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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 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 data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
#' Join [microorganisms] to a Data Set
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#'
#' Join the data set [microorganisms] easily to an existing data set or to a [character] vector.
#' @inheritSection lifecycle Stable Lifecycle
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#' @rdname join
#' @name join
#' @aliases join inner_join
#' @param x existing data set to join, or [character] vector. In case of a [character] vector, the resulting [data.frame] will contain a column 'x' with these values.
#' @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, only in place to allow future extensions
#' @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()] and [interaction()] functions from base \R will be used.
#' @inheritSection AMR Read more on Our Website!
#' @return a [data.frame]
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#' @export
#' @examples
#' left_join_microorganisms(as.mo("K. pneumoniae"))
#' left_join_microorganisms("B_KLBSL_PNMN")
#'
#' \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)
join_microorganisms(type = "inner_join", x = x, by = by, suffix = suffix, ...)
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}
#' @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)
join_microorganisms(type = "left_join", x = x, by = by, suffix = suffix, ...)
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}
#' @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)
join_microorganisms(type = "right_join", x = x, by = by, suffix = suffix, ...)
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}
#' @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)
join_microorganisms(type = "full_join", x = x, by = by, suffix = suffix, ...)
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}
#' @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)
join_microorganisms(type = "semi_join", x = x, by = by, ...)
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}
#' @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)
join_microorganisms(type = "anti_join", x = x, by = by, ...)
}
join_microorganisms <- function(type, x, by, suffix, ...) {
check_dataset_integrity()
if (!is.data.frame(x)) {
x <- data.frame(mo = x, stringsAsFactors = FALSE)
by <- "mo"
}
if (is.null(by)) {
by <- search_type_in_df(x, "mo", info = FALSE)
if (is.null(by) && NCOL(x) == 1) {
by <- colnames(x)[1L]
} else {
stop_if(is.null(by), "no column with microorganism names or codes found, set this column with `by`", call = -2)
}
message_('Joining, by = "', by, '"', add_fn = font_black, as_note = FALSE) # message same as dplyr::join functions
}
if (!all(x[, by, drop = TRUE] %in% MO_lookup$mo, na.rm = TRUE)) {
x$join.mo <- as.mo(x[, by, drop = TRUE])
by <- c("join.mo" = "mo")
} else {
x[, by] <- as.mo(x[, by, drop = TRUE])
}
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if (is.null(names(by))) {
# will always be joined to microorganisms$mo, so add name to that
by <- stats::setNames("mo", by)
}
# use dplyr if available - it's much faster than poorman alternatives
dplyr_join <- import_fn(name = type, pkg = "dplyr", error_on_fail = FALSE)
if (!is.null(dplyr_join)) {
join_fn <- dplyr_join
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} else {
# otherwise use poorman, see R/aa_helper_pm_functions.R
join_fn <- get(paste0("pm_", type), envir = asNamespace("AMR"))
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}
if (type %like% "full|left|right|inner") {
joined <- join_fn(x = x, y = AMR::microorganisms, by = by, suffix = suffix, ...)
} else {
joined <- join_fn(x = x, y = AMR::microorganisms, by = by, ...)
}
if ("join.mo" %in% colnames(joined)) {
if ("mo" %in% colnames(joined)) {
ind_mo <- which(colnames(joined) %in% c("mo", "join.mo"))
colnames(joined)[ind_mo[1L]] <- paste0("mo", suffix[1L])
colnames(joined)[ind_mo[2L]] <- paste0("mo", suffix[2L])
} else {
colnames(joined)[colnames(joined) == "join.mo"] <- "mo"
}
}
if (type %like% "full|left|right|inner" && NROW(joined) > NROW(x)) {
warning_("in `", type, "_join()`: the newly joined data set contains ", nrow(joined) - nrow(x), " rows more than the number of rows of `x`.")
}
joined
}