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
151af21f38
(v3.0.1.9005) re-add tidymodels implementation
2025-12-21 12:19:43 +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
640888f408
(v2.1.1.9064) update all microbial taxonomy, add mycobank, big documentation update
2024-07-16 14:53:17 +02:00
bc4f8515e2
new Norwegian link
2024-03-03 23:24:57 +01:00
7be4dabbc0
support veterinary MIC/disk translation
2024-02-24 15:16:52 +01:00
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
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
593d740b84
documentation, file permissions
2023-01-19 12:54:53 +01:00
f619fb683b
support new mo codes
2022-12-27 15:16:15 +01:00
Dr. Matthijs Berends
cd2acc4a29
New mo algorithm, prepare for 2.0
2022-10-05 09:12:22 +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
b84d647cac
(v1.8.1.9012) update prevalence of some genera
2022-06-03 13:28:55 +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
8f5e5a3fc2
(v1.7.1.9050) fix for as.mo
2021-10-05 14:00:35 +02:00
2ab21b7af3
(v1.7.1.9026) updated DDDs
2021-08-19 23:43:02 +02:00
a44283f998
(v1.7.1.9024) unit tests
2021-08-17 14:34:11 +02:00
4fbf9e1720
(v1.6.0.9064) prepare new release
2021-05-24 09:34:08 +02:00
a13fd98e8b
(v1.6.0.9063) prepare new release
2021-05-24 09:00:11 +02:00
04ef5b28e7
(v1.6.0.9050) printing NA in custom_eucast_rules()
2021-05-20 10:10:40 +02:00
29dbfa2f49
(v1.6.0.9021) join functions update
2021-05-12 18:15:03 +02:00
2eca8c3f01
(v1.5.0.9014) only_rsi_columns, is.rsi.eligible improvement
2021-02-02 23:57:35 +01:00
4eab095306
(v1.5.0.9006) major documentation update
2021-01-18 16:57:56 +01:00
8b52f9b1be
(v1.4.0.9047) unit tests
2020-12-27 00:30:28 +01:00
128ebcfd62
(v1.4.0.9043) documentation update
2020-12-22 00:51:17 +01:00
15c732703d
(v1.4.0.9015) bugfix
2020-11-10 16:35:56 +01:00
5a607abb36
(v1.4.0.9011) message formatting
2020-10-27 15:56:51 +01:00
4e9ccb4435
(v1.4.0.9001) is_gram_positive(), is_gram_negative(), parameter hardening
2020-10-19 17:09:19 +02:00
28e77680c5
(v1.4.0) matching score update
2020-10-08 11:16:03 +02:00
4e0374af29
(v1.3.0.9035) mdro() for EUCAST 3.2, examples cleanup
2020-09-29 23:35:46 +02:00
68e6e1e329
(v1.3.0.9034) eucast_rules summary fix
2020-09-29 10:40:25 +02:00
4e40e42011
(v1.3.0.9022) mo_matching_score(), poorman update, as.rsi() fix
2020-09-18 16:05:53 +02:00
c4b87fe241
(v1.3.0.9014) as.mo() speed improvement
2020-09-03 12:31:48 +02:00
6ab468362d
(v1.2.0.9034) code cleaning
2020-07-13 09:17:24 +02:00
76fc8e1b14
(v1.2.0.9026) move to github
2020-07-08 14:48:06 +02:00
93a158aebd
(v1.2.0.9011) mo_domain(), improved error handling
2020-06-22 11:18:40 +02:00
ac12392da3
(v1.2.0.9008) ab_class improvement
2020-06-17 15:14:37 +02:00
1b1e243d14
(v1.1.0.9016) small fix
2020-05-21 12:28:57 +02:00
218fd08097
(v1.1.0.9011) lose dependencies
2020-05-18 13:59:34 +02:00
bf0402a653
(v1.1.0.9009) lose dependencies
2020-05-18 10:30:53 +02:00
