mirror of https://github.com/msberends/AMR.git
63 lines
2.9 KiB
R
Executable File
63 lines
2.9 KiB
R
Executable File
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/join_microorganisms.R
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\name{join}
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\alias{join}
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\alias{inner_join_microorganisms}
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\alias{inner_join}
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\alias{left_join_microorganisms}
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\alias{right_join_microorganisms}
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\alias{full_join_microorganisms}
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\alias{semi_join_microorganisms}
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\alias{anti_join_microorganisms}
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\title{Join a table with \code{microorganisms}}
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\usage{
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inner_join_microorganisms(x, by = NULL, suffix = c("2", ""), ...)
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left_join_microorganisms(x, by = NULL, suffix = c("2", ""), ...)
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right_join_microorganisms(x, by = NULL, suffix = c("2", ""), ...)
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full_join_microorganisms(x, by = NULL, suffix = c("2", ""), ...)
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semi_join_microorganisms(x, by = NULL, ...)
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anti_join_microorganisms(x, by = NULL, ...)
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}
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\arguments{
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\item{x}{existing table to join, or character vector}
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\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")})}
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\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.}
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\item{...}{other parameters to pass on to \code{dplyr::\link[dplyr]{join}}.}
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}
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\description{
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Join the dataset \code{\link{microorganisms}} easily to an existing table or character vector.
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}
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\details{
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\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.
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}
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\section{Read more on our website!}{
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On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive 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}.
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}
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\examples{
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left_join_microorganisms(as.mo("K. pneumoniae"))
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left_join_microorganisms("B_KLBSL_PNE")
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library(dplyr)
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septic_patients \%>\% left_join_microorganisms()
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df <- data.frame(date = seq(from = as.Date("2018-01-01"),
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to = as.Date("2018-01-07"),
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by = 1),
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bacteria = as.mo(c("S. aureus", "MRSA", "MSSA", "STAAUR",
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"E. coli", "E. coli", "E. coli")),
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stringsAsFactors = FALSE)
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colnames(df)
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df_joined <- left_join_microorganisms(df, "bacteria")
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colnames(df_joined)
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}
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