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
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
640888f408
(v2.1.1.9064) update all microbial taxonomy, add mycobank, big documentation update
2024-07-16 14:53:17 +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
8d902410f9
unit tests
2023-02-18 14:56:06 +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
84ed8c32bb
documentation
2023-01-06 19:21:04 +01:00
a0ee86536a
unit tests
2023-01-05 14:43:18 +01:00
f619fb683b
support new mo codes
2022-12-27 15:16:15 +01:00
8da2467209
updated taxonomy
2022-12-12 00:14:56 +01:00
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
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
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
d04e83f494
(v1.7.1.9005) ab class selectors for R-3.0 and R-3.1
2021-06-22 12:16:42 +02:00
655b813e99
(v1.6.0.9022) unit test fix
2021-05-13 15:56:12 +02:00
29dbfa2f49
(v1.6.0.9021) join functions update
2021-05-12 18:15:03 +02:00
a9fd4aa49f
(v1.6.0.9013) website update
2021-04-29 17:16:30 +02:00
70b803dbb6
(v1.6.0.9008) unlike, bugfix for col_mo naming
2021-04-23 09:59:36 +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
81af41da3a
(v1.4.0.9041) updates based on review
2020-12-17 16:22:25 +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
36ec8b0d81
(v1.3.0.9033) skimr fix
2020-09-28 11:00:59 +02:00
050a9a04fb
(v1.3.0.9030) matching score update
2020-09-26 16:26:01 +02:00
4e40e42011
(v1.3.0.9022) mo_matching_score(), poorman update, as.rsi() fix
2020-09-18 16:05:53 +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
e88d7853f5
(v1.2.0.9010) documentation fix
2020-06-17 21:35:10 +02:00
2c8d600914
(v1.2.0.9002) fix for joins
2020-06-03 14:33:55 +02:00
5dc4c96b7d
(v1.2.0.9001) filter_ab_class() update
2020-06-03 11:48:00 +02:00
86d44054f0
(v1.1.0.9020) updated taxonomy
2020-05-27 16:37:49 +02:00
7f3da74b17
(v1.1.0.9004) lose dependencies
2020-05-16 13:05:47 +02:00
219cff403f
(v1.0.1.9004) Support dplyr 1.0.0
2020-03-14 14:05:43 +01:00
9b8b02960e
(v0.9.0.9023) EUCAST 2020 guidelines
2020-02-14 19:54:13 +01:00
