mirror of https://github.com/msberends/AMR.git
155 lines
6.0 KiB
R
Executable File
155 lines
6.0 KiB
R
Executable File
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# AUTHORS #
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# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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# #
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# LICENCE #
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# This package is free software; you can redistribute it and/or modify #
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# it under the terms of the GNU General Public License version 2.0, #
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# as published by the Free Software Foundation. #
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# #
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# This R package is distributed in the hope that it will be useful, #
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# but WITHOUT ANY WARRANTY; without even the implied warranty of #
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
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# GNU General Public License version 2.0 for more details. #
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# ==================================================================== #
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#' Join a table with \code{microorganisms}
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#'
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#' Join the dataset \code{\link{microorganisms}} easily to an existing table or character vector.
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#' @rdname join
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#' @name join
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#' @aliases join inner_join
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#' @param x existing table to join, or character vector
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#' @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")})
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#' @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.
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#' @param ... other parameters to pass on to \code{dplyr::\link[dplyr]{join}}.
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#' @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.
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#' @export
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#' @examples
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#' left_join_microorganisms(as.mo("K. pneumoniae"))
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#' left_join_microorganisms("B_KLBSL_PNE")
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#'
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#' library(dplyr)
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#' septic_patients %>% left_join_microorganisms()
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#'
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#' df <- data.frame(date = seq(from = as.Date("2018-01-01"),
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#' to = as.Date("2018-01-07"),
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#' by = 1),
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#' bacteria = as.mo(c("S. aureus", "MRSA", "MSSA", "STAAUR",
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#' "E. coli", "E. coli", "E. coli")),
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#' stringsAsFactors = FALSE)
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#' colnames(df)
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#' df_joined <- left_join_microorganisms(df, "bacteria")
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#' colnames(df_joined)
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inner_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
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checked <- joins_check_df(x, by)
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x <- checked$x
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by <- checked$by
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join <- suppressWarnings(
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dplyr::inner_join(x = x, y = AMR::microorganisms, by = by, suffix = suffix, ...)
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)
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if (nrow(join) > nrow(x)) {
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warning('The newly joined tbl contains ', nrow(join) - nrow(x), ' rows more that its original.')
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}
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join
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}
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#' @rdname join
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#' @export
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left_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
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checked <- joins_check_df(x, by)
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x <- checked$x
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by <- checked$by
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join <- suppressWarnings(
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dplyr::left_join(x = x, y = AMR::microorganisms, by = by, suffix = suffix, ...)
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)
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if (nrow(join) > nrow(x)) {
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warning('The newly joined tbl contains ', nrow(join) - nrow(x), ' rows more that its original.')
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}
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join
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}
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#' @rdname join
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#' @export
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right_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
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checked <- joins_check_df(x, by)
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x <- checked$x
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by <- checked$by
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join <- suppressWarnings(
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dplyr::right_join(x = x, y = AMR::microorganisms, by = by, suffix = suffix, ...)
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)
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if (nrow(join) > nrow(x)) {
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warning('The newly joined tbl contains ', nrow(join) - nrow(x), ' rows more that its original.')
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}
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join
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}
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#' @rdname join
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#' @export
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full_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
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checked <- joins_check_df(x, by)
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x <- checked$x
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by <- checked$by
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join <- suppressWarnings(
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dplyr::full_join(x = x, y = AMR::microorganisms, by = by, suffix = suffix, ...)
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)
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if (nrow(join) > nrow(x)) {
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warning('The newly joined tbl contains ', nrow(join) - nrow(x), ' rows more that its original.')
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}
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join
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}
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#' @rdname join
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#' @export
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semi_join_microorganisms <- function(x, by = NULL, ...) {
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checked <- joins_check_df(x, by)
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x <- checked$x
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by <- checked$by
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suppressWarnings(
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dplyr::semi_join(x = x, y = AMR::microorganisms, by = by, ...)
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)
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}
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#' @rdname join
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#' @export
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anti_join_microorganisms <- function(x, by = NULL, ...) {
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checked <- joins_check_df(x, by)
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x <- checked$x
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by <- checked$by
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suppressWarnings(
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dplyr::anti_join(x = x, y = AMR::microorganisms, by = by, ...)
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)
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}
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joins_check_df <- function(x, by) {
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if (!any(class(x) %in% c("data.frame", "matrix"))) {
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x <- data.frame(mo = as.character(x), stringsAsFactors = FALSE)
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if (is.null(by)) {
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by <- "mo"
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}
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}
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if (is.null(by)) {
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# search for column with class `mo` and return first one found
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by <- colnames(x)[lapply(x, is.mo) == TRUE][1]
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if (is.na(by)) {
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if ("mo" %in% colnames(x)) {
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by <- "mo"
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} else {
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stop("Cannot join - no column found with name or class `mo`.", call. = FALSE)
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}
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}
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message('Joining, by = "', by, '"') # message same as dplyr::join functions
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}
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if (is.null(names(by))) {
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joinby <- colnames(AMR::microorganisms)[1]
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names(joinby) <- by
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} else {
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joinby <- by
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}
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list(x = x,
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by = joinby)
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}
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