P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-09 08:52:15 +02:00
Code Releases Activity

(v0.9.0.9023) EUCAST 2020 guidelines

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2020-02-14 19:54:13 +01:00
parent 5a98e6b777
commit 9b8b02960e
43 changed files with 16588 additions and 14564 deletions
Download Patch File Download Diff File Expand all files Collapse all files

14
R/join_microorganisms.R
View File

@ -54,7 +54,7 @@ inner_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
x <- checked$x
by <- checked$by
join <- suppressWarnings(
dplyr::inner_join(x = x, y = AMR::microorganisms, by = by, suffix = suffix, ...)
dplyr::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.")
@ -69,7 +69,7 @@ left_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
x <- checked$x
by <- checked$by
join <- suppressWarnings(
dplyr::left_join(x = x, y = AMR::microorganisms, by = by, suffix = suffix, ...)
dplyr::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.")
@ -84,7 +84,7 @@ right_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
x <- checked$x
by <- checked$by
join <- suppressWarnings(
dplyr::right_join(x = x, y = AMR::microorganisms, by = by, suffix = suffix, ...)
dplyr::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.")
@ -99,7 +99,7 @@ full_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
x <- checked$x
by <- checked$by
join <- suppressWarnings(
dplyr::full_join(x = x, y = AMR::microorganisms, by = by, suffix = suffix, ...)
dplyr::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.")
@ -114,7 +114,7 @@ semi_join_microorganisms <- function(x, by = NULL, ...) {
x <- checked$x
by <- checked$by
suppressWarnings(
dplyr::semi_join(x = x, y = AMR::microorganisms, by = by, ...)
dplyr::semi_join(x = x, y = microorganisms, by = by, ...)
)
}
@ -125,7 +125,7 @@ anti_join_microorganisms <- function(x, by = NULL, ...) {
x <- checked$x
by <- checked$by
suppressWarnings(
dplyr::anti_join(x = x, y = AMR::microorganisms, by = by, ...)
dplyr::anti_join(x = x, y = microorganisms, by = by, ...)
)
}
@ -149,7 +149,7 @@ joins_check_df <- function(x, by) {
message('Joining, by = "', by, '"') # message same as dplyr::join functions
}
if (is.null(names(by))) {
joinby <- colnames(AMR::microorganisms)[1]
joinby <- colnames(microorganisms)[1]
names(joinby) <- by
} else {
joinby <- by