mirror of
https://github.com/msberends/AMR.git
synced 2024-12-25 20:06:12 +01:00
287 lines
11 KiB
R
Executable File
287 lines
11 KiB
R
Executable File
# ==================================================================== #
|
|
# TITLE #
|
|
# Antimicrobial Resistance (AMR) Analysis for R #
|
|
# #
|
|
# SOURCE #
|
|
# https://github.com/msberends/AMR #
|
|
# #
|
|
# LICENCE #
|
|
# (c) 2018-2021 Berends MS, Luz CF et al. #
|
|
# Developed at the University of Groningen, the Netherlands, in #
|
|
# collaboration with non-profit organisations Certe Medical #
|
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
|
# #
|
|
# 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. #
|
|
# We created this package for both routine data analysis and academic #
|
|
# research and it was publicly released in the hope that it will be #
|
|
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
|
|
# #
|
|
# Visit our website for the full manual and a complete tutorial about #
|
|
# how to conduct AMR analysis: https://msberends.github.io/AMR/ #
|
|
# ==================================================================== #
|
|
|
|
#' Join [microorganisms] to a data set
|
|
#'
|
|
#' Join the data set [microorganisms] easily to an existing table or character vector.
|
|
#' @inheritSection lifecycle Stable lifecycle
|
|
#' @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 [`mo`] (created with [as.mo()]) or will be `"mo"` if that column name exists in `x`, could otherwise be a column name of `x` with values that exist in `microorganisms$mo` (such as `by = "bacteria_id"`), or another column in [microorganisms] (but then it should be named, like `by = c("bacteria_id" = "fullname")`)
|
|
#' @param suffix if there are non-joined duplicate variables in `x` and `y`, these suffixes will be added to the output to disambiguate them. Should be a character vector of length 2.
|
|
#' @param ... ignored
|
|
#' @details **Note:** As opposed to the `join()` functions of `dplyr`, [character] vectors are supported and at default existing columns will get a suffix `"2"` and the newly joined columns will not get a suffix.
|
|
#'
|
|
#' If the `dplyr` package is installed, their join functions will be used. Otherwise, the much slower [merge()] function from base R will be used.
|
|
#' @inheritSection AMR Read more on our website!
|
|
#' @export
|
|
#' @examples
|
|
#' left_join_microorganisms(as.mo("K. pneumoniae"))
|
|
#' left_join_microorganisms("B_KLBSL_PNE")
|
|
#'
|
|
#' \donttest{
|
|
#' if (require("dplyr")) {
|
|
#' example_isolates %>%
|
|
#' left_join_microorganisms() %>%
|
|
#' colnames()
|
|
#'
|
|
#' df <- data.frame(date = seq(from = as.Date("2018-01-01"),
|
|
#' to = as.Date("2018-01-07"),
|
|
#' by = 1),
|
|
#' bacteria = as.mo(c("S. aureus", "MRSA", "MSSA", "STAAUR",
|
|
#' "E. coli", "E. coli", "E. coli")),
|
|
#' stringsAsFactors = FALSE)
|
|
#' colnames(df)
|
|
#' df_joined <- left_join_microorganisms(df, "bacteria")
|
|
#' colnames(df_joined)
|
|
#' }
|
|
#' }
|
|
inner_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
|
|
meet_criteria(x, allow_class = c("data.frame", "character"))
|
|
meet_criteria(by, allow_class = "character", allow_NULL = TRUE)
|
|
meet_criteria(suffix, allow_class = "character", has_length = 2)
|
|
|
|
check_dataset_integrity()
|
|
x <- check_groups_before_join(x, "inner_join_microorganisms")
|
|
checked <- joins_check_df(x, by)
|
|
x_class <- get_prejoined_class(x)
|
|
x <- checked$x
|
|
by <- checked$by
|
|
# use dplyr if available - it's much faster
|
|
dplyr_inner <- import_fn("inner_join", "dplyr", error_on_fail = FALSE)
|
|
if (!is.null(dplyr_inner)) {
|
|
join <- suppressWarnings(
|
|
dplyr_inner(x = x, y = microorganisms, by = by, suffix = suffix, ...)
|
|
)
|
|
} else {
|
|
join <- suppressWarnings(
|
|
pm_inner_join(x = x, y = microorganisms, by = by, suffix = suffix, ...)
|
|
)
|
|
}
|
|
if (NROW(join) > NROW(x)) {
|
|
warning_("The newly joined tbl contains ", nrow(join) - nrow(x), " rows more that its original.")
|
|
}
|
|
class(join) <- x_class
|
|
join
|
|
}
|
|
|
|
#' @rdname join
|
|
#' @export
|
|
left_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
|
|
meet_criteria(x, allow_class = c("data.frame", "character"))
|
|
meet_criteria(by, allow_class = "character", allow_NULL = TRUE)
|
|
meet_criteria(suffix, allow_class = "character", has_length = 2)
|
|
|
|
check_dataset_integrity()
|
|
x <- check_groups_before_join(x, "left_join_microorganisms")
|
|
checked <- joins_check_df(x, by)
|
|
x_class <- get_prejoined_class(x)
|
|
x <- checked$x
|
|
by <- checked$by
|
|
# use dplyr if available - it's much faster
|
|
dplyr_left <- import_fn("left_join", "dplyr", error_on_fail = FALSE)
|
|
if (!is.null(dplyr_left)) {
|
|
join <- suppressWarnings(
|
|
dplyr_left(x = x, y = microorganisms, by = by, suffix = suffix, ...)
|
|
)
|
|
} else {
|
|
join <- suppressWarnings(
|
|
pm_left_join(x = x, y = microorganisms, by = by, suffix = suffix, ...)
|
|
)
|
|
}
|
|
if (NROW(join) > NROW(x)) {
|
|
warning_("The newly joined tbl contains ", nrow(join) - nrow(x), " rows more that its original.")
|
|
}
|
|
class(join) <- x_class
|
|
join
|
|
}
|
|
|
|
#' @rdname join
|
|
#' @export
|
|
right_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
|
|
meet_criteria(x, allow_class = c("data.frame", "character"))
|
|
meet_criteria(by, allow_class = "character", allow_NULL = TRUE)
|
|
meet_criteria(suffix, allow_class = "character", has_length = 2)
|
|
|
|
check_dataset_integrity()
|
|
x <- check_groups_before_join(x, "right_join_microorganisms")
|
|
checked <- joins_check_df(x, by)
|
|
x_class <- get_prejoined_class(x)
|
|
x <- checked$x
|
|
by <- checked$by
|
|
# use dplyr if available - it's much faster
|
|
dplyr_right <- import_fn("right_join", "dplyr", error_on_fail = FALSE)
|
|
if (!is.null(dplyr_right)) {
|
|
join <- suppressWarnings(
|
|
dplyr_right(x = x, y = microorganisms, by = by, suffix = suffix, ...)
|
|
)
|
|
} else {
|
|
join <- suppressWarnings(
|
|
pm_right_join(x = x, y = microorganisms, by = by, suffix = suffix, ...)
|
|
)
|
|
}
|
|
if (NROW(join) > NROW(x)) {
|
|
warning_("The newly joined tbl contains ", nrow(join) - nrow(x), " rows more that its original.")
|
|
}
|
|
class(join) <- x_class
|
|
join
|
|
}
|
|
|
|
#' @rdname join
|
|
#' @export
|
|
full_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
|
|
meet_criteria(x, allow_class = c("data.frame", "character"))
|
|
meet_criteria(by, allow_class = "character", allow_NULL = TRUE)
|
|
meet_criteria(suffix, allow_class = "character", has_length = 2)
|
|
|
|
check_dataset_integrity()
|
|
x <- check_groups_before_join(x, "full_join_microorganisms")
|
|
checked <- joins_check_df(x, by)
|
|
x_class <- get_prejoined_class(x)
|
|
x <- checked$x
|
|
by <- checked$by
|
|
# use dplyr if available - it's much faster
|
|
dplyr_full <- import_fn("full_join", "dplyr", error_on_fail = FALSE)
|
|
if (!is.null(dplyr_full)) {
|
|
join <- suppressWarnings(
|
|
dplyr_full(x = x, y = microorganisms, by = by, suffix = suffix, ...)
|
|
)
|
|
} else {
|
|
join <- suppressWarnings(
|
|
pm_full_join(x = x, y = microorganisms, by = by, suffix = suffix, ...)
|
|
)
|
|
}
|
|
if (NROW(join) > NROW(x)) {
|
|
warning_("The newly joined tbl contains ", nrow(join) - nrow(x), " rows more that its original.")
|
|
}
|
|
class(join) <- x_class
|
|
join
|
|
}
|
|
|
|
#' @rdname join
|
|
#' @export
|
|
semi_join_microorganisms <- function(x, by = NULL, ...) {
|
|
meet_criteria(x, allow_class = c("data.frame", "character"))
|
|
meet_criteria(by, allow_class = "character", allow_NULL = TRUE)
|
|
|
|
check_dataset_integrity()
|
|
x <- check_groups_before_join(x, "semi_join_microorganisms")
|
|
x_class <- get_prejoined_class(x)
|
|
checked <- joins_check_df(x, by)
|
|
x <- checked$x
|
|
by <- checked$by
|
|
# use dplyr if available - it's much faster
|
|
dplyr_semi <- import_fn("semi_join", "dplyr", error_on_fail = FALSE)
|
|
if (!is.null(dplyr_semi)) {
|
|
join <- suppressWarnings(
|
|
dplyr_semi(x = x, y = microorganisms, by = by, ...)
|
|
)
|
|
} else {
|
|
join <- suppressWarnings(
|
|
pm_semi_join(x = x, y = microorganisms, by = by, ...)
|
|
)
|
|
}
|
|
class(join) <- x_class
|
|
join
|
|
}
|
|
|
|
#' @rdname join
|
|
#' @export
|
|
anti_join_microorganisms <- function(x, by = NULL, ...) {
|
|
meet_criteria(x, allow_class = c("data.frame", "character"))
|
|
meet_criteria(by, allow_class = "character", allow_NULL = TRUE)
|
|
|
|
check_dataset_integrity()
|
|
x <- check_groups_before_join(x, "anti_join_microorganisms")
|
|
checked <- joins_check_df(x, by)
|
|
x_class <- get_prejoined_class(x)
|
|
x <- checked$x
|
|
by <- checked$by
|
|
# use dplyr if available - it's much faster
|
|
dplyr_anti <- import_fn("anti_join", "dplyr", error_on_fail = FALSE)
|
|
if (!is.null(dplyr_anti)) {
|
|
join <- suppressWarnings(
|
|
dplyr_anti(x = x, y = microorganisms, by = by, ...)
|
|
)
|
|
} else {
|
|
join <- suppressWarnings(
|
|
pm_anti_join(x = x, y = microorganisms, by = by, ...)
|
|
)
|
|
}
|
|
class(join) <- x_class
|
|
join
|
|
}
|
|
|
|
joins_check_df <- function(x, by) {
|
|
if (!any(class(x) %in% c("data.frame", "matrix"))) {
|
|
x <- data.frame(mo = as.mo(x), stringsAsFactors = FALSE)
|
|
if (is.null(by)) {
|
|
by <- "mo"
|
|
}
|
|
}
|
|
x <- as.data.frame(x, stringsAsFactors = FALSE)
|
|
if (is.null(by)) {
|
|
# search for column with class `mo` and return first one found
|
|
by <- colnames(x)[lapply(x, is.mo) == TRUE][1]
|
|
if (is.na(by)) {
|
|
if ("mo" %in% colnames(x)) {
|
|
by <- "mo"
|
|
x[, "mo"] <- as.mo(x[, "mo"])
|
|
} else {
|
|
stop("Cannot join - no column found with name 'mo' or with class <mo>.", call. = FALSE)
|
|
}
|
|
}
|
|
message_('Joining, by = "', by, '"', add_fn = font_black, as_note = FALSE) # message same as dplyr::join functions
|
|
}
|
|
if (is.null(names(by))) {
|
|
joinby <- colnames(microorganisms)[1]
|
|
names(joinby) <- by
|
|
} else {
|
|
joinby <- by
|
|
}
|
|
list(x = x,
|
|
by = joinby)
|
|
}
|
|
|
|
get_prejoined_class <- function(x) {
|
|
if (is.data.frame(x)) {
|
|
class(x)
|
|
} else {
|
|
"data.frame"
|
|
}
|
|
}
|
|
|
|
check_groups_before_join <- function(x, fn) {
|
|
if (is.data.frame(x) && !is.null(attributes(x)$groups)) {
|
|
x <- pm_ungroup(x)
|
|
attr(x, "groups") <- NULL
|
|
class(x) <- class(x)[!class(x) %like% "group"]
|
|
warning_("Groups are dropped, since the ", fn, "() function relies on merge() from base R.", call = FALSE)
|
|
}
|
|
x
|
|
}
|