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(v3.0.0.9036) Modernise messaging infrastructure to use cli markup (#265)
* 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
GitHub
149
R/mo.R
149
R/mo.R
@@ -267,7 +267,7 @@ as.mo <- function(x,
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if (isTRUE(info) && message_not_thrown_before("as.mo", old, new, entire_session = TRUE) && any(is.na(old) & !is.na(new), na.rm = TRUE)) {
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message_(
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"Returning previously coerced value", ifelse(sum(is.na(old) & !is.na(new)) > 1, "s", ""),
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" for ", vector_and(x[is.na(old) & !is.na(new)]), ". Run `mo_reset_session()` to reset this. This note will be shown once per session for this input."
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" for ", vector_and(x[is.na(old) & !is.na(new)]), ". Run {.help [{.fun mo_reset_session}](AMR::mo_reset_session)} to reset this. This note will be shown once per session for this input."
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)
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}
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@@ -402,7 +402,14 @@ as.mo <- function(x,
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top_hits <- mo_to_search[order(m, decreasing = TRUE, na.last = NA)] # na.last = NA will remove the NAs
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if (length(top_hits) == 0) {
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warning_("No hits found for \"", x_search, "\" with minimum_matching_score = ", ifelse(is.null(minimum_matching_score), paste0("NULL (=", round(min(minimum_matching_score_current, na.rm = TRUE), 3), ")"), minimum_matching_score), ". Try setting this value lower or even to 0.", call = FALSE)
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warning_("No hits found for \"", x_search, "\" with minimum_matching_score = ",
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ifelse(is.null(minimum_matching_score),
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paste0("NULL (=", round(min(minimum_matching_score_current, na.rm = TRUE), 3), ")"),
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minimum_matching_score
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),
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". Try setting this value lower or even to 0.",
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call = FALSE
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)
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result_mo <- NA_character_
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} else {
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result_mo <- MO_lookup_current$mo[match(top_hits[1], MO_lookup_current$fullname)]
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@@ -448,8 +455,8 @@ as.mo <- function(x,
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if (length(AMR_env$mo_uncertainties$original_input) <= 3) {
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examples <- vector_and(
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paste0(
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'"', AMR_env$mo_uncertainties$original_input,
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'" (assumed ', italicise(AMR_env$mo_uncertainties$fullname), ")"
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"{.val ", AMR_env$mo_uncertainties$original_input,
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"} (assumed ", italicise(AMR_env$mo_uncertainties$fullname), ")"
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),
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quotes = FALSE
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)
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@@ -458,7 +465,7 @@ as.mo <- function(x,
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}
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msg <- c(msg, paste0(
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"Microorganism translation was uncertain for ", examples,
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". Run `mo_uncertainties()` to review ", plural[2], ", or use `add_custom_microorganisms()` to add custom entries."
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". Run {.help [{.fun mo_uncertainties}](AMR::mo_uncertainties)} to review ", plural[2], ", or use {.help [{.fun add_custom_microorganisms}](AMR::add_custom_microorganisms)} to add custom entries."
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))
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for (m in msg) {
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@@ -474,11 +481,11 @@ as.mo <- function(x,
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if (isFALSE(keep_synonyms)) {
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out[!is.na(out_current)] <- out_current[!is.na(out_current)]
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if (isTRUE(info) && length(AMR_env$mo_renamed$old) > 0) {
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print(mo_renamed(), extra_txt = " (use `keep_synonyms = TRUE` to leave uncorrected)")
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print(mo_renamed(), extra_txt = " (use {.arg keep_synonyms = TRUE} to leave uncorrected)")
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}
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} else if (is.null(getOption("AMR_keep_synonyms")) && length(AMR_env$mo_renamed$old) > 0 && message_not_thrown_before("as.mo", "keep_synonyms_warning", entire_session = TRUE)) {
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# keep synonyms is TRUE, so check if any do have synonyms
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warning_("Function `as.mo()` returned ", nr2char(length(unique(AMR_env$mo_renamed$old))), " outdated taxonomic name", ifelse(length(unique(AMR_env$mo_renamed$old)) > 1, "s", ""), ". Use `as.mo(..., keep_synonyms = FALSE)` to clean the input to currently accepted taxonomic names, or set the R option `AMR_keep_synonyms` to `FALSE`. This warning will be shown once per session.", call = FALSE)
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warning_("{.help [{.fun as.mo}](AMR::as.mo)} returned ", nr2char(length(unique(AMR_env$mo_renamed$old))), " outdated taxonomic name", ifelse(length(unique(AMR_env$mo_renamed$old)) > 1, "s", ""), ". Use {.arg keep_synonyms = FALSE} to clean the input to currently accepted taxonomic names, or set the R option {.code AMR_keep_synonyms} to {.code FALSE}. This warning will be shown once per session.", call = FALSE)
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}
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# Apply Becker ----
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@@ -495,7 +502,7 @@ as.mo <- function(x,
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)
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if (any(out %in% AMR_env$MO_lookup$mo[match(post_Becker, AMR_env$MO_lookup$fullname)])) {
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if (message_not_thrown_before("as.mo", "becker")) {
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warning_("in `as.mo()`: Becker ", font_italic("et al."), " (2014, 2019, 2020) does not contain these species named after their publication: ",
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warning_("in {.fun as.mo}: Becker ", font_italic("et al."), " (2014, 2019, 2020) does not contain these species named after their publication: ",
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vector_and(font_italic(gsub("Staphylococcus", "S.", post_Becker, fixed = TRUE), collapse = NULL), quotes = FALSE),
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". Categorisation to CoNS/CoPS was taken from the original scientific publication(s).",
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immediate = TRUE, call = FALSE
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@@ -540,7 +547,7 @@ as.mo <- function(x,
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out[is.na(out) & !is.na(x)] <- "UNKNOWN"
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AMR_env$mo_failures <- unique(x[out == "UNKNOWN" & !toupper(x) %in% c("UNKNOWN", "CON", "UNK") & !x %like_case% "^[(]unknown [a-z]+[)]$" & !is.na(x)])
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if (length(AMR_env$mo_failures) > 0) {
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warning_("The following input could not be coerced and was returned as \"UNKNOWN\": ", vector_and(AMR_env$mo_failures, quotes = TRUE), ".\nYou can retrieve this list with `mo_failures()`.", call = FALSE)
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warning_("The following input could not be coerced and was returned as \"UNKNOWN\": ", vector_and(AMR_env$mo_failures, quotes = TRUE), ".\nYou can retrieve this list with {.fun mo_failures}.", call = FALSE)
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}
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# Return class ----
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@@ -902,14 +909,16 @@ rep.mo <- function(x, ...) {
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print.mo_uncertainties <- function(x, n = 10, ...) {
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more_than_50 <- FALSE
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if (NROW(x) == 0) {
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cat(word_wrap("No uncertainties to show. Only uncertainties of the last call to `as.mo()` or any `mo_*()` function are stored.\n\n", add_fn = font_blue))
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message_("No uncertainties to show. Only uncertainties of the last call to {.help [{.fun as.mo}](AMR::as.mo)} or any {.help [{.fun mo_*}](AMR::mo_property)} function are stored.")
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return(invisible(NULL))
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} else if (NROW(x) > 50) {
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more_than_50 <- TRUE
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x <- x[1:50, , drop = FALSE]
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}
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cat(word_wrap("Matching scores are based on the resemblance between the input and the full taxonomic name, and the pathogenicity in humans. See `?mo_matching_score`.\n\n", add_fn = font_blue))
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message_("Matching scores are based on the resemblance between the input and the full taxonomic name, and the pathogenicity in humans. See {.help [{.fun mo_matching_score}](AMR::mo_matching_score)}.",
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as_note = FALSE
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)
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add_MO_lookup_to_AMR_env()
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@@ -919,12 +928,12 @@ print.mo_uncertainties <- function(x, n = 10, ...) {
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col_green <- function(x) font_green_bg(x, collapse = NULL)
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if (has_colour()) {
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cat(word_wrap("Colour keys: ",
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cat(word_wrap(
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"Colour keys: ",
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col_red(" 0.000-0.549 "),
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col_orange(" 0.550-0.649 "),
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col_yellow(" 0.650-0.749 "),
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col_green(" 0.750-1.000"),
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add_fn = font_blue
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col_green(" 0.750-1.000")
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), font_green_bg(" "), "\n", sep = "")
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}
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@@ -956,21 +965,6 @@ print.mo_uncertainties <- function(x, n = 10, ...) {
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# sort on descending scores
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candidates_formatted <- candidates_formatted[order(1 - scores)]
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scores_formatted <- scores_formatted[order(1 - scores)]
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candidates <- word_wrap(
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paste0(
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"Also matched: ",
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vector_and(
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paste0(
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candidates_formatted,
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font_blue(paste0(" (", scores_formatted, ")"), collapse = NULL)
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),
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quotes = FALSE, sort = FALSE
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)
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),
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extra_indent = nchar("Also matched: "),
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width = 0.9 * getOption("width", 100)
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)
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} else {
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candidates <- ""
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}
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@@ -980,46 +974,54 @@ print.mo_uncertainties <- function(x, n = 10, ...) {
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n = x[i, ]$fullname
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)
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score_formatted <- trimws(formatC(round(score, 3), format = "f", digits = 3))
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txt <- paste(txt,
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out <- paste0(
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paste0(
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"", strrep(font_grey("-"), times = getOption("width", 100) - 1), "\n",
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"{.val ", x[i, ]$original_input, "}",
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" -> ",
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paste0(
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"", strrep(font_grey("-"), times = getOption("width", 100)), "\n",
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'"', x[i, ]$original_input, '"',
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" -> ",
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paste0(
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font_bold(italicise(x[i, ]$fullname)),
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" (", x[i, ]$mo, ", ", score_set_colour(score_formatted, score), ")"
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)
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),
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collapse = "\n"
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font_bold(italicise(x[i, ]$fullname)),
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" (", x[i, ]$mo, ", ", score_set_colour(score_formatted, score), ")"
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)
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),
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ifelse(x[i, ]$mo %in% AMR_env$MO_lookup$mo[which(AMR_env$MO_lookup$status == "synonym")],
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paste0(
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strrep(" ", nchar(x[i, ]$original_input) + 6),
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ifelse(x[i, ]$keep_synonyms == FALSE,
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# Add note if result was coerced to accepted taxonomic name
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font_red(paste0("This outdated taxonomic name was converted to ", font_italic(AMR_env$MO_lookup$fullname[match(synonym_mo_to_accepted_mo(x[i, ]$mo), AMR_env$MO_lookup$mo)], collapse = NULL), " (", synonym_mo_to_accepted_mo(x[i, ]$mo), ")."), collapse = NULL),
|
||||
# Or add note if result is currently another taxonomic name
|
||||
font_red(paste0(font_bold("Note: "), "The current name is ", font_italic(AMR_env$MO_lookup$fullname[match(synonym_mo_to_accepted_mo(x[i, ]$mo), AMR_env$MO_lookup$mo)], collapse = NULL), " (", AMR_env$MO_lookup$ref[match(synonym_mo_to_accepted_mo(x[i, ]$mo), AMR_env$MO_lookup$mo)], ")."), collapse = NULL)
|
||||
)
|
||||
),
|
||||
""
|
||||
),
|
||||
candidates,
|
||||
sep = "\n"
|
||||
collapse = "\n"
|
||||
)
|
||||
txt <- gsub("[\n]+", "\n", txt)
|
||||
# remove first and last break
|
||||
txt <- gsub("(^[\n]|[\n]$)", "", txt)
|
||||
txt <- paste0("\n", txt, "\n")
|
||||
message_(out, as_note = FALSE)
|
||||
|
||||
if (x[i, ]$mo %in% AMR_env$MO_lookup$mo[which(AMR_env$MO_lookup$status == "synonym")]) {
|
||||
out2 <- paste0(
|
||||
strrep(" ", nchar(x[i, ]$original_input) + 6),
|
||||
ifelse(x[i, ]$keep_synonyms == FALSE,
|
||||
# Add note if result was coerced to accepted taxonomic name
|
||||
font_red(paste0("This outdated taxonomic name was converted to ", font_italic(AMR_env$MO_lookup$fullname[match(synonym_mo_to_accepted_mo(x[i, ]$mo), AMR_env$MO_lookup$mo)], collapse = NULL), " (", synonym_mo_to_accepted_mo(x[i, ]$mo), ")."), collapse = NULL),
|
||||
# Or add note if result is currently another taxonomic name
|
||||
font_red(paste0(font_bold("Note: "), "The current name is ", font_italic(AMR_env$MO_lookup$fullname[match(synonym_mo_to_accepted_mo(x[i, ]$mo), AMR_env$MO_lookup$mo)], collapse = NULL), " (", AMR_env$MO_lookup$ref[match(synonym_mo_to_accepted_mo(x[i, ]$mo), AMR_env$MO_lookup$mo)], ")."), collapse = NULL)
|
||||
)
|
||||
)
|
||||
message_(out2, as_note = FALSE)
|
||||
}
|
||||
|
||||
other_matches <- paste0(
|
||||
"Also matched: ",
|
||||
vector_and(
|
||||
paste0(
|
||||
candidates_formatted,
|
||||
font_blue(paste0(" (", scores_formatted, ")"), collapse = NULL)
|
||||
),
|
||||
quotes = FALSE, sort = FALSE
|
||||
)
|
||||
)
|
||||
message_(other_matches, as_note = FALSE)
|
||||
}
|
||||
|
||||
cat(txt)
|
||||
if (isTRUE(any_maxed_out)) {
|
||||
cat(font_blue(word_wrap("\nOnly the first ", n, " other matches of each record are shown. Run `print(mo_uncertainties(), n = ...)` to view more entries, or save `mo_uncertainties()` to an object.")))
|
||||
cat("\n")
|
||||
message_("Only the first ", n, " other matches of each record are shown. Run {.help [`print(mo_uncertainties(), n = ...)`](AMR::mo_uncertainties)} to view more entries, or save {.help [{.fun mo_uncertainties}](AMR::mo_uncertainties)} to an object.")
|
||||
}
|
||||
if (isTRUE(more_than_50)) {
|
||||
cat(font_blue(word_wrap("\nOnly the first 50 uncertainties are shown. Run `View(mo_uncertainties())` to view all entries, or save `mo_uncertainties()` to an object.")))
|
||||
cat("\n")
|
||||
message_("Only the first 50 uncertainties are shown. Run {.help [`View(mo_uncertainties())`](AMR::mo_uncertainties)} to view all entries, or save {.help [{.fun mo_uncertainties}](AMR::mo_uncertainties)} to an object.")
|
||||
}
|
||||
}
|
||||
|
||||
@@ -1028,7 +1030,7 @@ print.mo_uncertainties <- function(x, n = 10, ...) {
|
||||
#' @noRd
|
||||
print.mo_renamed <- function(x, extra_txt = "", n = 25, ...) {
|
||||
if (NROW(x) == 0) {
|
||||
cat(word_wrap("No renamed taxonomy to show. Only renamed taxonomy of the last call of `as.mo()` or any `mo_*()` function are stored.\n", add_fn = font_blue))
|
||||
message_("No renamed taxonomy to show. Only renamed taxonomy of the last call of {.help [{.fun as.mo}](AMR::as.mo)} or any {.help [{.fun mo_*}](AMR::mo_property)} function are stored.")
|
||||
return(invisible(NULL))
|
||||
}
|
||||
|
||||
@@ -1039,14 +1041,17 @@ print.mo_renamed <- function(x, extra_txt = "", n = 25, ...) {
|
||||
|
||||
rows <- seq_len(min(NROW(x), n))
|
||||
|
||||
message_(
|
||||
"The following microorganism", ifelse(NROW(x) > 1, "s were", " was"), " taxonomically renamed", extra_txt, ":\n",
|
||||
paste0(" ", AMR_env$bullet_icon, " ", font_italic(x$old[rows], collapse = NULL), x$ref_old[rows],
|
||||
" -> ", font_italic(x$new[rows], collapse = NULL), x$ref_new[rows],
|
||||
collapse = "\n"
|
||||
),
|
||||
ifelse(NROW(x) > n, paste0("\n\nOnly the first ", n, " (out of ", NROW(x), ") are shown. Run `print(mo_renamed(), n = ...)` to view more entries (might be slow), or save `mo_renamed()` to an object."), "")
|
||||
)
|
||||
message_("The following microorganism", ifelse(NROW(x) > 1, "s were", " was"), " taxonomically renamed", extra_txt, ":")
|
||||
old_format <- format(paste0(font_italic(x$old[rows], collapse = NULL), x$ref_old[rows])) # format() will set trailing spaces for textual alignment
|
||||
old_format <- gsub(" ", "\u00a0", old_format, fixed = TRUE)
|
||||
for (old_tax in rows) {
|
||||
message_("\u00a0\u00a0", AMR_env$bullet_icon, " ", old_format[old_tax], " -> ", font_italic(x$new[old_tax]), x$ref_new[old_tax], as_note = FALSE)
|
||||
}
|
||||
if (NROW(x) > n) {
|
||||
message_("\u00a0\u00a0Only the first ", n, " (out of ", NROW(x), ") are shown. Run {.code print(mo_renamed(), n = ...)} to view more entries (might be slow), or save {.fun mo_renamed} to an object.",
|
||||
as_note = FALSE
|
||||
)
|
||||
}
|
||||
}
|
||||
|
||||
# UNDOCUMENTED HELPER FUNCTIONS -------------------------------------------
|
||||
@@ -1251,14 +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"),
|
||||
|
||||
Reference in New Issue
Block a user