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Code Releases Activity

- Added new function guess_bactid to determine the ID of a microorganism based on genus/species

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- Renamed `ablist` to `antibiotics`
- Added support for character vector in join functions
- Altered `%like%` to make it case insensitive
This commit is contained in:
dr. M.S. (Matthijs) Berends
2018-03-19 12:43:22 +01:00
parent 0fec64a240
commit 502a44eb25
23 changed files with 312 additions and 103 deletions
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17
man/join.Rd
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@ -11,39 +11,42 @@
\alias{anti_join_bactlist}
\title{Join a table with \code{bactlist}}
\usage{
inner_join_bactlist(x, by = "bactid", ...)
inner_join_bactlist(x, by = "bactid", suffix = c("2", ""), ...)
left_join_bactlist(x, by = "bactid", ...)
left_join_bactlist(x, by = "bactid", suffix = c("2", ""), ...)
right_join_bactlist(x, by = "bactid", ...)
right_join_bactlist(x, by = "bactid", suffix = c("2", ""), ...)
full_join_bactlist(x, by = "bactid", ...)
full_join_bactlist(x, by = "bactid", suffix = c("2", ""), ...)
semi_join_bactlist(x, by = "bactid", ...)
anti_join_bactlist(x, by = "bactid", ...)
}
\arguments{
\item{x}{existing table to join}
\item{x}{existing table to join, also supports character vectors}
\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")})}
\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 list of microorganisms \code{\link{bactlist}} easily to an existing table.
}
\details{
As opposed to the \code{\link[dplyr]{join}} functions of \code{dplyr}, 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.
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_bactlist("STAAUR")
df <- data.frame(date = seq(from = as.Date("2018-01-01"),
to = as.Date("2018-01-07"),
by = 1),
bacteria_id = c("STAAUR", "STAAUR", "STAAUR", "STAAUR",
"ESCCOL", "ESCCOL", "ESCCOL"),
stringsAsFactors = FALSE)
colnames(df)
df2 <- left_join_bactlist(df, "bacteria_id")
colnames(df2)