Claude
ad31fba556
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
2026-03-18 12:10:17 +00:00
46f80b1378
(v2.1.1.9288) mdro fix
2025-06-01 15:35:04 +02:00
4b171745de
(v2.1.1.9276) mdro() fix
2025-05-15 10:39:48 +02:00
abee2a954e
(v2.1.1.9252) fix MIC for >= and <=
2025-04-25 10:19:40 +02:00
40d7a971c3
(v2.1.1.9236) documentation
2025-04-12 11:46:42 +02:00
36fd99e1f4
(v2.1.1.9235) New website!
2025-04-08 15:54:30 +01:00
1fdab84103
(v2.1.1.9233) chore: make all argument texts full sentences
2025-03-31 14:53:24 +02:00
63099cd81e
(v2.1.1.9232) is.mic() iteration, documentation cleanup
2025-03-31 10:51:31 +02:00
f7938289eb
(v2.1.1.9186) replace antibiotics with antimicrobials!
2025-03-07 20:43:26 +01:00
07efc292bc
(v2.1.1.9163) cleanup
2025-02-27 14:04:29 +01:00
92c4fc0f94
(v2.1.1.9125) replace 'antibiotic selectors' with 'antimicrobial selectors'
2025-01-17 12:09:39 +01:00
ddb23b6e73
(v2.1.1.9071) update veterinary SIR interpretation, add only_fungi
2024-09-19 11:44:56 +02:00
640888f408
(v2.1.1.9064) update all microbial taxonomy, add mycobank, big documentation update
2024-07-16 14:53:17 +02:00
0d8a91db49
rename pre-commit hook to pre-commit checks (no-check)
2024-04-23 10:55:48 +02:00
acb534102b
new species groups, updated clinical breakpoints
2023-07-08 17:30:05 +02:00
9591688811
documentation update
2023-05-27 10:39:22 +02:00
dad25302f2
make rsi work in more cases, documentation update
2023-02-22 14:38:57 +01:00
19fd0ef121
sort sir history
2023-01-23 15:01:21 +01:00
Dr. Matthijs Berends
98e62c9af2
Replace RSI with SIR
2023-01-21 23:47:20 +01:00
f619fb683b
support new mo codes
2022-12-27 15:16:15 +01:00
f6862a139d
expert rules 12.0
2022-11-14 15:20:39 +01:00
7ca44fb756
cleanup and new intro logo
2022-11-13 13:44:25 +01:00
85e2fbe4a3
remove warnings from unit tests
2022-10-19 11:47:57 +02:00
76bcd3528c
move object assignment to AMR_env
2022-10-14 13:02:50 +02:00
Dr. Matthijs Berends
cd2acc4a29
New mo algorithm, prepare for 2.0
2022-10-05 09:12:22 +02:00
fbd5d32541
small fixes
2022-08-29 09:35:36 +02:00
4d050aef7c
styled, unit test fix
2022-08-28 10:31:50 +02:00
3864ab2fb8
Feather and Parquet files
2022-08-26 22:25:15 +02:00
952d16de33
new, automated website
2022-08-21 16:37:20 +02:00
3b2b2be5f8
(v1.8.0.9002) as.rsi() cleanup, more informative warnings
2022-03-02 15:38:55 +01:00
25cef46c59
(v1.8.0) prerelease 1.8.0
2021-12-23 18:56:28 +01:00
77ba4318ea
(v1.7.1.9064) eucast 3.3 for mdro(), major change to repeated calling
2021-12-11 13:41:31 +01:00
e18c49ed93
(v1.7.1.9063) not_intrinsic_resistant
2021-12-09 10:48:25 +01:00
694cf5ba77
(v1.7.1.9054) mdro() update - fixes #49 , first_isolate() speedup
2021-11-28 23:01:26 +01:00
e6ce25162e
(v1.7.1.9031) dplyr grouping fix on windows?
2021-08-30 14:07:46 +02:00
4e1efd902c
(v1.7.1.9022) rely on vctrs for ab selectors
2021-07-23 21:42:11 +02:00
3e26929838
(v1.7.1.9009) fix for ab class selectors
2021-07-03 21:56:53 +02:00
4fbf9e1720
(v1.6.0.9064) prepare new release
2021-05-24 09:34:08 +02:00
29dbfa2f49
(v1.6.0.9021) join functions update
2021-05-12 18:15:03 +02:00
93683a4ae2
(v1.6.0.9010) big first_isolate() update
2021-04-26 23:57:37 +02:00
4e0a9533ad
(v1.5.0.9041) SNOMED update
2021-03-11 21:42:30 +01:00
4a84894f79
(v1.5.0.9016) only_rsi_columns update, documentation
2021-02-08 14:18:42 +01:00
8fda473e49
(v1.5.0.9015) unit test fix, grouped first isolates
2021-02-04 16:48:16 +01:00
2eca8c3f01
(v1.5.0.9014) only_rsi_columns, is.rsi.eligible improvement
2021-02-02 23:57:35 +01:00
1ba44776a1
(v1.5.0.9008) Internal data sets to pkg, speed for auto col determination
2021-01-22 10:20:41 +01:00
4eab095306
(v1.5.0.9006) major documentation update
2021-01-18 16:57:56 +01:00
7ebc534ccd
(v1.5.0.9003) verbose output of mdro()
2021-01-15 22:44:52 +01:00
526f8afb08
(v1.4.0.9052) replaced all sapply's with type-safe vapply's
2020-12-28 22:24:33 +01:00
8b52f9b1be
(v1.4.0.9047) unit tests
2020-12-27 00:30:28 +01:00
e03b3c96d3
(v1.4.0.9030) as.mo() fix for known lab codes
2020-12-03 16:59:04 +01:00
