Claude
8760c6d85a
Add {.topic} markup for non-function help page references
...
Replace {.code ?AMR-options} and backtick-style ?AMR-options / ?AMR-deprecated
references with proper {.topic AMR-options} / {.topic AMR-deprecated} cli markup
in count.R, interpretive_rules.R, proportion.R, and zz_deprecated.R.
Add {.topic} fallback handler to format_message() in aa_helper_functions.R:
plain-text environments render {.topic foo} as ?foo, and the [text](topic)
link form extracts just the display text (same pattern as {.help}).
Also convert remaining backtick function/arg references in proportion.R to
{.help [{.fun ...}](AMR::...)}, {.arg}, and {.code} markup for consistency.
Note: zzz.R intentionally keeps the backtick form since its startup message
goes through packageStartupMessage() which bypasses our cli infrastructure.
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
2026-03-18 22:41:43 +00:00
12cf144b19
(v3.0.1.9021) add guideline to resistance() and susceptibility()
2026-02-12 20:34:06 +01:00
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
d94bdd2c6a
(v3.0.0.9008) fix ggplot_sir(), support lighter green for SDD
2025-07-17 17:05:41 +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
a2c2be23c1
(v2.1.1.9190) antibiotics deprecation in antibiogram()
2025-03-09 10:41:11 +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
baea4323c7
(v2.1.1.9140) WISCA fix
2025-02-05 20:48:35 +01:00
92c4fc0f94
(v2.1.1.9125) replace 'antibiotic selectors' with 'antimicrobial selectors'
2025-01-17 12:09:39 +01:00
5c4d8fcd2a
(v2.1.1.9095) Python support
2024-10-15 17:12:55 +02:00
ef79d22daf
(v2.1.1.9093) New brand names
2024-10-06 22:30:52 +02:00
ac1c40d8bb
(v2.1.1.9081) HUGE microorganisms update for fungi!
2024-09-29 22:17:56 +02:00
640888f408
(v2.1.1.9064) update all microbial taxonomy, add mycobank, big documentation update
2024-07-16 14:53:17 +02:00
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
0039cb05d6
update MIC comparisons
2024-04-05 16:44:43 +02:00
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
80cfc503c2
check for 2.0
2023-03-12 13:02:37 +01:00
9179e98e12
patient ID in first isolate
2023-03-11 17:13:19 +01:00
7ad8635994
documentation for 'data.table' AB selectors
2023-03-11 16:54:02 +01:00
dad25302f2
make rsi work in more cases, documentation update
2023-02-22 14:38:57 +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
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
d40e0ef20b
completely updated antibiotics
2022-10-30 14:31:45 +01:00
4bebba3610
fix for scoped dplyr verbs
2022-10-21 15:13:19 +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
25cef46c59
(v1.8.0) prerelease 1.8.0
2021-12-23 18:56:28 +01:00
56f1ce328a
(v1.7.1.9067) Support for Swedish and Russian
2021-12-12 09:42:03 +01:00
99be4c7e7e
(v1.7.1.9002) ab class selectors update
2021-06-14 22:04:04 +02:00
a13fd98e8b
(v1.6.0.9063) prepare new release
2021-05-24 09:00:11 +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
