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75 lines
2.8 KiB
R
Executable File
75 lines
2.8 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 \link{microorganisms} to a Data Set}
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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 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.}
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\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")})}
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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 \link{character} vector of length 2.}
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\item{...}{ignored, only in place to allow future extensions}
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}
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\value{
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a \link{data.frame}
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}
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\description{
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Join the data set \link{microorganisms} easily to an existing data set or to a \link{character} vector.
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}
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\details{
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\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.
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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.
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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_PNMN")
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df <- data.frame(
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date = seq(
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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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),
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bacteria = as.mo(c(
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"S. aureus", "MRSA", "MSSA", "STAAUR",
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"E. coli", "E. coli", "E. coli"
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)),
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stringsAsFactors = FALSE
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)
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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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\donttest{
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if (require("dplyr")) {
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example_isolates \%>\%
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left_join_microorganisms() \%>\%
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colnames()
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}
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}
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}
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