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fixes

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2026-03-20 16:10:02 +01:00
parent 9f73571832
commit 92ae56eaaa
7 changed files with 20 additions and 22 deletions
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2
R/aa_helper_functions.R
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@@ -1061,7 +1061,7 @@ get_current_data <- function(arg_name, call) {
} else {
examples <- ""
}
stop_("this function must be used inside a {.pkg dplyr} verb or {.code data.frame} call",
stop_("this function must be used inside a {.pkg dplyr} verb or {.cls data.frame} call",
examples,
call = call
)

24
R/ab.R
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@@ -484,7 +484,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
}
message_(
"Antimicrobial translation was uncertain for ", examples,
". If required, use `add_custom_antimicrobials()` to add custom entries."
". If required, use {.help [{.fun add_custom_antimicrobials}](AMR::add_custom_antimicrobials)} to add custom entries."
)
}
}
@@ -556,21 +556,21 @@ print.ab <- function(x, ...) {
function_name <- attributes(x)$amr_selector
if (pkg_is_available("cli", min_version = "3.0.0")) {
cli::cli_inform(c(
"i" = paste0("This {.cls ab} vector was retrieved using {.fun ", function_name, "}, which should normally be used inside a {.pkg dplyr} verb or {.code data.frame} call, e.g.:"),
"*" = highlight_code(paste0("your_data %>% select(", function_name, "()")),
"*" = highlight_code(paste0("your_data %>% select(column_a, column_b, ", function_name, "()")),
"*" = highlight_code(paste0("your_data %>% filter(any(", function_name, "() == \"R\"))")),
"*" = highlight_code(paste0("your_data[, ", function_name, "()]")),
"*" = highlight_code(paste0("your_data[, c(\"column_a\", \"column_b\", ", function_name, "())]"))
"i" = paste0("This {.cls ab} vector was retrieved using {.fun ", function_name, "}, which should normally be used inside a {.pkg dplyr} verb or {.cls data.frame} call, e.g.:"),
paste0("\u00a0\u00a0", AMR_env$bullet_icon, " ", highlight_code(paste0("your_data %>% select(", function_name, "())"))),
paste0("\u00a0\u00a0", AMR_env$bullet_icon, " ", highlight_code(paste0("your_data %>% select(column_a, column_b, ", function_name, "())"))),
paste0("\u00a0\u00a0", AMR_env$bullet_icon, " ", highlight_code(paste0("your_data %>% filter(any(", function_name, "() == \"R\"))"))),
paste0("\u00a0\u00a0", AMR_env$bullet_icon, " ", highlight_code(paste0("your_data[, ", function_name, "()]"))),
paste0("\u00a0\u00a0", AMR_env$bullet_icon, " ", highlight_code(paste0("your_data[, c(\"column_a\", \"column_b\", ", function_name, "())]")))
))
} else {
message(word_wrap(paste0(
"This 'ab' vector was retrieved using `", function_name, "()`, which should normally be used inside a dplyr verb or data.frame call, e.g.:\n",
" ", AMR_env$bullet_icon, " your_data %>% select(", function_name, "())\n",
" ", AMR_env$bullet_icon, " your_data %>% select(column_a, column_b, ", function_name, "())\n",
" ", AMR_env$bullet_icon, " your_data %>% filter(any(", function_name, "() == \"R\"))\n",
" ", AMR_env$bullet_icon, " your_data[, ", function_name, "()]\n",
" ", AMR_env$bullet_icon, " your_data[, c(\"column_a\", \"column_b\", ", function_name, "())]"
"\u00a0\u00a0", AMR_env$bullet_icon, " your_data %>% select(", function_name, "())\n",
"\u00a0\u00a0", AMR_env$bullet_icon, " your_data %>% select(column_a, column_b, ", function_name, "())\n",
"\u00a0\u00a0", AMR_env$bullet_icon, " your_data %>% filter(any(", function_name, "() == \"R\"))\n",
"\u00a0\u00a0", AMR_env$bullet_icon, " your_data[, ", function_name, "()]\n",
"\u00a0\u00a0", AMR_env$bullet_icon, " your_data[, c(\"column_a\", \"column_b\", ", function_name, "())]"
), as_note = TRUE))
}
}

4
R/amr_selectors.R
View File

@@ -722,7 +722,7 @@ amr_select_exec <- function(function_name,
if (any(untreatable %in% names(ab_in_data))) {
if (message_not_thrown_before(function_name, "amr_class", "untreatable")) {
warning_(
"in `", function_name, "()`: some drugs were ignored since they cannot be used for treatment: ",
"in {.help [{.fun ", function_name, "}](AMR::", function_name, ")}: some drugs were ignored since they cannot be used for treatment: ",
vector_and(
ab_name(names(ab_in_data)[names(ab_in_data) %in% untreatable],
language = NULL,
@@ -797,7 +797,7 @@ amr_select_exec <- function(function_name,
if (only_treatable == TRUE) {
if (message_not_thrown_before(function_name, "amr_class", "untreatable")) {
message_(
"in `", function_name, "()`: ",
"in {.help [{.fun ", function_name, "}](AMR::", function_name, ")}: ",
vector_and(
paste0(
ab_name(abx[abx %in% untreatable],

4
R/custom_mdro_guideline.R
View File

@@ -235,9 +235,9 @@ print.custom_mdro_guideline <- function(x, ...) {
for (i in seq_len(length(x))) {
rule <- x[[i]]
rule$query <- format_custom_query_rule(rule$query)
cat(" ", i, ". ", font_bold("If "), font_blue(rule$query), font_bold(" then: "), font_red(rule$value), "\n", sep = "")
cat("\u00a0\u00a0", i, ". ", font_bold("If "), font_blue(rule$query), font_bold(" then: "), font_red(rule$value), "\n", sep = "")
}
cat(" ", i + 1, ". ", font_bold("Otherwise: "), font_red(paste0("Negative")), "\n", sep = "")
cat("\u00a0\u00a0", i + 1, ". ", font_bold("Otherwise: "), font_red(paste0("Negative")), "\n", sep = "")
cat("\nUnmatched rows will return ", font_red("NA"), ".\n", sep = "")
if (isTRUE(attributes(x)$as_factor)) {
cat("Results will be of class 'factor', with ordered levels: ", paste0(attributes(x)$values, collapse = " < "), "\n", sep = "")

4
R/mo.R
View File

@@ -977,8 +977,8 @@ print.mo_uncertainties <- function(x, n = 10, ...) {
out <- paste0(
paste0(
"", strrep(font_grey("-"), times = getOption("width", 100)), "\n",
'"', x[i, ]$original_input, '"',
"", strrep(font_grey("-"), times = getOption("width", 100) - 1), "\n",
"{.val ", x[i, ]$original_input, "}",
" -> ",
paste0(
font_bold(italicise(x[i, ]$fullname)),

2
R/sir.R
View File

@@ -1946,7 +1946,7 @@ as_sir_method <- function(method_short,
message_(notes[i], as_note = FALSE)
}
} else {
# message(word_wrap(" ", AMR_env$bullet_icon, " There were multiple notes. Print or View `sir_interpretation_history()` to examine them, or use `as.sir(..., verbose = TRUE)` next time to directly print them here.", add_fn = font_black))
# message(word_wrap("\u00a0\u00a0", AMR_env$bullet_icon, " There were multiple notes. Print or View `sir_interpretation_history()` to examine them, or use `as.sir(..., verbose = TRUE)` next time to directly print them here.", add_fn = font_black))
}
} else {
message(font_green_bg(" OK "))

2
tests/testthat/test-mo.R
View File

@@ -272,8 +272,6 @@ test_that("test-mo.R", {
)
x <- as.mo("Sta. aur")
# many hits
expect_output(print(mo_uncertainties()))
# no viruses
expect_equal(suppressWarnings(as.mo("Virus")), as.mo("UNKNOWN"))