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count_all and some fixes

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dr. M.S. (Matthijs) Berends
2018-10-12 16:35:18 +02:00
parent e7d937d36e
commit 5b5b95a47b
22 changed files with 232 additions and 246 deletions
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29
man/join.Rd
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@@ -11,22 +11,22 @@
\alias{anti_join_microorganisms}
\title{Join a table with \code{microorganisms}}
\usage{
inner_join_microorganisms(x, by = "mo", suffix = c("2", ""), ...)
inner_join_microorganisms(x, by = NULL, suffix = c("2", ""), ...)
left_join_microorganisms(x, by = "mo", suffix = c("2", ""), ...)
left_join_microorganisms(x, by = NULL, suffix = c("2", ""), ...)
right_join_microorganisms(x, by = "mo", suffix = c("2", ""), ...)
right_join_microorganisms(x, by = NULL, suffix = c("2", ""), ...)
full_join_microorganisms(x, by = "mo", suffix = c("2", ""), ...)
full_join_microorganisms(x, by = NULL, suffix = c("2", ""), ...)
semi_join_microorganisms(x, by = "mo", ...)
semi_join_microorganisms(x, by = NULL, ...)
anti_join_microorganisms(x, by = "mo", ...)
anti_join_microorganisms(x, by = NULL, ...)
}
\arguments{
\item{x}{existing table to join, also supports character vectors}
\item{x}{existing table to join, or character vector}
\item{by}{a variable to join by - could be a column name of \code{x} with values that exist in \code{microorganisms$mo} (like \code{by = "bacteria_id"}), or another column in \code{\link{microorganisms}} (but then it should be named, like \code{by = c("my_genus_species" = "fullname")})}
\item{by}{a variable to join by - if left empty will search for a column with class \code{mo} (created with \code{\link{as.mo}}) or will be \code{"mo"} if that column name exists in \code{x}, could otherwise be a column name of \code{x} with values that exist in \code{microorganisms$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")})}
\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.}
@@ -36,10 +36,11 @@ anti_join_microorganisms(x, by = "mo", ...)
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.
\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.
}
\examples{
left_join_microorganisms("STAAUR")
left_join_microorganisms(as.mo("K. pneumoniae"))
left_join_microorganisms("B_KLBSL_PNE")
library(dplyr)
septic_patients \%>\% left_join_microorganisms()
@@ -47,10 +48,10 @@ septic_patients \%>\% left_join_microorganisms()
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"),
bacteria = as.mo(c("S. aureus", "MRSA", "MSSA", "STAAUR",
"E. coli", "E. coli", "E. coli")),
stringsAsFactors = FALSE)
colnames(df)
df2 <- left_join_microorganisms(df, "bacteria_id")
colnames(df2)
df_joined <- left_join_microorganisms(df, "bacteria")
colnames(df_joined)
}