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nope, but this might be

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dr. M.S. (Matthijs) Berends 2022-10-04 23:38:08 +02:00
parent aa06aad4ea
commit 4e9de9eb5d
5 changed files with 18 additions and 19 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 1.8.2.9028 Version: 1.8.2.9029
Date: 2022-10-04 Date: 2022-10-04
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR) Description: Functions to simplify and standardise antimicrobial resistance (AMR)

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 1.8.2.9028 # AMR 1.8.2.9029
This version will eventually become v2.0! We're happy to reach a new major milestone soon! This version will eventually become v2.0! We're happy to reach a new major milestone soon!

28
R/aa_helper_functions.R
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@ -1369,12 +1369,12 @@ trimws2 <- function(..., whitespace = "[\u0009\u000A\u000B\u000C\u000D\u0020\u00
# Faster data.table implementations ---- # Faster data.table implementations ----
match <- function(x, ...) { match <- function(x, table, ...) {
if (isTRUE(AMR_env$has_data.table) && is.character(x)) { if (isTRUE(AMR_env$has_data.table) && is.character(x) && is.character(table)) {
# data.table::chmatch() is 35% faster than base::match() for character # data.table::chmatch() is 35% faster than base::match() for character
getExportedValue(name = "chmatch", ns = asNamespace("data.table"))(x, ...) getExportedValue(name = "chmatch", ns = asNamespace("data.table"))(x, table, ...)
} else { } else {
base::match(x, ...) base::match(x, table, ...)
} }
} }
`%in%` <- function(x, table) { `%in%` <- function(x, table) {
@ -1490,7 +1490,16 @@ if (getRversion() < "3.5.0") {
isFALSE <- function(x) { isFALSE <- function(x) {
is.logical(x) && length(x) == 1L && !is.na(x) && !x is.logical(x) && length(x) == 1L && !is.na(x) && !x
} }
# trims() was introduced in 3.3.0, but its argument `whitespace` only in 3.5.0 }
if (getRversion() < "3.6.0") {
str2lang <- function(s) {
stopifnot(length(s) == 1L)
ex <- parse(text = s, keep.source = FALSE)
stopifnot(length(ex) == 1L)
ex[[1L]]
}
# trims() was introduced in 3.3.0, but its argument `whitespace` only in 3.6.0
trimws <- function(x, which = c("both", "left", "right"), whitespace = "[ \t\r\n]") { trimws <- function(x, which = c("both", "left", "right"), whitespace = "[ \t\r\n]") {
which <- match.arg(which) which <- match.arg(which)
mysub <- function(re, x) sub(re, "", x, perl = TRUE) mysub <- function(re, x) sub(re, "", x, perl = TRUE)
@ -1502,15 +1511,6 @@ if (getRversion() < "3.5.0") {
} }
} }
if (getRversion() < "3.6.0") {
str2lang <- function(s) {
stopifnot(length(s) == 1L)
ex <- parse(text = s, keep.source = FALSE)
stopifnot(length(ex) == 1L)
ex[[1L]]
}
}
if (getRversion() < "4.0.0") { if (getRversion() < "4.0.0") {
deparse1 <- function(expr, collapse = " ", width.cutoff = 500L, ...) { deparse1 <- function(expr, collapse = " ", width.cutoff = 500L, ...) {
paste(deparse(expr, width.cutoff, ...), collapse = collapse) paste(deparse(expr, width.cutoff, ...), collapse = collapse)

1
R/mo.R
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@ -826,7 +826,6 @@ print.mo_uncertainties <- function(x, ...) {
" -> ", " -> ",
paste0( paste0(
font_bold(font_italic(x[i, ]$fullname)), font_bold(font_italic(x[i, ]$fullname)),
ifelse(!is.na(x[i, ]$renamed_to), paste(", renamed to", font_italic(x[i, ]$renamed_to)), ""),
" (", x[i, ]$mo, ", ", score_set_colour(score_formatted, score), ")" " (", x[i, ]$mo, ", ", score_set_colour(score_formatted, score), ")"
) )
), ),

4
tests/tinytest.R
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@ -54,11 +54,11 @@ if (identical(Sys.getenv("R_RUN_TINYTEST"), "true")) {
} }
if (getRversion() < "3.5.0") { if (getRversion() < "3.5.0") {
isFALSE <- AMR:::isFALSE isFALSE <- AMR:::isFALSE
# trims() was introduced in 3.3.0, but its argument `whitespace` only in 3.5.0
trimws <- AMR:::trimws
} }
if (getRversion() < "3.6.0") { if (getRversion() < "3.6.0") {
str2lang <- AMR:::str2lang str2lang <- AMR:::str2lang
# trims() was introduced in 3.3.0, but its argument `whitespace` only in 3.6.0
trimws <- AMR:::trimws
} }
if (getRversion() < "4.0.0") { if (getRversion() < "4.0.0") {
deparse1 <- AMR:::deparse1 deparse1 <- AMR:::deparse1