Claude
1dabd4df3d
Replace bare backticks with cli inline markup across all messaging calls
...
- {.arg} for argument names in stop_/warning_/message_ calls
- {.cls} after "of class" text in format_class() and elsewhere
- {.fun} for function names (replaces `fn()` pattern)
- {.pkg} for tidyverse package names (dplyr, ggplot2)
- {.code} for code literals (TRUE, FALSE, expressions)
- Rewrite print.ab: use cli named-vector with * bullets and code
highlighting when cli >= 3.0.0; keep plain-text fallback otherwise
- Fix typo in as.sir(): "of must be" -> "or must be"
- switch sir.R verbose notes from message() to message_()
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
2026-03-19 08:35:26 +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
38cebc1541
(v2.1.1.9279) fix documentation, add foreign S3 exports to functions
2025-05-16 16:55:29 +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
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
aa8f6af185
(v2.1.1.9155) new mic_p50() and mic_p90() - updated AMR intro
2025-02-23 11:18:08 +01:00
1149360b27
(v2.1.1.9129) unit test fix
2025-01-27 16:17:03 +01:00
6efa317a81
(v2.1.1.9128) fix for bug-drug combinations
2025-01-27 11:51:40 +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
5c4d8fcd2a
(v2.1.1.9095) Python support
2024-10-15 17:12:55 +02:00
ac1c40d8bb
(v2.1.1.9081) HUGE microorganisms update for fungi!
2024-09-29 22:17:56 +02:00
127892430d
(v2.1.1.9078) 12 new formatting formats for antibiogram(), prepare for Bayesian WISCA
2024-09-22 11:45:51 +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
fc269e667d
unit test fix
2024-05-20 18:58:35 +02:00
08a27922a8
new SDD and N for as.sir()
2024-05-20 15:27:04 +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
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
dad25302f2
make rsi work in more cases, documentation update
2023-02-22 14:38:57 +01:00
ba255ddb00
website
2023-02-18 11:57:17 +01:00
45a9697c84
unit tests
2023-02-12 17:10:48 +01:00
c740967cf2
fix for binding rows
2023-02-12 11:20:14 +01:00
c51fb24363
pm_bind_rows
2023-02-11 22:28:48 +01:00
2007c3eef3
bind_rows
2023-02-10 17:09:48 +01:00
03294c7901
fix for Salmonella group A, unit tests
2023-02-10 16:47:25 +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
aa48c6bf53
pm fixes
2023-02-08 16:51:41 +01:00
822e9de82c
pm update, unit test fix?
2023-02-08 13:48:06 +01:00
9e99e66f01
use dplyr where available, new antibiogram() for WISCA, fixed Salmonella Typhi/Paratyphi
2023-02-06 11:57:22 +01:00
Dr. Matthijs Berends
98e62c9af2
Replace RSI with SIR
2023-01-21 23:47:20 +01:00
593d740b84
documentation, file permissions
2023-01-19 12:54:53 +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
c2801ba7a1
new rsi_translation
2022-10-22 22:00:15 +02:00
aa2c0639d0
add confidence intervals ( fixed #70 ), remove combine_IR
2022-10-20 16:08:01 +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
3f2f60ab77
language updates
2022-08-19 12:33:14 +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
