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
ba4c159154
(v3.0.1.9019) Wildtype/Non-wildtype support, and start with interpretive_rules()
...
Fixes #246
Fixes #254
Fixes #255
Fixes #256
2026-02-08 23:15:40 +01:00
10ba36821e
(v3.0.0.9034) fix MycoBank synonyms
2025-09-18 13:58:34 +01:00
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
8ba2e4ed94
(v2.1.1.9141) new AMR selectors, eucast overwrite arg
2025-02-07 18:01:22 +01:00
66833b4f5a
(v2.1.1.9126) implemented WISCA! Also added top_n_microorganisms() and fixed Python wrapper
2025-01-26 23:01:17 +01:00
8907e8e4af
(v2.1.1.9083) update for first_isolate()
2024-09-30 19:13:53 +02:00
681fe011fe
(v2.1.1.9082) algorithm updates
2024-09-30 18:46:55 +02:00
640888f408
(v2.1.1.9064) update all microbial taxonomy, add mycobank, big documentation update
2024-07-16 14:53:17 +02:00
9bf7584d58
(v2.1.1.9049) new 2024 breakpoints, add AMO, set NI instead of N
2024-06-14 22:39:01 +02:00
08a27922a8
new SDD and N for as.sir()
2024-05-20 15:27:04 +02:00
c7461766ce
Remove RSI from package, add extra MIC scale functions
2023-12-03 11:34:48 +01:00
7cda9e575b
prepare for CRAN
2023-10-20 14:51:48 +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
0bcf55d3b6
improve as.mo()
2023-05-24 15:55:53 +02:00
3018fb87a9
icu_exclude in first_isolate(), fixes #110
2023-05-17 22:12:10 +02:00
9179e98e12
patient ID in first isolate
2023-03-11 17:13:19 +01:00
262598b8d7
support for old rsi arguments
2023-03-11 14:24:34 +01:00
dad25302f2
make rsi work in more cases, documentation update
2023-02-22 14:38:57 +01:00
6016547f1f
support for dplyr 1.1.0
2023-02-15 17:02:10 +01:00
45a9697c84
unit tests
2023-02-12 17:10:48 +01:00
bc434db835
bring back antibiogram(), without deps
2023-02-10 16:18:00 +01:00
70a7ba0206
fix first isolate
2023-02-10 13:13:17 +01:00
1a0dc4bf46
revert back to pre-antibiogram
2023-02-09 13:07:39 +01:00
9e99e66f01
use dplyr where available, new antibiogram() for WISCA, fixed Salmonella Typhi/Paratyphi
2023-02-06 11:57:22 +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
aa2c0639d0
add confidence intervals ( fixed #70 ), remove combine_IR
2022-10-20 16:08:01 +02:00
85e2fbe4a3
remove warnings from unit tests
2022-10-19 11:47:57 +02:00
4fe90092c7
fix for NA in as.ab()
2022-10-10 15:44:59 +02:00
Dr. Matthijs Berends
cd2acc4a29
New mo algorithm, prepare for 2.0
2022-10-05 09:12:22 +02:00
71db246d5c
unit test fix
2022-08-28 19:17:12 +02:00
4d050aef7c
styled, unit test fix
2022-08-28 10:31:50 +02:00
303d61b473
new tibble export
2022-08-27 20:49:37 +02:00
952d16de33
new, automated website
2022-08-21 16:37:20 +02:00
25cef46c59
(v1.8.0) prerelease 1.8.0
2021-12-23 18:56:28 +01:00
76dee66852
(v1.7.1.9074) as.mo() improvement, ASCII replacements for unit tests
2021-12-14 22:39:23 +01:00
1e66a3daf3
(v1.7.1.9068) new logo, unit tests
2021-12-12 11:07:02 +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
694cf5ba77
(v1.7.1.9054) mdro() update - fixes #49 , first_isolate() speedup
2021-11-28 23:01:26 +01:00
81a1a432bd
(v1.7.1.9038) dplyr grouping fix on windows?
2021-09-01 16:52:55 +02:00
