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(v3.0.0.9036) Modernise messaging infrastructure to use cli markup (#265)

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* Modernise messaging infrastructure with cli support

Rewrites message_(), warning_(), stop_() to use cli::cli_inform(),
cli::cli_warn(), and cli::cli_abort() when the cli package is available,
with a fully functional plain-text fallback for environments without cli.

Key changes:
- New cli_to_plain() helper converts cli inline markup ({.fun}, {.arg},
  {.val}, {.field}, {.cls}, {.pkg}, {.href}, {.url}, etc.) to readable
  plain-text equivalents for the non-cli fallback path
- word_wrap() simplified: drops add_fn, ANSI re-index algorithm, RStudio
  link injection, and operator spacing hack; returns pasted input unchanged
  when cli is available
- stop_() no longer references AMR_env$cli_abort; uses pkg_is_available()
  directly; passes sys.call() objects to cli::cli_abort() call= argument
- Removed add_fn parameter from message_(), warning_(), and word_wrap()
- All call sites across R/ updated: add_fn arguments removed, some paste0-
  based string construction converted to cli glue syntax ({.fun as.mo},
  {.arg col_mo}, {n} results, etc.)
- cli already listed in Suggests; no DESCRIPTION dependency changes needed

https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b

* Replace {.fun} with {.help} for all exported functions in messaging

All function names referenced via {.fun …} in cli-style messages are
exported in NAMESPACE, so {.help …} is the appropriate markup — it
renders as a clickable help link rather than plain function styling.

https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b

* Qualify all {.help} tags with AMR:: and convert backtick ?func references

- Add AMR:: namespace prefix and trailing () to all {.help} cli markup
  so they render as clickable help links (e.g. {.help AMR::as.sir}())
- Convert `?funcname` backtick-quoted help references to {.help AMR::funcname}()
  in aa_helper_functions.R, custom_eucast_rules.R, interpretive_rules.R,
  key_antimicrobials.R, mo.R, plotting.R, resistance_predict.R, and sir.R
- Skipped `?proportion` in sir_calc.R as 'proportion' is not exported

https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b

* Require cli >= 3.0.0 for cli_inform/cli_warn/cli_abort availability checks

cli_inform, cli_warn, and cli_abort were introduced in cli 3.0.0.
Add min_version = "3.0.0" (as character) to all four pkg_is_available("cli")
checks so older cli versions fall back to base R messaging.

https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b

* Implement cli::code_highlight() for R code examples in messages (issue #191)

Add highlight_code() helper that wraps cli::code_highlight() when cli >= 3.0.0
is available, falling back to plain code otherwise. Apply it to all inline
R code examples embedded in message/warning/stop strings across the package.

Also convert remaining backtick-quoted function and argument references in
messaging calls to proper cli markup: {.help AMR::fn}(), {.arg arg},
{.code expr}, and {.pkg pkg} throughout ab.R, ab_from_text.R, av_from_text.R,
amr_selectors.R, count.R, custom_antimicrobials.R, custom_microorganisms.R,
interpretive_rules.R, mo.R, mo_property.R, sir.R, sir_calc.R.

Fixes #191

https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b

* Fix {.help} markup to use correct cli link format [{.fun fn}](AMR::fn)

Replace all instances of {.help AMR::fn}() (incorrect format with manual
parentheses outside the link) with {.help [{.fun fn}](AMR::fn)} which is
the correct cli hyperlink syntax: the display text [{.fun fn}] renders the
function name with parentheses automatically, and (AMR::fn) is the link target.

Also update the plain-text fallback handler in aa_helper_functions.R to
extract the display text from the [text](topic) markdown link format,
so that non-cli environments show just the function name (e.g. `fn()`),
not the raw link markup.

Dynamic cases in amr_selectors.R and mo_property.R also updated.

https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b

* Add {.topic} markup for non-function help page references

Replace {.code ?AMR-options} and backtick-style ?AMR-options / ?AMR-deprecated
references with proper {.topic AMR-options} / {.topic AMR-deprecated} cli markup
in count.R, interpretive_rules.R, proportion.R, and zz_deprecated.R.

Add {.topic} fallback handler to format_message() in aa_helper_functions.R:
plain-text environments render {.topic foo} as ?foo, and the [text](topic)
link form extracts just the display text (same pattern as {.help}).

Also convert remaining backtick function/arg references in proportion.R to
{.help [{.fun ...}](AMR::...)}, {.arg}, and {.code} markup for consistency.

Note: zzz.R intentionally keeps the backtick form since its startup message
goes through packageStartupMessage() which bypasses our cli infrastructure.

https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b

* Fix {.topic} to use required pkg::topic format with display text

{.topic} in cli requires a package-qualified topic reference to generate
a valid x-r-help:pkg::topic URI. Bare {.topic AMR-options} produced a
malformed x-r-help:AMR-options URI (no package prefix).

Use the [display_text](pkg::topic) form throughout:
  {.topic [AMR-options](AMR::AMR-options)}
  {.topic [AMR-deprecated](AMR::AMR-deprecated)}

The hyphen in the topic name is fine as a URI string even though
AMR::AMR-options is not a valid R symbol expression.

The fallback handler in format_message() already handles the [text](uri)
form by extracting the display text, so plain-text output is unchanged.

https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b

* Fix regexec() calls: remove perl=TRUE unsupported in older R

regexec() only gained the perl argument in R 4.1.0. The CI matrix
covers oldrel-1 through oldrel-4 (R 3.x/4.0.x), so perl=TRUE caused
an 'unused argument' error on every message_() call in those
environments.

All four affected regexec() calls use POSIX-extended compatible
patterns, so dropping perl=TRUE is safe.

https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b

* Slim CI matrix for PRs to ubuntu-latest / r-release only

For pull requests, check-recent now runs a single job (ubuntu-latest,
r-release) via a setup job that emits the matrix as JSON. On push and
schedule the full matrix is unchanged (devel + release on all OSes,
oldrel-1 through oldrel-4).

Also removed the pull_request trigger from check-recent-dev-pkgs; the
dev-packages check only needs to run on push/schedule.

https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b

* Restrict dev-versions and old-tinytest CI to main branch only

Both workflows were triggering on every push to every branch.
Narrowed push trigger to [main] so they only run after merging,
not on every feature/PR branch push.

https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b

* Update NEWS.md to continuous log + add concise style rules to CLAUDE.md

NEWS.md is now a single continuous log under one heading per dev series,
not a new section per version bump. CLAUDE.md documents: only replace
line 1 (heading), append new entries, keep them extremely concise with
no trailing full stop.

Merged 9035 and 9036 entries into one section; condensed verbose 9036
bullets; added CI workflow change entry.

https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b

* Replace single-quoted literals in messaging calls with cli markup

Converted bare 'value' strings inside stop_(), warning_(), message_()
to appropriate cli markup:
- {.val}: option values ('drug', 'dose', 'administration', 'SDD', 'logbook')
- {.cls}: class names ('sir', 'mo')
- {.field}: column names ('mo' in mo_source)
- {.code}: object/dataset names ('clinical_breakpoints')

Files changed: ab_from_text.R, av_from_text.R, sir.R, sir_calc.R, mo_source.R

https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b

* Apply {.topic}, {.cls}, and {.field} markup in sir.R messaging

- 'clinical_breakpoints' (dataset): {.code} -> {.topic [clinical_breakpoints](AMR::clinical_breakpoints)}
- "is of class" context: extract bad_col/bad_cls/exp_cls vars and use {.cls} + {.field} in glue syntax
- Column references in as.sir() messages: font_bold(col) with surrounding quotes -> {.field {col}}

https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b

* Replace glue-style dynamic markup with paste0() construction

{.field {variable}} and {.cls {variable}} patterns rely on glue
evaluation which is not safe in a zero-dependency package. Replace
all four occurrences with paste0("{.field ", var, "}") so the value
is baked into the markup string before reaching message_()/stop_().

https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b

* Limit push trigger to main in check-recent workflow

push: branches: '**' caused both the push event (9-worker matrix) and
the pull_request event (1-worker matrix) to fire simultaneously on every
PR commit. Restricting push to [main] means PR pushes only trigger the
pull_request path (1 worker), while direct pushes to main still get the
full 9-worker matrix.

https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b

* Limit push trigger to main in code-coverage workflow

Same fix as check-recent: push: branches: '**' caused the workflow to
run twice per PR commit (once for push, once for pull_request). Restricting
push to [main] ensures coverage runs only once per PR update.

https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b

* Replace bare backticks with cli inline markup across all messaging calls

- {.arg} for argument names in stop_/warning_/message_ calls
- {.cls} after "of class" text in format_class() and elsewhere
- {.fun} for function names (replaces `fn()` pattern)
- {.pkg} for tidyverse package names (dplyr, ggplot2)
- {.code} for code literals (TRUE, FALSE, expressions)
- Rewrite print.ab: use cli named-vector with * bullets and code
  highlighting when cli >= 3.0.0; keep plain-text fallback otherwise
- Fix typo in as.sir(): "of must be" -> "or must be"
- switch sir.R verbose notes from message() to message_()

https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b

* Pre-evaluate inline expressions, add format_inline_(), fix print.ab

- All bare {variable}/{expression} in message_()/warning_()/stop_() calls
  are now pre-evaluated via paste0(), so users without cli/glue never see
  raw template syntax (mo_source.R, first_isolate.R, join_microorganisms.R,
  antibiogram.R, atc_online.R)
- Add format_inline_() helper: formats a cli-markup string and returns it
  (not emits it), using cli::format_inline() when available and cli_to_plain()
  otherwise
- Rewrite .onAttach to use format_inline_() for all packageStartupMessage
  calls; also adds {.topic} link and {.code} markup for option names
- print.ab: pre-evaluate function_name via paste0 (no .envir needed),
  apply highlight_code() to each example bullet for R syntax highlighting
- join_microorganisms: pre-evaluate {type} and {nrow(...)} expressions

https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b

* fixes

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

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

* fixes

* definitive

* version fix

---------

Co-authored-by: Claude <noreply@anthropic.com>
This commit is contained in:
Matthijs Berends
2026-03-20 17:01:34 +01:00
committed by GitHub
parent 8439e9c1d2
commit 4171d5b778
50 changed files with 567 additions and 546 deletions
Download Patch File Download Diff File Expand all files Collapse all files

69
R/sir.R
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@@ -441,7 +441,7 @@ is_sir_eligible <- function(x, threshold = 0.05) {
return(unname(vapply(FUN.VALUE = logical(1), x, is_sir_eligible)))
}
stop_if(NCOL(x) > 1, "`x` must be a one-dimensional vector.")
stop_if(NCOL(x) > 1, "{.arg x} must be a one-dimensional vector.")
if (any(c(
"numeric",
"integer",
@@ -529,10 +529,10 @@ as.sir.default <- function(x,
if (all(x %unlike% "(S|I|R)", na.rm = TRUE) && !all(x %in% c(1, 2, 3, 4, 5), na.rm = TRUE)) {
# check if they are actually MICs or disks
if (all_valid_mics(x)) {
warning_("in `as.sir()`: input values were guessed to be MIC values - preferably transform them with `as.mic()` before running `as.sir()`.")
warning_("in {.help [{.fun as.sir}](AMR::as.sir)}: input values were guessed to be MIC values - preferably transform them with {.help [{.fun as.mic}](AMR::as.mic)} before running {.help [{.fun as.sir}](AMR::as.sir)}.")
return(as.sir(as.mic(x), ...))
} else if (all_valid_disks(x)) {
warning_("in `as.sir()`: input values were guessed to be disk diffusion values - preferably transform them with `as.disk()` before running `as.sir()`.")
warning_("in {.help [{.fun as.sir}](AMR::as.sir)}: input values were guessed to be disk diffusion values - preferably transform them with {.help [{.fun as.disk}](AMR::as.disk)} before running {.help [{.fun as.sir}](AMR::as.sir)}.")
return(as.sir(as.disk(x), ...))
}
}
@@ -601,7 +601,7 @@ as.sir.default <- function(x,
ifelse(length(out7) > 0, paste0("7 as \"", out7, "\""), NA_character_),
ifelse(length(out8) > 0, paste0("8 as \"", out8, "\""), NA_character_)
)
message_("in `as.sir()`: Interpreting input value ", vector_and(out[!is.na(out)], quotes = FALSE, sort = FALSE))
message_("in {.help [{.fun as.sir}](AMR::as.sir)}: Interpreting input value ", vector_and(out[!is.na(out)], quotes = FALSE, sort = FALSE))
}
if (na_before != na_after) {
@@ -610,7 +610,7 @@ as.sir.default <- function(x,
sort() %pm>%
vector_and(quotes = TRUE)
cur_col <- get_current_column()
warning_("in `as.sir()`: ", na_after - na_before, " result",
warning_("in {.help [{.fun as.sir}](AMR::as.sir)}: ", na_after - na_before, " result",
ifelse(na_after - na_before > 1, "s", ""),
ifelse(is.null(cur_col), "", paste0(" in column '", cur_col, "'")),
" truncated (",
@@ -783,10 +783,10 @@ as.sir.data.frame <- function(x,
# -- host
if (missing(breakpoint_type) && any(host %in% clinical_breakpoints$host[!clinical_breakpoints$host %in% c("human", "ECOFF")], na.rm = TRUE)) {
if (isTRUE(info)) message_("Assuming `breakpoint_type = \"animal\"` since `host` contains animal species.")
if (isTRUE(info)) message_("Assuming {.code breakpoint_type = \"animal\"} since {.arg host} contains animal species.")
breakpoint_type <- "animal"
} else if (any(!suppressMessages(convert_host(host, lang = language)) %in% c("human", "ECOFF"), na.rm = TRUE)) {
if (isTRUE(info)) message_("Assuming `breakpoint_type = \"animal\"`.")
if (isTRUE(info)) message_("Assuming {.code breakpoint_type = \"animal\"}.")
breakpoint_type <- "animal"
}
if (breakpoint_type == "animal") {
@@ -816,7 +816,7 @@ as.sir.data.frame <- function(x,
# column found, transform to logical
stop_if(
length(col_uti) != 1 | !col_uti %in% colnames(x),
"argument `uti` must be a [logical] vector, of must be a single column name of `x`"
"argument {.arg uti} must be a [logical] vector, or must be a single column name of {.arg x}"
)
uti <- as.logical(x[, col_uti, drop = TRUE])
}
@@ -835,8 +835,7 @@ as.sir.data.frame <- function(x,
message_(
"Assuming value", plural[1], " ",
vector_and(col_values, quotes = TRUE),
" in column '", font_bold(col_specimen),
"' reflect", plural[2], " ", plural[3], "urinary tract infection", plural[1],
" in column ", paste0("{.field ", col_specimen, "}"), " reflect", plural[2], " ", plural[3], "urinary tract infection", plural[1],
".\n Use `as.sir(uti = FALSE)` to prevent this."
)
}
@@ -883,7 +882,7 @@ as.sir.data.frame <- function(x,
types[types == "" & !vapply(FUN.VALUE = logical(1), x.bak[, ab_cols, drop = FALSE], is.sir)] <- "sir"
if (any(types %in% c("mic", "disk"), na.rm = TRUE)) {
# now we need an mo column
stop_if(is.null(col_mo), "`col_mo` must be set")
stop_if(is.null(col_mo), "{.arg col_mo} must be set")
# if not null, we already found it, now find again so a message will show
if (is.null(col_mo.bak)) {
col_mo <- search_type_in_df(x = x, type = "mo", info = info)
@@ -898,7 +897,7 @@ as.sir.data.frame <- function(x,
cl <- tryCatch(parallel::makeCluster(n_cores, type = "PSOCK"),
error = function(e) {
if (isTRUE(info)) {
message_("Could not create parallel cluster, using single-core computation. Error message: ", conditionMessage(e), add_fn = font_red)
message_("Could not create parallel cluster, using single-core computation. Error message: ", conditionMessage(e))
}
return(NULL)
}
@@ -975,7 +974,7 @@ as.sir.data.frame <- function(x,
if (!all(x[, ab, drop = TRUE] %in% c("S", "SDD", "I", "R", "NI", NA), na.rm = TRUE)) {
show_message <- TRUE
if (isTRUE(info)) {
message_("Cleaning values in column '", font_bold(ab), "' (",
message_("Cleaning values in column ", paste0("{.field ", ab, "}"), " (",
ifelse(ab_coerced != toupper(ab), paste0(ab_coerced, ", "), ""),
ab_name(ab_coerced, tolower = TRUE, info = info), ")... ",
appendLF = FALSE,
@@ -985,7 +984,7 @@ as.sir.data.frame <- function(x,
} else if (!is.sir(x.bak[, ab, drop = TRUE])) {
show_message <- TRUE
if (isTRUE(info)) {
message_("Assigning class 'sir' to already clean column '", font_bold(ab), "' (",
message_("Assigning class {.cls sir} to already clean column ", paste0("{.field ", ab, "}"), " (",
ifelse(ab_coerced != toupper(ab), paste0(ab_coerced, ", "), ""),
ab_name(ab_coerced, tolower = TRUE, language = NULL, info = info), ")... ",
appendLF = FALSE,
@@ -1029,14 +1028,14 @@ as.sir.data.frame <- function(x,
if (isTRUE(info)) {
message_(font_green_bg(" DONE "), as_note = FALSE)
message()
message_("Run `sir_interpretation_history()` to retrieve a logbook with all details of the breakpoint interpretations.", add_fn = font_green)
message_("Run {.help [{.fun sir_interpretation_history}](AMR::sir_interpretation_history)} to retrieve a logbook with all details of the breakpoint interpretations.")
}
} else {
# sequential mode (non-parallel)
if (isTRUE(info) && n_cores > 1 && NROW(x) * NCOL(x) > 10000) {
# give a note that parallel mode might be better
message()
message_("Running in sequential mode. Consider setting `parallel = TRUE` to speed up processing on multiple cores.\n", add_fn = font_red)
message_("Running in sequential mode. Consider setting {.arg parallel} to {.code TRUE} to speed up processing on multiple cores.\n")
}
# this will contain a progress bar already
result_list <- lapply(seq_along(ab_cols), run_as_sir_column)
@@ -1168,13 +1167,13 @@ as_sir_method <- function(method_short,
dots <- list(...)
dots <- dots[which(!names(dots) %in% c("warn", "mo.bak", "is_data.frame"))]
if (length(dots) != 0) {
warning_("These arguments in `as.sir()` are no longer used: ", vector_and(names(dots), quotes = "`"), ".", call = FALSE)
warning_("These arguments in {.help [{.fun as.sir}](AMR::as.sir)} are no longer used: ", vector_and(names(dots), quotes = "`"), ".", call = FALSE)
}
current_sir_interpretation_history <- NROW(AMR_env$sir_interpretation_history)
if (isTRUE(info) && message_not_thrown_before("as.sir", "sir_interpretation_history")) {
message_("Run `sir_interpretation_history()` afterwards to retrieve a logbook with all details of the breakpoint interpretations.\n\n", add_fn = font_green)
message_("Run {.help [{.fun sir_interpretation_history}](AMR::sir_interpretation_history)} afterwards to retrieve a logbook with all details of the breakpoint interpretations.\n\n")
}
current_df <- tryCatch(get_current_data(NA, 0), error = function(e) NULL)
@@ -1190,13 +1189,13 @@ as_sir_method <- function(method_short,
if (is.null(host)) {
host <- "dogs"
if (isTRUE(info) && message_not_thrown_before("as.sir", "host_missing")) {
message_("Animal hosts not set in `host`, assuming `host = \"dogs\"`, since these have the highest breakpoint availability.\n\n")
message_("Animal hosts not set in {.arg host}, assuming {.code host = \"dogs\"}, since these have the highest breakpoint availability.\n\n")
}
}
} else {
if (!is.null(host) && !all(toupper(as.character(host)) %in% c("HUMAN", "ECOFF"))) {
if (isTRUE(info) && message_not_thrown_before("as.sir", "assumed_breakpoint_animal")) {
message_("Assuming `breakpoint_type = \"animal\"`, since `host` is set.", ifelse(guideline_coerced %like% "EUCAST", " Do you also need to set `guideline = \"CLSI\"`?", ""), "\n\n")
message_("Assuming {.code breakpoint_type = \"animal\"}, since {.arg host} is set.", ifelse(guideline_coerced %like% "EUCAST", " Do you also need to set {.code guideline = \"CLSI\"}?", ""), "\n\n")
}
breakpoint_type <- "animal"
} else {
@@ -1276,9 +1275,9 @@ as_sir_method <- function(method_short,
mo_var_found <- ""
}
if (is.null(mo)) {
stop_("No information was supplied about the microorganisms (missing argument `mo` and no column of class 'mo' found). See ?as.sir.\n\n",
"To transform certain columns with e.g. mutate(), use `data %>% mutate(across(..., as.sir, mo = x))`, where x is your column with microorganisms.\n",
"To transform all ", method_long, " in a data set, use `data %>% as.sir()` or `data %>% mutate_if(is.", method_short, ", as.sir)`.",
stop_("No information was supplied about the microorganisms (missing argument {.arg mo} and no column of class {.cls mo} found). See {.help [{.fun as.sir}](AMR::as.sir)}.\n\n",
"To transform certain columns with e.g. mutate(), use ", highlight_code("data %>% mutate(across(..., as.sir, mo = x))"), ", where x is your column with microorganisms.\n",
"To transform all ", method_long, " in a data set, use ", highlight_code("data %>% as.sir()"), " or ", highlight_code(paste0("data %>% mutate_if(is.", method_short, ", as.sir)")), ".",
call = FALSE
)
}
@@ -1312,7 +1311,7 @@ as_sir_method <- function(method_short,
if (length(ab) == 1 && ab %like% paste0("as.", method_short)) {
stop_("No unambiguous name was supplied about the antibiotic (argument `ab`). See ?as.sir.", call = FALSE)
stop_("No unambiguous name was supplied about the antibiotic (argument {.arg ab}). See {.help [{.fun as.sir}](AMR::as.sir)}.", call = FALSE)
}
ab.bak <- trimws2(ab)
@@ -1328,8 +1327,7 @@ as_sir_method <- function(method_short,
if (all(is.na(ab))) {
if (isTRUE(info)) {
message_("Returning NAs for unknown antibiotic: ", vector_and(ab.bak, sort = FALSE, quotes = TRUE),
". Rename this column to a valid name or code, and check the output with `as.ab()`.",
add_fn = font_red,
". Rename this column to a valid name or code, and check the output with {.help [{.fun as.ab}](AMR::as.ab)}.",
as_note = FALSE
)
}
@@ -1353,9 +1351,7 @@ as_sir_method <- function(method_short,
}
if (isTRUE(add_intrinsic_resistance) && guideline_coerced %unlike% "EUCAST") {
if (isTRUE(info) && message_not_thrown_before("as.sir", "intrinsic")) {
message_("in `as.sir()`: using 'add_intrinsic_resistance' is only useful when using EUCAST guidelines, since the rules for intrinsic resistance are based on EUCAST.",
add_fn = font_red
)
message_("in {.help [{.fun as.sir}](AMR::as.sir)}: using {.arg add_intrinsic_resistance} is only useful when using EUCAST guidelines, since the rules for intrinsic resistance are based on EUCAST.")
}
}
@@ -1724,7 +1720,7 @@ as_sir_method <- function(method_short,
pm_filter(uti == FALSE)
notes_current <- paste0(
notes_current, "\n",
paste0("Breakpoints for UTI ", font_bold("and"), " non-UTI available for ", ab_formatted, " in ", mo_formatted, " - assuming ", site, ". Use argument `uti` to set which isolates are from urine. See `?as.sir`.")
paste0("Breakpoints for UTI ", font_bold("and"), " non-UTI available for ", ab_formatted, " in ", mo_formatted, " - assuming ", site, ". Use argument {.arg uti} to set which isolates are from urine. See {.help [{.fun as.sir}](AMR::as.sir)}.")
)
} else if (nrow(breakpoints_current) > 1 && length(unique(breakpoints_current$site)) > 1 && all(breakpoints_current$uti == FALSE, na.rm = TRUE) && message_not_thrown_before("as.sir", "siteOther", mo_current, ab_current)) {
# breakpoints for multiple body sites available
@@ -1947,10 +1943,10 @@ as_sir_method <- function(method_short,
# if (isTRUE(verbose) || length(notes) == 1 || NROW(AMR_env$sir_interpretation_history) == 0) {
if (isTRUE(verbose)) {
for (i in seq_along(notes)) {
message(word_wrap(" ", AMR_env$bullet_icon, " ", notes[i], add_fn = font_black))
message_(notes[i], as_note = FALSE)
}
} else {
# message(word_wrap(" ", AMR_env$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 "))
@@ -1991,7 +1987,7 @@ sir_interpretation_history <- function(clean = FALSE) {
#' @noRd
print.sir_log <- function(x, ...) {
if (NROW(x) == 0) {
message_("No results to print. First run `as.sir()` on MIC values or disk diffusion zones (or on a `data.frame` containing any of these) to print a 'logbook' data set here.")
message_("No results to print. First run {.help [{.fun as.sir}](AMR::as.sir)} on MIC values or disk diffusion zones (or on a {.cls data.frame} containing any of these) to print a {.val logbook} data set here.")
return(invisible(NULL))
}
class(x) <- class(x)[class(x) != "sir_log"]
@@ -2230,10 +2226,13 @@ check_reference_data <- function(reference_data, .call_depth) {
class_sir <- vapply(FUN.VALUE = character(1), AMR::clinical_breakpoints, function(x) paste0("<", class(x), ">", collapse = " and "))
class_ref <- vapply(FUN.VALUE = character(1), reference_data, function(x) paste0("<", class(x), ">", collapse = " and "))
if (!all(names(class_sir) == names(class_ref))) {
stop_("`reference_data` must have the same column names as the 'clinical_breakpoints' data set.", call = .call_depth)
stop_("{.arg reference_data} must have the same column names as the {.topic [clinical_breakpoints](AMR::clinical_breakpoints)} data set.", call = .call_depth)
}
if (!all(class_sir == class_ref)) {
stop_("`reference_data` must be the same structure as the 'clinical_breakpoints' data set. Column '", names(class_ref[class_sir != class_ref][1]), "' is of class ", class_ref[class_sir != class_ref][1], ", but should be of class ", class_sir[class_sir != class_ref][1], ".", call = .call_depth)
bad_col <- names(class_ref[class_sir != class_ref][1])
bad_cls <- gsub("<|>", "", class_ref[class_sir != class_ref][1])
exp_cls <- gsub("<|>", "", class_sir[class_sir != class_ref][1])
stop_("{.arg reference_data} must be the same structure as the {.topic [clinical_breakpoints](AMR::clinical_breakpoints)} data set. Column ", paste0("{.field ", bad_col, "}"), " is of class ", paste0("{.cls ", bad_cls, "}"), ", but should be of class ", paste0("{.cls ", exp_cls, "}"), call = .call_depth)
}
}
}