mirror of https://github.com/msberends/AMR.git
287 lines
11 KiB
R
Executable File
287 lines
11 KiB
R
Executable File
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis for R #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2021 Berends MS, Luz CF et al. #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# #
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# Visit our website for the full manual and a complete tutorial about #
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# how to conduct AMR analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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#' Join [microorganisms] to a Data Set
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#'
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#' Join the data set [microorganisms] easily to an existing table or character vector.
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#' @inheritSection lifecycle Stable Lifecycle
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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 [`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")`)
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#' @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.
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#' @param ... ignored
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#' @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.
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#'
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#' If the `dplyr` package is installed, their join functions will be used. Otherwise, the much slower [merge()] function from base R will be used.
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#' @inheritSection AMR Read more on Our Website!
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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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#' \donttest{
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#' if (require("dplyr")) {
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#' example_isolates %>%
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#' left_join_microorganisms() %>%
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#' colnames()
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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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#' }
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#' }
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inner_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
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meet_criteria(x, allow_class = c("data.frame", "character"))
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meet_criteria(by, allow_class = "character", allow_NULL = TRUE)
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meet_criteria(suffix, allow_class = "character", has_length = 2)
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check_dataset_integrity()
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x <- check_groups_before_join(x, "inner_join_microorganisms")
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checked <- joins_check_df(x, by)
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x_class <- get_prejoined_class(x)
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x <- checked$x
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by <- checked$by
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# use dplyr if available - it's much faster
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dplyr_inner <- import_fn("inner_join", "dplyr", error_on_fail = FALSE)
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if (!is.null(dplyr_inner)) {
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join <- suppressWarnings(
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dplyr_inner(x = x, y = microorganisms, by = by, suffix = suffix, ...)
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)
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} else {
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join <- suppressWarnings(
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pm_inner_join(x = x, y = microorganisms, by = by, suffix = suffix, ...)
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)
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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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class(join) <- x_class
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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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meet_criteria(x, allow_class = c("data.frame", "character"))
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meet_criteria(by, allow_class = "character", allow_NULL = TRUE)
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meet_criteria(suffix, allow_class = "character", has_length = 2)
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check_dataset_integrity()
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x <- check_groups_before_join(x, "left_join_microorganisms")
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checked <- joins_check_df(x, by)
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x_class <- get_prejoined_class(x)
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x <- checked$x
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by <- checked$by
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# use dplyr if available - it's much faster
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dplyr_left <- import_fn("left_join", "dplyr", error_on_fail = FALSE)
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if (!is.null(dplyr_left)) {
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join <- suppressWarnings(
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dplyr_left(x = x, y = microorganisms, by = by, suffix = suffix, ...)
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)
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} else {
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join <- suppressWarnings(
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pm_left_join(x = x, y = microorganisms, by = by, suffix = suffix, ...)
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)
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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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class(join) <- x_class
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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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meet_criteria(x, allow_class = c("data.frame", "character"))
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meet_criteria(by, allow_class = "character", allow_NULL = TRUE)
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meet_criteria(suffix, allow_class = "character", has_length = 2)
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check_dataset_integrity()
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x <- check_groups_before_join(x, "right_join_microorganisms")
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checked <- joins_check_df(x, by)
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x_class <- get_prejoined_class(x)
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x <- checked$x
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by <- checked$by
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# use dplyr if available - it's much faster
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dplyr_right <- import_fn("right_join", "dplyr", error_on_fail = FALSE)
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if (!is.null(dplyr_right)) {
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join <- suppressWarnings(
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dplyr_right(x = x, y = microorganisms, by = by, suffix = suffix, ...)
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)
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} else {
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join <- suppressWarnings(
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pm_right_join(x = x, y = microorganisms, by = by, suffix = suffix, ...)
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)
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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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class(join) <- x_class
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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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meet_criteria(x, allow_class = c("data.frame", "character"))
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meet_criteria(by, allow_class = "character", allow_NULL = TRUE)
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meet_criteria(suffix, allow_class = "character", has_length = 2)
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check_dataset_integrity()
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x <- check_groups_before_join(x, "full_join_microorganisms")
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checked <- joins_check_df(x, by)
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x_class <- get_prejoined_class(x)
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x <- checked$x
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by <- checked$by
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# use dplyr if available - it's much faster
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dplyr_full <- import_fn("full_join", "dplyr", error_on_fail = FALSE)
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if (!is.null(dplyr_full)) {
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join <- suppressWarnings(
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dplyr_full(x = x, y = microorganisms, by = by, suffix = suffix, ...)
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)
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} else {
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join <- suppressWarnings(
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pm_full_join(x = x, y = microorganisms, by = by, suffix = suffix, ...)
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)
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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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class(join) <- x_class
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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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meet_criteria(x, allow_class = c("data.frame", "character"))
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meet_criteria(by, allow_class = "character", allow_NULL = TRUE)
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check_dataset_integrity()
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x <- check_groups_before_join(x, "semi_join_microorganisms")
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x_class <- get_prejoined_class(x)
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checked <- joins_check_df(x, by)
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x <- checked$x
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by <- checked$by
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# use dplyr if available - it's much faster
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dplyr_semi <- import_fn("semi_join", "dplyr", error_on_fail = FALSE)
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if (!is.null(dplyr_semi)) {
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join <- suppressWarnings(
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dplyr_semi(x = x, y = microorganisms, by = by, ...)
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)
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} else {
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join <- suppressWarnings(
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pm_semi_join(x = x, y = microorganisms, by = by, ...)
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)
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}
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class(join) <- x_class
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join
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}
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#' @rdname join
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#' @export
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anti_join_microorganisms <- function(x, by = NULL, ...) {
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meet_criteria(x, allow_class = c("data.frame", "character"))
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meet_criteria(by, allow_class = "character", allow_NULL = TRUE)
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check_dataset_integrity()
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x <- check_groups_before_join(x, "anti_join_microorganisms")
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checked <- joins_check_df(x, by)
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x_class <- get_prejoined_class(x)
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x <- checked$x
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by <- checked$by
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# use dplyr if available - it's much faster
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dplyr_anti <- import_fn("anti_join", "dplyr", error_on_fail = FALSE)
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if (!is.null(dplyr_anti)) {
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join <- suppressWarnings(
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dplyr_anti(x = x, y = microorganisms, by = by, ...)
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)
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} else {
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join <- suppressWarnings(
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pm_anti_join(x = x, y = microorganisms, by = by, ...)
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)
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}
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class(join) <- x_class
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join
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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.mo(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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x <- as.data.frame(x, stringsAsFactors = FALSE)
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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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x[, "mo"] <- as.mo(x[, "mo"])
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} else {
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stop("Cannot join - no column found with name 'mo' or with class <mo>.", call. = FALSE)
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}
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}
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message_('Joining, by = "', by, '"', add_fn = font_black, as_note = FALSE) # 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(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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get_prejoined_class <- function(x) {
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if (is.data.frame(x)) {
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class(x)
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} else {
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"data.frame"
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}
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}
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check_groups_before_join <- function(x, fn) {
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if (is.data.frame(x) && !is.null(attributes(x)$groups)) {
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x <- pm_ungroup(x)
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attr(x, "groups") <- NULL
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class(x) <- class(x)[!class(x) %like% "group"]
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warning_("Groups are dropped, since the ", fn, "() function relies on merge() from base R.", call = FALSE)
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}
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x
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}
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