AMR/R/join_microorganisms.R

# ==================================================================== #
# TITLE                                                                #
# Antimicrobial Resistance (AMR) Analysis                              #
#                                                                      #
# AUTHORS                                                              #
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)           #
#                                                                      #
# LICENCE                                                              #
# This package is free software; you can redistribute it and/or modify #
# it under the terms of the GNU General Public License version 2.0,    #
# as published by the Free Software Foundation.                        #
#                                                                      #
# This R package is distributed in the hope that it will be useful,    #
# but WITHOUT ANY WARRANTY; without even the implied warranty of       #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the        #
# GNU General Public License version 2.0 for more details.             #
# ==================================================================== #

#' Join a table with \code{microorganisms}
#'
#' Join the dataset \code{\link{microorganisms}} easily to an existing table or character vector.
#' @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 \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$mo} (like \code{by = "bacteria_id"}), or another column in \code{\link{microorganisms}} (but then it should be named, like \code{by = c("my_genus_species" = "fullname")})
#' @param suffix if there are non-joined duplicate variables in \code{x} and \code{y}, these suffixes will be added to the output to disambiguate them. Should be a character vector of length 2.
#' @param ... other parameters to pass on to \code{dplyr::\link[dplyr]{join}}.
#' @details \strong{Note:} As opposed to the \code{\link[dplyr]{join}} functions of \code{dplyr}, characters vectors are supported and at default existing columns will get a suffix \code{"2"} and the newly joined columns will not get a suffix. See \code{\link[dplyr]{join}} for more information.
#' @export
#' @examples
#' left_join_microorganisms(as.mo("K. pneumoniae"))
#' left_join_microorganisms("B_KLBSL_PNE")
#'
#' library(dplyr)
#' septic_patients %>% left_join_microorganisms()
#'
#' df <- data.frame(date = seq(from = as.Date("2018-01-01"),
#'                             to = as.Date("2018-01-07"),
#'                             by = 1),
#'                  bacteria = as.mo(c("S. aureus", "MRSA", "MSSA", "STAAUR",
#'                                     "E. coli", "E. coli", "E. coli")),
#'                  stringsAsFactors = FALSE)
#' colnames(df)
#' df_joined <- left_join_microorganisms(df, "bacteria")
#' colnames(df_joined)
inner_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
  checked <- joins_check_df(x, by)
  x <- checked$x
  by <- checked$by
  join <- suppressWarnings(
    dplyr::inner_join(x = x, y = AMR::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.')
  }
  join
}

#' @rdname join
#' @export
left_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
  checked <- joins_check_df(x, by)
  x <- checked$x
  by <- checked$by
  join <- suppressWarnings(
    dplyr::left_join(x = x, y = AMR::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.')
  }
  join
}

#' @rdname join
#' @export
right_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
  checked <- joins_check_df(x, by)
  x <- checked$x
  by <- checked$by
  join <- suppressWarnings(
    dplyr::right_join(x = x, y = AMR::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.')
  }
  join
}

#' @rdname join
#' @export
full_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
  checked <- joins_check_df(x, by)
  x <- checked$x
  by <- checked$by
  join <- suppressWarnings(
    dplyr::full_join(x = x, y = AMR::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.')
  }
  join
}

#' @rdname join
#' @export
semi_join_microorganisms <- function(x, by = NULL, ...) {
  checked <- joins_check_df(x, by)
  x <- checked$x
  by <- checked$by
  suppressWarnings(
    dplyr::semi_join(x = x, y = AMR::microorganisms, by = by, ...)
  )
}

#' @rdname join
#' @export
anti_join_microorganisms <- function(x, by = NULL, ...) {
  checked <- joins_check_df(x, by)
  x <- checked$x
  by <- checked$by
  suppressWarnings(
    dplyr::anti_join(x = x, y = AMR::microorganisms, by = by, ...)
  )
}

joins_check_df <- function(x, by) {
  if (!any(class(x) %in% c("data.frame", "matrix"))) {
    x <- data.frame(mo = as.character(x), stringsAsFactors = FALSE)
    if (is.null(by)) {
      by <- "mo"
    }
  }
  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"
      } else {
        stop("Cannot join - no column found with name or class  `mo`.", call. = FALSE)
      }
    }
    message('Joining, by = "', by, '"') # message same as dplyr::join functions
  }
  if (is.null(names(by))) {
    joinby <- colnames(AMR::microorganisms)[1]
    names(joinby) <- by
  } else {
    joinby <- by
  }
  list(x = x,
       by = joinby)
}