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
b6211931f8
(v3.0.1.9022) add ceftibuten/avibactam (CTA), kasugamycin (KAS), ostreogrycin (OST), thiostrepton (THS), xeruborbactam (XER), zorbamycin (ZOR)
2026-03-03 15:41:08 +01:00
12cf144b19
(v3.0.1.9021) add guideline to resistance() and susceptibility()
2026-02-12 20:34:06 +01:00
d94bdd2c6a
(v3.0.0.9008) fix ggplot_sir(), support lighter green for SDD
2025-07-17 17:05:41 +02:00
e70f3de02e
(v2.1.1.9286) deprecate antibiotics better, add ATC for ceftaroline
2025-06-01 11:54:40 +02:00
38cebc1541
(v2.1.1.9279) fix documentation, add foreign S3 exports to functions
2025-05-16 16:55:29 +02:00
4e7fca3b38
(v2.1.1.9253) parallel computing
2025-04-26 15:47:00 +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
a905303296
(v2.1.1.9234) fix CLSI
2025-04-07 17:36:01 +01:00
b972bbb96f
(v2.1.1.9230) deprecated resistance_predict(), data set folder name without space
2025-03-28 16:48:56 +01:00
a2c2be23c1
(v2.1.1.9190) antibiotics deprecation in antibiogram()
2025-03-09 10:41:11 +01:00
b67613ce08
(v2.1.1.9187) WISCA fix
2025-03-07 22:27:21 +01:00
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
d94efb0f5e
(v2.1.1.9147) scale fixes and WISCA update, fix conserved capped values
2025-02-14 14:16:46 +01:00
22afd918e6
(v2.1.1.9136) console colours, updated Suggests, added as.ab() improvement
2025-01-31 16:01:52 +01:00
92c4fc0f94
(v2.1.1.9125) replace 'antibiotic selectors' with 'antimicrobial selectors'
2025-01-17 12:09:39 +01:00
08ddbaa930
(v2.1.1.9123) add EFF code to antibiotics data set
2025-01-15 16:14:09 +01:00
4e96a56b6a
(v2.1.1.9073) unit tests
2024-09-19 13:57:36 +02:00
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
2dee1d71dc
(v2.1.1.9053) add verbose to as.sir(), unit test fix
2024-06-17 10:38:45 +02:00
bdbf5198a2
(v2.1.1.9050) vctrs fix for sir, small documentation fixes
2024-06-15 15:33:49 +02:00
de17de1be9
(v2.1.1.9048) vctrs update for sir
2024-06-13 20:55:17 +02:00
2899b3c840
new mo_group_members()
2024-04-19 10:18:21 +02:00
94e9a4d99b
update MIC implementation
2024-04-07 20:22:59 +02:00
0039cb05d6
update MIC comparisons
2024-04-05 16:44:43 +02:00
35963ca3dc
vctrs fix
2024-02-24 18:51:37 +01:00
4aa5413641
fix unit test
2024-02-24 18:14:50 +01:00
7be4dabbc0
support veterinary MIC/disk translation
2024-02-24 15:16:52 +01:00
c7461766ce
Remove RSI from package, add extra MIC scale functions
2023-12-03 11:34:48 +01:00
7a4628b73f
Added C. freundii complex and Y. pseudotuberculosis complex
2023-07-14 10:49:06 +02:00
8df1cd8d97
interpretation fixes
2023-07-11 09:50:45 +02:00
a4e2e25e3f
reftbl in plots, speedup for as.sir() and mo_validate
2023-07-10 16:43:46 +02:00
acb534102b
new species groups, updated clinical breakpoints
2023-07-08 17:30:05 +02:00
Dr. Matthijs Berends
f065945d7b
Update clinical breakpoints and fix some as.mo() bugs ( #117 )
...
* Updates clinical breakpoints EUCAST/CLSI 2023, fixes #102 , fixes #112 , fixes #113 , fixes #114 , fixes #115
* docs
* implement ecoffs
* unit tests
2023-06-22 15:10:59 +02:00
9591688811
documentation update
2023-05-27 10:39:22 +02:00
c28cfa3a77
fix documentation
2023-03-16 08:55:37 +01:00
80cfc503c2
check for 2.0
2023-03-12 13:02:37 +01:00
049baf0a71
fix for antibiograms on R < 3.5
2023-02-24 09:43:10 +01:00
e70f2cd32c
knitr format
2023-02-23 16:27:40 +01:00
8d902410f9
unit tests
2023-02-18 14:56:06 +01:00
bc434db835
bring back antibiogram(), without deps
2023-02-10 16:18:00 +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
b94bc6c67b
adding mo fixes
2023-01-14 19:50:25 +01:00
1db74e86cd
good start-up practice
2022-12-29 16:23:57 +01:00
