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4171d5b778901ed6fb25ef217e7e90bcab372d5e
AMR/tests/testthat/test-mo.R
Matthijs Berends 4171d5b778 (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>
2026-03-20 17:01:34 +01:00

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# ==================================================================== #
# TITLE: #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE CODE: #
# https://github.com/msberends/AMR #
# #
# PLEASE CITE THIS SOFTWARE AS: #
# Berends MS, Luz CF, Friedrich AW, et al. (2022). #
# AMR: An R Package for Working with Antimicrobial Resistance Data. #
# Journal of Statistical Software, 104(3), 1-31. #
# https://doi.org/10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many #
# colleagues from around the world, see our website. #
# #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# We created this package for both routine data analysis and academic #
# research and it was publicly released in the hope that it will be #
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-mo.R", {
skip_on_cran()
MOs <- subset(microorganisms, !is.na(mo) & nchar(mo) > 3)
expect_identical(as.character(MOs$mo), as.character(as.mo(MOs$mo, keep_synonyms = TRUE)))
expect_identical(
as.character(as.mo(c("E. coli", "H. influenzae"), keep_synonyms = FALSE)),
c("B_ESCHR_COLI", "B_HMPHL_INFL")
)
expect_equal(as.character(as.mo("Escherichia coli")), "B_ESCHR_COLI")
expect_equal(as.character(as.mo("Escherichia coli")), "B_ESCHR_COLI")
expect_equal(as.character(as.mo(112283007)), "B_ESCHR_COLI")
expect_equal(as.character(as.mo("Escherichia species")), "B_ESCHR")
expect_equal(as.character(as.mo("Escherichia")), "B_ESCHR")
expect_equal(as.character(as.mo("Eschr spp.")), "B_ESCHR")
expect_equal(as.character(as.mo(" B_ESCHR_COLI ")), "B_ESCHR_COLI")
expect_equal(as.character(as.mo("e coli")), "B_ESCHR_COLI") # not Campylobacter
expect_equal(as.character(as.mo("klpn")), "B_KLBSL_PNMN")
expect_equal(as.character(as.mo("Klebsiella")), "B_KLBSL")
expect_equal(as.character(as.mo("K. pneumo rhino")), "B_KLBSL_PNMN_RHNS") # K. pneumoniae subspp. rhinoscleromatis
expect_equal(as.character(as.mo("Bartonella")), "B_BRTNL")
expect_equal(as.character(as.mo("C. difficile")), "B_CRDDS_DFFC")
expect_equal(as.character(as.mo("L. pneumophila")), "B_LGNLL_PNMP")
expect_equal(as.character(as.mo("Streptococcus")), "B_STRPT") # not Peptostreptoccus
expect_equal(as.character(as.mo("Estreptococos grupo B")), "B_STRPT_GRPB")
expect_equal(as.character(as.mo("Group B Streptococci")), "B_STRPT_GRPB")
expect_equal(as.character(as.mo(c("GAS", "GBS", "haemoly strep"))), c("B_STRPT_GRPA", "B_STRPT_GRPB", "B_STRPT_HAEM"))
expect_equal(as.character(as.mo("S. pyo")), "B_STRPT_PYGN") # not Actinomyces pyogenes
# GLIMS
expect_equal(as.character(as.mo("bctfgr")), "B_BCTRD_FRGL")
expect_equal(as.character(as.mo("MRSE")), "B_STPHY_EPDR")
expect_equal(as.character(as.mo("VRE")), "B_ENTRC")
expect_equal(as.character(as.mo("MRPA")), "B_PSDMN_AERG")
expect_equal(as.character(as.mo("PISP")), "B_STRPT_PNMN")
expect_equal(as.character(as.mo("PRSP")), "B_STRPT_PNMN")
expect_equal(as.character(as.mo("VISP")), "B_STRPT_PNMN")
expect_equal(as.character(as.mo("VRSP")), "B_STRPT_PNMN")
expect_equal(as.character(as.mo("CNS")), "B_STPHY_CONS")
expect_equal(as.character(as.mo("CoNS")), "B_STPHY_CONS")
expect_equal(as.character(as.mo("CPS")), "B_STPHY_COPS")
expect_equal(as.character(as.mo("CoPS")), "B_STPHY_COPS")
expect_equal(as.character(as.mo("VGS")), "B_STRPT_VIRI")
expect_equal(as.character(as.mo("streptococcus milleri")), "B_STRPT_MILL")
expect_equal(as.character(as.mo(c("Gram negative", "Gram positive"))), c("B_GRAMN", "B_GRAMP"))
# expect_warning(as.mo("Acinetobacter calcoaceticus/baumannii complex"))
# prevalent MO
expect_identical(
suppressWarnings(as.character(
as.mo(c(
"stau", # WHONET code
"STAU",
"staaur",
"S. aureus",
"S aureus",
"Sthafilokkockus aureus", # handles incorrect spelling
"Staphylococcus aureus (MRSA)",
"MRSA", # Methicillin Resistant S. aureus
"VISA", # Vancomycin Intermediate S. aureus
"VRSA", # Vancomycin Resistant S. aureus
115329001 # SNOMED CT code
))
)),
rep("B_STPHY_AURS", 11)
)
expect_identical(
as.character(
as.mo(c("EHEC", "EPEC", "EIEC", "STEC", "ATEC", "UPEC"))
),
rep("B_ESCHR_COLI", 6)
)
# unprevalent MO
expect_identical(
as.character(
as.mo(c(
"parnod",
"Paraburkholderia nodosa"
))
),
rep("B_PRBRK_NODS", 2)
)
# empty values
expect_identical(as.character(as.mo(c("", " ", NA, NaN))), rep(NA_character_, 4))
expect_identical(as.character(as.mo(" ")), NA_character_)
# too few characters
# expect_warning(as.mo("ab"))
expect_identical(
suppressWarnings(as.character(as.mo(c("Qq species", "MRSA", "K. pneu rhino", "esco")))),
c("UNKNOWN", "B_STPHY_AURS", "B_KLBSL_PNMN_RHNS", "B_ESCHR_COLI")
)
# check for Becker classification
expect_identical(as.character(as.mo("S. epidermidis", Becker = FALSE)), "B_STPHY_EPDR")
expect_identical(as.character(as.mo("S. epidermidis", Becker = TRUE)), "B_STPHY_CONS")
expect_identical(as.character(as.mo("STAEPI", Becker = TRUE)), "B_STPHY_CONS")
expect_identical(as.character(as.mo("Sta intermedius", Becker = FALSE)), "B_STPHY_INTR")
expect_identical(as.character(as.mo("Sta intermedius", Becker = TRUE)), "B_STPHY_COPS")
expect_identical(as.character(as.mo("STAINT", Becker = TRUE)), "B_STPHY_COPS")
# aureus must only be influenced if Becker = "all"
expect_identical(as.character(as.mo("STAAUR", Becker = FALSE)), "B_STPHY_AURS")
expect_identical(as.character(as.mo("STAAUR", Becker = TRUE)), "B_STPHY_AURS")
expect_identical(as.character(as.mo("STAAUR", Becker = "all")), "B_STPHY_COPS")
# check for Lancefield classification
expect_identical(as.character(as.mo("S. pyogenes", Lancefield = FALSE)), "B_STRPT_PYGN")
expect_identical(as.character(as.mo("S. pyogenes", Lancefield = TRUE)), "B_STRPT_GRPA")
expect_identical(as.character(as.mo("STCPYO", Lancefield = TRUE)), "B_STRPT_GRPA") # group A
expect_identical(as.character(as.mo("S. agalactiae", Lancefield = FALSE)), "B_STRPT_AGLC")
expect_identical(as.character(as.mo("S. agalactiae", Lancefield = TRUE)), "B_STRPT_GRPB") # group B
expect_identical(as.character(suppressWarnings(as.mo("estreptococos grupo B"))), "B_STRPT_GRPB")
expect_identical(as.character(as.mo("S. equi", Lancefield = FALSE)), "B_STRPT_EQUI")
expect_identical(as.character(as.mo("S. equi", Lancefield = TRUE)), "B_STRPT_GRPC") # group C
# Enterococci must only be influenced if Lancefield = "all"
expect_identical(as.character(as.mo("E. faecium", Lancefield = FALSE)), "B_ENTRC_FACM")
expect_identical(as.character(as.mo("E. faecium", Lancefield = TRUE)), "B_ENTRC_FACM")
expect_identical(as.character(as.mo("E. faecium", Lancefield = "all")), "B_STRPT_GRPD") # group D
expect_identical(as.character(as.mo("S. anginosus", Lancefield = FALSE)), "B_STRPT_ANGN")
expect_identical(as.character(as.mo("S. anginosus", Lancefield = TRUE)), "B_STRPT_GRPF") # group F
expect_identical(as.character(as.mo("S. sanguinis", Lancefield = FALSE)), "B_STRPT_SNGN")
expect_identical(as.character(as.mo("S. sanguinis", Lancefield = TRUE)), "B_STRPT_GRPH") # group H
expect_identical(as.character(as.mo("S. salivarius", Lancefield = FALSE)), "B_STRPT_SLVR")
expect_identical(as.character(as.mo("S. salivarius", Lancefield = TRUE)), "B_STRPT_GRPK") # group K
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
# select with one column
expect_identical(
example_isolates %>%
slice(1:10) %>%
left_join_microorganisms() %>%
select(genus) %>%
as.mo() %>%
as.character(),
c(
"B_ESCHR", "B_ESCHR", "B_STPHY", "B_STPHY", "B_STPHY",
"B_STPHY", "B_STPHY", "B_STPHY", "B_STPHY", "B_STPHY"
)
)
# select with two columns
expect_identical(
example_isolates %>%
slice(1:10) %>%
pull(mo),
example_isolates %>%
slice(1:10) %>%
left_join_microorganisms() %>%
select(genus, species) %>%
as.mo()
)
# too many columns
expect_error(example_isolates %>% select(1:3) %>% as.mo())
# test pull
expect_equal(
nrow(example_isolates %>% mutate(mo = as.mo(mo))),
2000
)
expect_true(example_isolates %>% pull(mo) %>% is.mo())
}
# print
expect_output(print(as.mo(c("B_ESCHR_COLI", NA))))
# test data.frame
expect_equal(
nrow(data.frame(test = as.mo("B_ESCHR_COLI"))),
1
)
# check empty values
expect_equal(
as.character(as.mo("")),
NA_character_
)
# check less prevalent MOs
expect_equal(as.character(as.mo("Actinosynnema pretiosum auranticum")), "B_ANNMA_PRTS_ARNT")
# expect_equal(as.character(as.mo("Actinosynnema preti aura")), "B_ANNMA_PRTS_ARNT")
# expect_equal(as.character(as.mo("A pre aur")), "B_ANNMA_PRTS_ARNT")
expect_equal(as.character(as.mo("Actinosynnema pretiosum")), "B_ANNMA_PRTS")
expect_equal(as.character(as.mo("Actinosynnema")), "B_ANNMA")
expect_equal(as.character(as.mo(" B_ANNMA_PRTS ")), "B_ANNMA_PRTS")
# check old names
expect_equal(suppressMessages(as.character(as.mo("Escherichia blattae"))), "B_SHMWL_BLTT")
expect_equal(suppressMessages(as.character(as.mo(c("E. coli", "Chlamydo psittaci")))), c("B_ESCHR_COLI", "B_CHLMY_PSTT"))
expect_equal(suppressMessages(mo_name("eubcom")), "Clostridium combesii")
# predefined reference_df
expect_equal(
as.character(as.mo("TestingOwnID",
reference_df = data.frame(mycol = "TestingOwnID", mo = "B_ESCHR_COLI")
)),
"B_ESCHR_COLI"
)
expect_equal(
as.character(as.mo(c("TestingOwnID", "E. coli"),
reference_df = data.frame(mycol = "TestingOwnID", mo = "B_ESCHR_COLI")
)),
c("B_ESCHR_COLI", "B_ESCHR_COLI")
)
# # expect_warning(as.mo("TestingOwnID", reference_df = NULL))
expect_error(as.mo("E. coli", reference_df = data.frame(mycol = "TestingOwnID")))
# combination of existing mo and other code
expect_identical(
suppressWarnings(as.character(as.mo(c("B_ESCHR_COL", "ESCCOL")))),
c("B_ESCHR_COLI", "B_ESCHR_COLI")
)
# from different sources
expect_equal(
as.character(as.mo(
c("PRTMIR", "bclcer", "B_ESCHR_COLI")
)),
c("B_PROTS_MRBL", "B_BCLLS_CERS", "B_ESCHR_COLI")
)
# hard to find
expect_equal(
as.character(suppressMessages(as.mo(
c(
"Microbacterium paraoxidans",
"Streptococcus suis (bovis gr)",
"Raoultella (here some text) terrigena"
)
))),
c("B_MCRBC_PRXY", "B_STRPT_SUIS", "B_KLBSL_TRRG")
)
x <- as.mo("Sta. aur")
# no viruses
expect_equal(suppressWarnings(as.mo("Virus")), as.mo("UNKNOWN"))
# summary
expect_equal(length(summary(example_isolates$mo)), 6)
# WHONET codes and NA/NaN
expect_true(all(is.na(as.mo(c("xxx", "na", "nan")))))
expect_equal(as.character(as.mo(c("con", "eco"))), c("UNKNOWN", "B_ESCHR_COLI"))
expect_equal(
as.character(suppressWarnings(as.mo(c("other", "none", "unknown")))),
rep("UNKNOWN", 3)
)
# ..coccus
expect_equal(
as.character(as.mo(c("meningococ", "gonococ", "pneumococ"))),
c("B_NESSR_MNNG", "B_NESSR_GNRR", "B_STRPT_PNMN")
)
# yeasts and fungi
expect_equal(
suppressWarnings(as.character(as.mo(c("yeasts", "fungi")))),
c("F_YEAST", "F_FUNGUS")
)
if (AMR:::pkg_is_available("tibble")) {
# print tibble
expect_output(print(tibble::tibble(mo = as.mo("B_ESCHR_COLI"))))
}
# assigning and subsetting
x <- example_isolates$mo
expect_inherits(x[1], "mo")
expect_inherits(x[[1]], "mo")
expect_inherits(c(x[1], x[9]), "mo")
# expect_warning(x[1] <- "invalid code")
# expect_warning(x[[1]] <- "invalid code")
# expect_warning(c(x[1], "test"))
# ignoring patterns
expect_true(is.na(as.mo("E. coli ignorethis", ignore_pattern = "this")))
# frequency tables
if (AMR:::pkg_is_available("cleaner")) {
expect_inherits(cleaner::freq(example_isolates$mo), "freq")
}
# skimr
if (AMR:::pkg_is_available("skimr", min_version = "2.0.0", also_load = TRUE)) {
expect_named(
skim(example_isolates$mo),
c("skim_type", "skim_variable", "n_missing", "complete_rate", "mo.n_unique", "mo.gram_negative", "mo.gram_positive", "mo.yeast", "mo.top_genus", "mo.top_species")
)
}
})
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