mirror of
https://github.com/msberends/AMR.git
synced 2024-12-26 22:46:12 +01:00
58 lines
2.5 KiB
R
Executable File
58 lines
2.5 KiB
R
Executable File
% 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 \code{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{mo} (created with \code{\link{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 \code{\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{dplyr::\link[dplyr]{join}}.}
|
|
}
|
|
\description{
|
|
Join the dataset \code{\link{microorganisms}} easily to an existing table or character vector.
|
|
}
|
|
\details{
|
|
\strong{Note:} As opposed to the \code{\link[dplyr]{join}} functions of \code{dplyr}, characters 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}} for more information.
|
|
}
|
|
\examples{
|
|
left_join_microorganisms(as.mo("K. pneumoniae"))
|
|
left_join_microorganisms("B_KLBSL_PNE")
|
|
|
|
library(dplyr)
|
|
septic_patients \%>\% 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)
|
|
}
|