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Replace all "in \funcname()\:" with {.help [{.fun funcname}](AMR::funcname)}

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Converts all "in `funcname()`:" prefixes in warning_()/message_()/stop_()
calls to the full {.help} link format for clickable help in supported
terminals. Also fixes adjacent backtick argument names to {.arg}.

Files changed: ab.R, ab_property.R, av.R, av_property.R, antibiogram.R,
key_antimicrobials.R, mdro.R, mic.R, mo.R, plotting.R

https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
This commit is contained in:
Claude
2026-03-20 14:30:26 +00:00
parent d28671c34d
commit 9f73571832
12 changed files with 24 additions and 23 deletions
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2
DESCRIPTION
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@@ -1,5 +1,5 @@
Package: AMR
Version: 3.0.1.9038
Version: 3.0.1.9039
Date: 2026-03-19
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)

3
NEWS.md
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@@ -1,4 +1,4 @@
# AMR 3.0.1.9038
# AMR 3.0.1.9039
### New
* Integration with the **tidymodels** framework to allow seamless use of SIR, MIC and disk data in modelling pipelines via `recipes`
@@ -33,6 +33,7 @@
* Replaced all bare backtick-quoted text in `message_()`, `warning_()`, and `stop_()` calls with proper cli inline markup (`{.arg}`, `{.cls}`, `{.fun}`, `{.pkg}`, `{.code}`); rewrote `print.ab` to use a cli named-vector with `*` bullets and code highlighting when cli is available
* Added `format_inline_()` helper that formats a cli-markup string and returns it (rather than emitting it), using `cli::format_inline()` when available and `cli_to_plain()` otherwise; used this in `.onAttach` to replace the duplicated cli/non-cli startup message pattern
* All inline `{variable}` / `{expression}` in messaging calls are now pre-evaluated via `paste0()`, so users without cli or glue never see raw template syntax
* All `"in `funcname()`:"` patterns in `warning_()`/`message_()`/`stop_()` replaced with `{.help [{.fun funcname}](AMR::funcname)}` for clickable help links
* `mdro()` now infers resistance for a _missing_ base drug column from an _available_ corresponding drug+inhibitor combination showing resistance (e.g., piperacillin is absent but required, while piperacillin/tazobactam available and resistant). Can be set with the new argument `infer_from_combinations`, which defaults to `TRUE` (#209). Note that this can yield a higher MDRO detection (which is a good thing as it has become more reliable).
* `susceptibility()` and `resistance()` gained the argument `guideline`, which defaults to EUCAST, for interpreting the 'I' category correctly.
* Added to the `antimicrobials` data set: cefepime/taniborbactam (`FTA`), ceftibuten/avibactam (`CTA`), clorobiocin (`CLB`), kasugamycin (`KAS`), ostreogrycin (`OST`), taniborbactam (`TAN`), thiostrepton (`THS`), xeruborbactam (`XER`), and zorbamycin (`ZOR`)

4
R/ab.R
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@@ -445,7 +445,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
# take failed ATC codes apart from rest
if (length(x_unknown_ATCs) > 0 && fast_mode == FALSE) {
warning_(
"in `as.ab()`: these ATC codes are not (yet) in the antimicrobials data set: ",
"in {.help [{.fun as.ab}](AMR::as.ab)}: these ATC codes are not (yet) in the antimicrobials data set: ",
vector_and(x_unknown_ATCs), "."
)
}
@@ -459,7 +459,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
x_unknown <- x_unknown[!x_unknown %in% c("", NA)]
if (length(x_unknown) > 0 && fast_mode == FALSE) {
warning_(
"in `as.ab()`: ", ifelse(length(unique(x_unknown)) == 1, "this value", "these values"), " could not be coerced to a valid antimicrobial ID: ",
"in {.help [{.fun as.ab}](AMR::as.ab)}: ", ifelse(length(unique(x_unknown)) == 1, "this value", "these values"), " could not be coerced to a valid antimicrobial ID: ",
vector_and(x_unknown), "."
)
}

6
R/ab_property.R
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@@ -265,7 +265,7 @@ ab_ddd <- function(x, administration = "oral", ...) {
if (any(ab_name(x, language = NULL) %like% "/" & is.na(out))) {
warning_(
"in `ab_ddd()`: DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package.",
"in {.help [{.fun ab_ddd}](AMR::ab_ddd)}: DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package.",
"Please refer to the WHOCC website:\n",
"atcddd.fhi.no/ddd/list_of_ddds_combined_products/"
)
@@ -285,7 +285,7 @@ ab_ddd_units <- function(x, administration = "oral", ...) {
if (any(ab_name(x, language = NULL) %like% "/" & is.na(out))) {
warning_(
"in `ab_ddd_units()`: DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package.",
"in {.help [{.fun ab_ddd_units}](AMR::ab_ddd_units)}: DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package.",
"Please refer to the WHOCC website:\n",
"atcddd.fhi.no/ddd/list_of_ddds_combined_products/"
)
@@ -424,7 +424,7 @@ set_ab_names <- function(data, ..., property = "name", language = get_AMR_locale
)
if (any(x %in% c("", NA))) {
warning_(
"in `set_ab_names()`: no ", property, " found for column(s): ",
"in {.help [{.fun set_ab_names}](AMR::set_ab_names)}: no ", property, " found for column(s): ",
vector_and(vars[x %in% c("", NA)], sort = FALSE)
)
x[x %in% c("", NA)] <- vars[x %in% c("", NA)]

6
R/antibiogram.R
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@@ -583,9 +583,9 @@ antibiogram.default <- function(x,
if (length(existing_ab_combined_cols) > 0 && !is.null(ab_transform)) {
ab_transform <- NULL
warning_(
"Detected column name(s) containing the '+' character, which conflicts with the expected syntax in `antibiogram()`: the '+' is used to combine separate antimicrobial drug columns (e.g., \"AMP+GEN\").\n\n",
"To avoid incorrectly guessing which antimicrobials this represents, `ab_transform` was automatically set to `NULL`.\n\n",
"If this is unintended, please rename the column(s) to avoid using '+' in the name, or set `ab_transform = NULL` explicitly to suppress this message."
"Detected column name(s) containing the '+' character, which conflicts with the expected syntax in {.help [{.fun antibiogram}](AMR::antibiogram)}: the '+' is used to combine separate antimicrobial drug columns (e.g., \"AMP+GEN\").\n\n",
"To avoid incorrectly guessing which antimicrobials this represents, {.arg ab_transform} was automatically set to {.code NULL}.\n\n",
"If this is unintended, please rename the column(s) to avoid using '+' in the name, or set {.code ab_transform = NULL} explicitly to suppress this message."
)
}
antimicrobials <- ab_trycatch

4
R/av.R
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@@ -475,7 +475,7 @@ as.av <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
# take failed ATC codes apart from rest
if (length(x_unknown_ATCs) > 0 && fast_mode == FALSE) {
warning_(
"in `as.av()`: these ATC codes are not (yet) in the antivirals data set: ",
"in {.help [{.fun as.av}](AMR::as.av)}: these ATC codes are not (yet) in the antivirals data set: ",
vector_and(x_unknown_ATCs), "."
)
}
@@ -486,7 +486,7 @@ as.av <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
)
if (length(x_unknown) > 0 && fast_mode == FALSE) {
warning_(
"in `as.av()`: these values could not be coerced to a valid antiviral drug ID: ",
"in {.help [{.fun as.av}](AMR::as.av)}: these values could not be coerced to a valid antiviral drug ID: ",
vector_and(x_unknown), "."
)
}

4
R/av_property.R
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@@ -162,7 +162,7 @@ av_ddd <- function(x, administration = "oral", ...) {
if (any(av_name(x, language = NULL) %like% "/" & is.na(out))) {
warning_(
"in `av_ddd()`: DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package.",
"in {.help [{.fun av_ddd}](AMR::av_ddd)}: DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package.",
"Please refer to the WHOCC website:\n",
"atcddd.fhi.no/ddd/list_of_ddds_combined_products/"
)
@@ -182,7 +182,7 @@ av_ddd_units <- function(x, administration = "oral", ...) {
if (any(av_name(x, language = NULL) %like% "/" & is.na(out))) {
warning_(
"in `av_ddd_units()`: DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package.",
"in {.help [{.fun av_ddd_units}](AMR::av_ddd_units)}: DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package.",
"Please refer to the WHOCC website:\n",
"atcddd.fhi.no/ddd/list_of_ddds_combined_products/"
)

2
R/key_antimicrobials.R
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@@ -182,7 +182,7 @@ key_antimicrobials <- function(x = NULL,
any(filter, na.rm = TRUE) &&
message_not_thrown_before("key_antimicrobials", name)) {
warning_(
"in `key_antimicrobials()`: ",
"in {.help [{.fun key_antimicrobials}](AMR::key_antimicrobials)}: ",
ifelse(values_new_length == 0,
"No columns available ",
paste0("Only using ", values_new_length, " out of ", values_old_length, " defined columns ")

4
R/mdro.R
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@@ -1888,8 +1888,8 @@ mdro <- function(x = NULL,
if (any(x$MDRO == -1, na.rm = TRUE)) {
if (message_not_thrown_before("mdro", "availability")) {
warning_(
"in `mdro()`: NA introduced for isolates where the available percentage of antimicrobial classes was below ",
percentage(pct_required_classes), " (set with `pct_required_classes`)"
"in {.help [{.fun mdro}](AMR::mdro)}: NA introduced for isolates where the available percentage of antimicrobial classes was below ",
percentage(pct_required_classes), " (set with {.arg pct_required_classes})"
)
}
# set these -1s to NA

2
R/mic.R
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@@ -331,7 +331,7 @@ rescale_mic <- function(x, mic_range, keep_operators = "edges", as.mic = TRUE, r
}
stop_ifnot(
all(mic_range %in% c(VALID_MIC_LEVELS, NA)),
"Values in `mic_range` must be valid MIC values. ",
"Values in {.arg mic_range} must be valid MIC values. ",
"The allowed range is ", format(as.double(as.mic(VALID_MIC_LEVELS)[1]), scientific = FALSE), " to ", format(as.double(as.mic(VALID_MIC_LEVELS)[length(VALID_MIC_LEVELS)]), scientific = FALSE), ". ",
"Unvalid: ", vector_and(mic_range[!mic_range %in% c(VALID_MIC_LEVELS, NA)], quotes = FALSE), "."
)

6
R/mo.R
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@@ -1256,14 +1256,14 @@ replace_old_mo_codes <- function(x, property) {
}
if (property != "mo") {
warning_(
"in `mo_", property, "()`: the input contained ", n_matched,
"in {.help [{.fun mo_", property, "}](AMR::mo_", property, ")}: the input contained ", n_matched,
" old MO code", ifelse(n_matched == 1, "", "s"),
" (", n_unique, "from a previous AMR package version). ",
"Please update your MO codes with `as.mo()` to increase speed."
"Please update your MO codes with {.help [{.fun as.mo}](AMR::as.mo)} to increase speed."
)
} else {
warning_(
"in `as.mo()`: the input contained ", n_matched,
"in {.help [{.fun as.mo}](AMR::as.mo)}: the input contained ", n_matched,
" old MO code", ifelse(n_matched == 1, "", "s"),
" (", n_unique, "from a previous AMR package version). ",
n_solved, " old MO code", ifelse(n_solved == 1, "", "s"),

2
R/plotting.R
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@@ -1590,7 +1590,7 @@ expand_SIR_colours <- function(colours_SIR, unname = TRUE) {
# named input: match and reorder
stop_ifnot(
all(names(colours_SIR) %in% sir_order),
"Unknown names in `colours_SIR`. Expected any of: ", vector_or(levels(NA_sir_), quotes = FALSE, sort = FALSE), "."
"Unknown names in {.arg colours_SIR}. Expected any of: ", vector_or(levels(NA_sir_), quotes = FALSE, sort = FALSE), "."
)
if (length(colours_SIR) == 4) {
# add colours for SI (same as S) and IR (same as R)