mirror of
https://github.com/msberends/AMR.git
synced 2024-12-26 21:26:12 +01:00
99 lines
3.2 KiB
R
99 lines
3.2 KiB
R
|
#' Join van tabel en \code{bactlist}
|
||
|
|
#'
|
||
|
|
#' Join the list of microorganisms \code{\link{bactlist}} easily to an existing table.
|
||
|
|
#' @rdname join
|
||
|
|
#' @name join
|
||
|
|
#' @aliases join inner_join
|
||
|
|
#' @param x existing table to join
|
||
|
|
#' @param 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")})
|
||
|
|
#' @param ... other parameters to pass trhough to \code{dplyr::\link[dplyr]{join}}.
|
||
|
|
#' @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.
|
||
|
|
#' @export
|
||
|
|
inner_join_bactlist <- function(x, by = 'bactid', ...) {
|
||
|
|
# no name set to `by` parameter
|
||
|
|
if (is.null(names(by))) {
|
||
|
|
joinby <- colnames(AMR::bactlist)[1]
|
||
|
|
names(joinby) <- by
|
||
|
|
} else {
|
||
|
|
joinby <- by
|
||
|
|
}
|
||
|
|
join <- dplyr::inner_join(x = x, y = AMR::bactlist, by = joinby, suffix = c("2", ""), ...)
|
||
|
|
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_bactlist <- function(x, by = 'bacteriecode', ...) {
|
||
|
|
# no name set to `by` parameter
|
||
|
|
if (is.null(names(by))) {
|
||
|
|
joinby <- colnames(AMR::bactlist)[1]
|
||
|
|
names(joinby) <- by
|
||
|
|
} else {
|
||
|
|
joinby <- by
|
||
|
|
}
|
||
|
|
join <- dplyr::left_join(x = x, y = AMR::bactlist, by = joinby, suffix = c("2", ""), ...)
|
||
|
|
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_bactlist <- function(x, by = 'bacteriecode', ...) {
|
||
|
|
# no name set to `by` parameter
|
||
|
|
if (is.null(names(by))) {
|
||
|
|
joinby <- colnames(AMR::bactlist)[1]
|
||
|
|
names(joinby) <- by
|
||
|
|
} else {
|
||
|
|
joinby <- by
|
||
|
|
}
|
||
|
|
join <- dplyr::right_join(x = x, y = AMR::bactlist, by = joinby, suffix = c("2", ""), ...)
|
||
|
|
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_bactlist <- function(x, by = 'bacteriecode', ...) {
|
||
|
|
# no name set to `by` parameter
|
||
|
|
if (is.null(names(by))) {
|
||
|
|
joinby <- colnames(AMR::bactlist)[1]
|
||
|
|
names(joinby) <- by
|
||
|
|
} else {
|
||
|
|
joinby <- by
|
||
|
|
}
|
||
|
|
dplyr::full_join(x = x, y = AMR::bactlist, by = joinby, suffix = c("2", ""), ...)
|
||
|
|
}
|
||
|
|
|
||
|
|
#' @rdname join
|
||
|
|
#' @export
|
||
|
|
semi_join_bactlist <- function(x, by = 'bacteriecode', ...) {
|
||
|
|
# no name set to `by` parameter
|
||
|
|
if (is.null(names(by))) {
|
||
|
|
joinby <- colnames(AMR::bactlist)[1]
|
||
|
|
names(joinby) <- by
|
||
|
|
} else {
|
||
|
|
joinby <- by
|
||
|
|
}
|
||
|
|
dplyr::semi_join(x = x, y = AMR::bactlist, by = joinby, ...)
|
||
|
|
}
|
||
|
|
|
||
|
|
#' @rdname join
|
||
|
|
#' @export
|
||
|
|
anti_join_bactlist <- function(x, by = 'bacteriecode', ...) {
|
||
|
|
# no name set to `by` parameter
|
||
|
|
if (is.null(names(by))) {
|
||
|
|
joinby <- colnames(AMR::bactlist)[1]
|
||
|
|
names(joinby) <- by
|
||
|
|
} else {
|
||
|
|
joinby <- by
|
||
|
|
}
|
||
|
|
dplyr::anti_join(x = x, y = AMR::bactlist, by = joinby, ...)
|
||
|
|
}
|