mirror of https://github.com/msberends/AMR.git
159 lines
6.3 KiB
R
Executable File
159 lines
6.3 KiB
R
Executable File
# ==================================================================== #
|
|
# TITLE #
|
|
# Antimicrobial Resistance (AMR) Analysis #
|
|
# #
|
|
# SOURCE #
|
|
# https://gitlab.com/msberends/AMR #
|
|
# #
|
|
# LICENCE #
|
|
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
|
# #
|
|
# This R package is free software; you can freely use and distribute #
|
|
# it for both personal and commercial purposes under the terms of the #
|
|
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
|
|
# the Free Software Foundation. #
|
|
# #
|
|
# This R package was created for academic research and was publicly #
|
|
# released in the hope that it will be useful, but it comes WITHOUT #
|
|
# ANY WARRANTY OR LIABILITY. #
|
|
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
|
|
# ==================================================================== #
|
|
|
|
#' Join a table with \code{microorganisms}
|
|
#'
|
|
#' Join the dataset \code{\link{microorganisms}} easily to an existing table or character vector.
|
|
#' @rdname join
|
|
#' @name join
|
|
#' @aliases join inner_join
|
|
#' @param x existing table to join, or character vector
|
|
#' @param 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$mo} (like \code{by = "bacteria_id"}), or another column in \code{\link{microorganisms}} (but then it should be named, like \code{by = c("my_genus_species" = "fullname")})
|
|
#' @param suffix if there are non-joined duplicate variables in \code{x} and \code{y}, these suffixes will be added to the output to disambiguate them. Should be a character vector of length 2.
|
|
#' @param ... other parameters to pass on to \code{dplyr::\link[dplyr]{join}}.
|
|
#' @details \strong{Note:} As opposed to the \code{\link[dplyr]{join}} functions of \code{dplyr}, characters vectors are supported and at default existing columns will get a suffix \code{"2"} and the newly joined columns will not get a suffix. See \code{\link[dplyr]{join}} for more information.
|
|
#' @inheritSection AMR Read more on our website!
|
|
#' @export
|
|
#' @examples
|
|
#' left_join_microorganisms(as.mo("K. pneumoniae"))
|
|
#' left_join_microorganisms("B_KLBSL_PNE")
|
|
#'
|
|
#' library(dplyr)
|
|
#' septic_patients %>% left_join_microorganisms()
|
|
#'
|
|
#' df <- data.frame(date = seq(from = as.Date("2018-01-01"),
|
|
#' to = as.Date("2018-01-07"),
|
|
#' by = 1),
|
|
#' bacteria = as.mo(c("S. aureus", "MRSA", "MSSA", "STAAUR",
|
|
#' "E. coli", "E. coli", "E. coli")),
|
|
#' stringsAsFactors = FALSE)
|
|
#' colnames(df)
|
|
#' df_joined <- left_join_microorganisms(df, "bacteria")
|
|
#' colnames(df_joined)
|
|
inner_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
|
|
checked <- joins_check_df(x, by)
|
|
x <- checked$x
|
|
by <- checked$by
|
|
join <- suppressWarnings(
|
|
dplyr::inner_join(x = x, y = AMR::microorganisms, by = by, suffix = suffix, ...)
|
|
)
|
|
if (nrow(join) > nrow(x)) {
|
|
warning('The newly joined tbl contains ', nrow(join) - nrow(x), ' rows more that its original.')
|
|
}
|
|
join
|
|
}
|
|
|
|
#' @rdname join
|
|
#' @export
|
|
left_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
|
|
checked <- joins_check_df(x, by)
|
|
x <- checked$x
|
|
by <- checked$by
|
|
join <- suppressWarnings(
|
|
dplyr::left_join(x = x, y = AMR::microorganisms, by = by, suffix = suffix, ...)
|
|
)
|
|
if (nrow(join) > nrow(x)) {
|
|
warning('The newly joined tbl contains ', nrow(join) - nrow(x), ' rows more that its original.')
|
|
}
|
|
join
|
|
}
|
|
|
|
#' @rdname join
|
|
#' @export
|
|
right_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
|
|
checked <- joins_check_df(x, by)
|
|
x <- checked$x
|
|
by <- checked$by
|
|
join <- suppressWarnings(
|
|
dplyr::right_join(x = x, y = AMR::microorganisms, by = by, suffix = suffix, ...)
|
|
)
|
|
if (nrow(join) > nrow(x)) {
|
|
warning('The newly joined tbl contains ', nrow(join) - nrow(x), ' rows more that its original.')
|
|
}
|
|
join
|
|
}
|
|
|
|
#' @rdname join
|
|
#' @export
|
|
full_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
|
|
checked <- joins_check_df(x, by)
|
|
x <- checked$x
|
|
by <- checked$by
|
|
join <- suppressWarnings(
|
|
dplyr::full_join(x = x, y = AMR::microorganisms, by = by, suffix = suffix, ...)
|
|
)
|
|
if (nrow(join) > nrow(x)) {
|
|
warning('The newly joined tbl contains ', nrow(join) - nrow(x), ' rows more that its original.')
|
|
}
|
|
join
|
|
}
|
|
|
|
#' @rdname join
|
|
#' @export
|
|
semi_join_microorganisms <- function(x, by = NULL, ...) {
|
|
checked <- joins_check_df(x, by)
|
|
x <- checked$x
|
|
by <- checked$by
|
|
suppressWarnings(
|
|
dplyr::semi_join(x = x, y = AMR::microorganisms, by = by, ...)
|
|
)
|
|
}
|
|
|
|
#' @rdname join
|
|
#' @export
|
|
anti_join_microorganisms <- function(x, by = NULL, ...) {
|
|
checked <- joins_check_df(x, by)
|
|
x <- checked$x
|
|
by <- checked$by
|
|
suppressWarnings(
|
|
dplyr::anti_join(x = x, y = AMR::microorganisms, by = by, ...)
|
|
)
|
|
}
|
|
|
|
joins_check_df <- function(x, by) {
|
|
if (!any(class(x) %in% c("data.frame", "matrix"))) {
|
|
x <- data.frame(mo = as.character(x), stringsAsFactors = FALSE)
|
|
if (is.null(by)) {
|
|
by <- "mo"
|
|
}
|
|
}
|
|
if (is.null(by)) {
|
|
# search for column with class `mo` and return first one found
|
|
by <- colnames(x)[lapply(x, is.mo) == TRUE][1]
|
|
if (is.na(by)) {
|
|
if ("mo" %in% colnames(x)) {
|
|
by <- "mo"
|
|
} else {
|
|
stop("Cannot join - no column found with name or class `mo`.", call. = FALSE)
|
|
}
|
|
}
|
|
message('Joining, by = "', by, '"') # message same as dplyr::join functions
|
|
}
|
|
if (is.null(names(by))) {
|
|
joinby <- colnames(AMR::microorganisms)[1]
|
|
names(joinby) <- by
|
|
} else {
|
|
joinby <- by
|
|
}
|
|
list(x = x,
|
|
by = joinby)
|
|
}
|