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- For functions first_isolate, EUCAST_rules the antibiotic column names are case-insensitive

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- Functions `first_isolate`, `EUCAST_rules` and `rsi_predict` supports tidyverse-like evaluation of parameters (no need to quote columns them anymore)
- Functions `clipboard_import` and `clipboard_export` as helper functions to quickly copy and paste from/to software like Excel and SPSS
- Renamed dataset `bactlist` to `microorganisms`
This commit is contained in:
dr. M.S. (Matthijs) Berends
2018-03-23 14:46:02 +01:00
parent e1e19af625
commit 53464ff1c8
29 changed files with 693 additions and 373 deletions
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36
man/join.Rd
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@@ -2,47 +2,47 @@
% Please edit documentation in R/join.R
\name{join}
\alias{join}
\alias{inner_join_bactlist}
\alias{inner_join_microorganisms}
\alias{inner_join}
\alias{left_join_bactlist}
\alias{right_join_bactlist}
\alias{full_join_bactlist}
\alias{semi_join_bactlist}
\alias{anti_join_bactlist}
\title{Join a table with \code{bactlist}}
\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_bactlist(x, by = "bactid", suffix = c("2", ""), ...)
inner_join_microorganisms(x, by = "bactid", suffix = c("2", ""), ...)
left_join_bactlist(x, by = "bactid", suffix = c("2", ""), ...)
left_join_microorganisms(x, by = "bactid", suffix = c("2", ""), ...)
right_join_bactlist(x, by = "bactid", suffix = c("2", ""), ...)
right_join_microorganisms(x, by = "bactid", suffix = c("2", ""), ...)
full_join_bactlist(x, by = "bactid", suffix = c("2", ""), ...)
full_join_microorganisms(x, by = "bactid", suffix = c("2", ""), ...)
semi_join_bactlist(x, by = "bactid", ...)
semi_join_microorganisms(x, by = "bactid", ...)
anti_join_bactlist(x, by = "bactid", ...)
anti_join_microorganisms(x, by = "bactid", ...)
}
\arguments{
\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$bactid} (like \code{by = "bacteria_id"}), or another column in \code{\link{bactlist}} (but then it should be named, like \code{by = c("my_genus_species" = "fullname")})}
\item{by}{a variable to join by - could be a column name of \code{x} with values that exist in \code{microorganisms$bactid} (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 list of microorganisms \code{\link{bactlist}} easily to an existing table.
Join the dataset \code{\link{microorganisms}} easily to an existing table or character vector.
}
\details{
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")
left_join_microorganisms("STAAUR")
library(dplyr)
septic_patients \%>\% left_join_bactlist()
septic_patients \%>\% left_join_microorganisms()
df <- data.frame(date = seq(from = as.Date("2018-01-01"),
to = as.Date("2018-01-07"),
@@ -51,6 +51,6 @@ df <- data.frame(date = seq(from = as.Date("2018-01-01"),
"ESCCOL", "ESCCOL", "ESCCOL"),
stringsAsFactors = FALSE)
colnames(df)
df2 <- left_join_bactlist(df, "bacteria_id")
df2 <- left_join_microorganisms(df, "bacteria_id")
colnames(df2)
}