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(v1.1.0.9004) lose dependencies

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dr. M.S. (Matthijs) Berends
2020-05-16 13:05:47 +02:00
parent 9fce546901
commit 7f3da74b17
111 changed files with 3211 additions and 2345 deletions
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20
R/join_microorganisms.R
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@ -19,7 +19,7 @@
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
#' Join a table with [microorganisms]
#' Join [microorganisms] to a data set
#'
#' Join the data set [microorganisms] easily to an existing table or character vector.
#' @inheritSection lifecycle Stable lifecycle
@ -30,13 +30,16 @@
#' @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$mo` (like `by = "bacteria_id"`), or another column in [microorganisms] (but then it should be named, like `by = c("my_genus_species" = "fullname")`)
#' @param suffix if there are non-joined duplicate variables in `x` and `y`, these suffixes will be added to the output to disambiguate them. Should be a character vector of length 2.
#' @param ... other parameters to pass on to [dplyr::join()]
#' @details **Note:** As opposed to the [dplyr::join()] functions of `dplyr`, [`character`] vectors are supported and at default existing columns will get a suffix `"2"` and the newly joined columns will not get a suffix. See [dplyr::join()] for more information.
#' @details **Note:** As opposed to the [join()] functions of `dplyr`, [`character`] vectors are supported and at default existing columns will get a suffix `"2"` and the newly joined columns will not get a suffix.
#'
#' These functions rely on [merge()], a base R function to do joins.
#' @inheritSection AMR Read more on our website!
#' @export
#' @examples
#' left_join_microorganisms(as.mo("K. pneumoniae"))
#' left_join_microorganisms("B_KLBSL_PNE")
#'
#' \dontrun{
#' library(dplyr)
#' example_isolates %>% left_join_microorganisms()
#'
@ -49,13 +52,14 @@
#' colnames(df)
#' df_joined <- left_join_microorganisms(df, "bacteria")
#' colnames(df_joined)
#' }
inner_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
check_dataset_integrity()
checked <- joins_check_df(x, by)
x <- checked$x
by <- checked$by
join <- suppressWarnings(
dplyr::inner_join(x = x, y = microorganisms, by = by, suffix = suffix, ...)
inner_join(x = x, y = microorganisms, by = by, suffix = suffix, ...)
)
if (NROW(join) > NROW(x)) {
warning("The newly joined tbl contains ", nrow(join) - nrow(x), " rows more that its original.")
@ -71,7 +75,7 @@ left_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
x <- checked$x
by <- checked$by
join <- suppressWarnings(
dplyr::left_join(x = x, y = microorganisms, by = by, suffix = suffix, ...)
left_join(x = x, y = microorganisms, by = by, suffix = suffix, ...)
)
if (NROW(join) > NROW(x)) {
warning("The newly joined tbl contains ", nrow(join) - nrow(x), " rows more that its original.")
@ -87,7 +91,7 @@ right_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
x <- checked$x
by <- checked$by
join <- suppressWarnings(
dplyr::right_join(x = x, y = microorganisms, by = by, suffix = suffix, ...)
right_join(x = x, y = microorganisms, by = by, suffix = suffix, ...)
)
if (NROW(join) > NROW(x)) {
warning("The newly joined tbl contains ", nrow(join) - nrow(x), " rows more that its original.")
@ -103,7 +107,7 @@ full_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
x <- checked$x
by <- checked$by
join <- suppressWarnings(
dplyr::full_join(x = x, y = microorganisms, by = by, suffix = suffix, ...)
full_join(x = x, y = microorganisms, by = by, suffix = suffix, ...)
)
if (NROW(join) > NROW(x)) {
warning("The newly joined tbl contains ", nrow(join) - nrow(x), " rows more that its original.")
@ -119,7 +123,7 @@ semi_join_microorganisms <- function(x, by = NULL, ...) {
x <- checked$x
by <- checked$by
suppressWarnings(
dplyr::semi_join(x = x, y = microorganisms, by = by, ...)
semi_join(x = x, y = microorganisms, by = by, ...)
)
}
@ -131,7 +135,7 @@ anti_join_microorganisms <- function(x, by = NULL, ...) {
x <- checked$x
by <- checked$by
suppressWarnings(
dplyr::anti_join(x = x, y = microorganisms, by = by, ...)
anti_join(x = x, y = microorganisms, by = by, ...)
)
}