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 a table with \link{microorganisms}}
\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 table to join, or character vector}

\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} (like \code{by = "bacteria_id"}), or another column in \link{microorganisms} (but then it should be named, like \code{by = c("my_genus_species" = "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{...}{other parameters to pass on to \code{\link[dplyr:join]{dplyr::join()}}}
}
\description{
Join the data set \link{microorganisms} easily to an existing table or character vector.
}
\details{
\strong{Note:} As opposed to the \code{\link[dplyr:join]{dplyr::join()}} functions of \code{dplyr}, \code{\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. See \code{\link[dplyr:join]{dplyr::join()}} for more information.
}
\section{Stable lifecycle}{

\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.

If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will continue to work but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
}

\section{Read more on our website!}{

On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
}

\examples{
left_join_microorganisms(as.mo("K. pneumoniae"))
left_join_microorganisms("B_KLBSL_PNE")

library(dplyr)
example_isolates \%>\% left_join_microorganisms()

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)
}