, ...)

anti_join_microorganisms(x, by = NULL, ...)
}
\arguments{
\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 \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 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()}} and \code{\link[=interaction]{interaction()}} functions from base \R will be used.
}
\examples{
left_join_microorganisms(as.mo("K. pneumoniae"))
left_join_microorganisms("B_KLBSL_PNMN")

df <- data.frame(
  date = seq(
    from = as.Date("2018-01-01"),
    to = as.Date("2018-01-07"),
    by = 1
  ),
  bacteria = as.mo(c(
    "S. aureus", "MRSA", "MSSA", "STAAUR",
    "E. coli", "E. coli", "E. coli"
  )),
  stringsAsFactors = FALSE
)
colnames(df)

df_joined <- left_join_microorganisms(df, "bacteria")
colnames(df_joined)

\donttest{
if (require("dplyr")) {
  example_isolates \%>\%
    left_join_microorganisms() \%>\%
    colnames()
}
}
}