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(v1.3.0.9022) mo_matching_score(), poorman update, as.rsi() fix

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dr. M.S. (Matthijs) Berends
2020-09-18 16:05:53 +02:00
parent 89401ede9f
commit 4e40e42011
138 changed files with 2923 additions and 1472 deletions
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14
R/join_microorganisms.R
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@ -30,7 +30,7 @@
#' @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$mo` (like `by = "bacteria_id"`), or another column in [microorganisms] (but then it should be named, like `by = c("my_genus_species" = "fullname")`)
#' @param suffix if there are non-joined duplicate variables in `x` and `y`, these suffixes will be added to the output to disambiguate them. Should be a character vector of length 2.
#' @param ... ignored
#' @details **Note:** As opposed to the `join()` functions of `dplyr`, [`character`] vectors are supported and at default existing columns will get a suffix `"2"` and the newly joined columns will not get a suffix.
#' @details **Note:** As opposed to the `join()` functions of `dplyr`, [character] vectors are supported and at default existing columns will get a suffix `"2"` and the newly joined columns will not get a suffix.
#'
#' These functions rely on [merge()], a base R function to do joins.
#' @inheritSection AMR Read more on our website!
@ -61,7 +61,7 @@ inner_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
x <- checked$x
by <- checked$by
join <- suppressWarnings(
inner_join(x = x, y = microorganisms, by = by, suffix = suffix, ...)
pm_inner_join(x = x, y = microorganisms, by = by, suffix = suffix, ...)
)
if (NROW(join) > NROW(x)) {
warning("The newly joined tbl contains ", nrow(join) - nrow(x), " rows more that its original.")
@ -80,7 +80,7 @@ left_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
x <- checked$x
by <- checked$by
join <- suppressWarnings(
left_join(x = x, y = microorganisms, by = by, suffix = suffix, ...)
pm_left_join(x = x, y = microorganisms, by = by, suffix = suffix, ...)
)
if (NROW(join) > NROW(x)) {
warning("The newly joined tbl contains ", nrow(join) - nrow(x), " rows more that its original.")
@ -99,7 +99,7 @@ right_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
x <- checked$x
by <- checked$by
join <- suppressWarnings(
right_join(x = x, y = microorganisms, by = by, suffix = suffix, ...)
pm_right_join(x = x, y = microorganisms, by = by, suffix = suffix, ...)
)
if (NROW(join) > NROW(x)) {
warning("The newly joined tbl contains ", nrow(join) - nrow(x), " rows more that its original.")
@ -118,7 +118,7 @@ full_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
x <- checked$x
by <- checked$by
join <- suppressWarnings(
full_join(x = x, y = microorganisms, by = by, suffix = suffix, ...)
pm_full_join(x = x, y = microorganisms, by = by, suffix = suffix, ...)
)
if (NROW(join) > NROW(x)) {
warning("The newly joined tbl contains ", nrow(join) - nrow(x), " rows more that its original.")
@ -137,7 +137,7 @@ semi_join_microorganisms <- function(x, by = NULL, ...) {
x <- checked$x
by <- checked$by
join <- suppressWarnings(
semi_join(x = x, y = microorganisms, by = by, ...)
pm_semi_join(x = x, y = microorganisms, by = by, ...)
)
class(join) <- x_class
join
@ -153,7 +153,7 @@ anti_join_microorganisms <- function(x, by = NULL, ...) {
x <- checked$x
by <- checked$by
join <- suppressWarnings(
anti_join(x = x, y = microorganisms, by = by, ...)
pm_anti_join(x = x, y = microorganisms, by = by, ...)
)
class(join) <- x_class
join