mirror of
https://github.com/msberends/AMR.git
synced 2025-11-04 09:14:01 +01:00
193 lines
8.3 KiB
R
Executable File
193 lines
8.3 KiB
R
Executable File
# ==================================================================== #
|
|
# TITLE: #
|
|
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
|
# #
|
|
# SOURCE CODE: #
|
|
# https://github.com/msberends/AMR #
|
|
# #
|
|
# PLEASE CITE THIS SOFTWARE AS: #
|
|
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
|
|
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
|
|
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
|
# https://doi.org/10.18637/jss.v104.i03 #
|
|
# #
|
|
# Developed at the University of Groningen and the University Medical #
|
|
# Center Groningen in The Netherlands, in collaboration with many #
|
|
# colleagues from around the world, see our website. #
|
|
# #
|
|
# 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
|
|
#'
|
|
#' Join the data set [microorganisms] easily to an existing data set or to a [character] vector.
|
|
#' @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.
|
|
#' @return a [data.frame]
|
|
#' @export
|
|
#' @examples
|
|
#' left_join_microorganisms(as.mo("K. pneumoniae"))
|
|
#' left_join_microorganisms("B_KLBSL_PNMN")
|
|
#'
|
|
#' 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)
|
|
#'
|
|
#' \donttest{
|
|
#' if (require("dplyr")) {
|
|
#' example_isolates %>%
|
|
#' left_join_microorganisms() %>%
|
|
#' colnames()
|
|
#' }
|
|
#' }
|
|
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, ...)
|
|
}
|
|
|
|
#' @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, ...)
|
|
}
|
|
|
|
#' @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, ...)
|
|
}
|
|
|
|
#' @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, ...)
|
|
}
|
|
|
|
#' @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, ...)
|
|
}
|
|
|
|
#' @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, ...) {
|
|
add_MO_lookup_to_AMR_env()
|
|
|
|
if (!is.data.frame(x)) {
|
|
if (pkg_is_available("tibble")) {
|
|
x <- import_fn("tibble", "tibble")(mo = x)
|
|
} else {
|
|
x <- data.frame(mo = x, stringsAsFactors = FALSE)
|
|
}
|
|
by <- "mo"
|
|
}
|
|
x.bak <- x
|
|
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% AMR_env$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])
|
|
}
|
|
|
|
if (is.null(names(by))) {
|
|
# will always be joined to microorganisms$mo, so add name to that
|
|
by <- stats::setNames("mo", by)
|
|
}
|
|
|
|
# use dplyr if available - it's much faster than poorman alternatives
|
|
dplyr_join <- import_fn(name = type, pkg = "dplyr", error_on_fail = FALSE)
|
|
if (!is.null(dplyr_join)) {
|
|
join_fn <- dplyr_join
|
|
} else {
|
|
# otherwise use poorman, see R/aa_helper_pm_functions.R
|
|
join_fn <- get(paste0("pm_", type), envir = asNamespace("AMR"))
|
|
}
|
|
MO_df <- AMR_env$MO_lookup[, colnames(AMR::microorganisms), drop = FALSE]
|
|
if (type %like% "full|left|right|inner") {
|
|
joined <- join_fn(x = x, y = MO_df, by = by, suffix = suffix, ...)
|
|
} else {
|
|
joined <- join_fn(x = x, y = MO_df, 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, "_microorganisms()`: the newly joined data set contains ", nrow(joined) - nrow(x), " rows more than the number of rows of `x`.")
|
|
}
|
|
|
|
as_original_data_class(joined, class(x.bak)) # will remove tibble groups
|
|
}
|