mirror of https://github.com/msberends/AMR.git
57 lines
2.2 KiB
R
57 lines
2.2 KiB
R
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/join.R
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\name{join}
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\alias{join}
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\alias{inner_join_bactlist}
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\alias{inner_join}
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\alias{left_join_bactlist}
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\alias{right_join_bactlist}
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\alias{full_join_bactlist}
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\alias{semi_join_bactlist}
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\alias{anti_join_bactlist}
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\title{Join a table with \code{bactlist}}
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\usage{
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inner_join_bactlist(x, by = "bactid", suffix = c("2", ""), ...)
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left_join_bactlist(x, by = "bactid", suffix = c("2", ""), ...)
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right_join_bactlist(x, by = "bactid", suffix = c("2", ""), ...)
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full_join_bactlist(x, by = "bactid", suffix = c("2", ""), ...)
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semi_join_bactlist(x, by = "bactid", ...)
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anti_join_bactlist(x, by = "bactid", ...)
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}
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\arguments{
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\item{x}{existing table to join, also supports character vectors}
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\item{by}{a variable to join by - could be a column name of \code{x} with values that exist in \code{bactlist$bactid} (like \code{by = "bacteria_id"}), or another column in \code{\link{bactlist}} (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 list of microorganisms \code{\link{bactlist}} easily to an existing table.
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}
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\details{
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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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\examples{
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left_join_bactlist("STAAUR")
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library(dplyr)
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septic_patients \%>\% left_join_bactlist()
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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_id = c("STAAUR", "STAAUR", "STAAUR", "STAAUR",
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"ESCCOL", "ESCCOL", "ESCCOL"),
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stringsAsFactors = FALSE)
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colnames(df)
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df2 <- left_join_bactlist(df, "bacteria_id")
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colnames(df2)
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}
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