Claude
3928a3de55
Fix {.help} markup to use correct cli link format [{.fun fn}](AMR::fn)
...
Replace all instances of {.help AMR::fn}() (incorrect format with manual
parentheses outside the link) with {.help [{.fun fn}](AMR::fn)} which is
the correct cli hyperlink syntax: the display text [{.fun fn}] renders the
function name with parentheses automatically, and (AMR::fn) is the link target.
Also update the plain-text fallback handler in aa_helper_functions.R to
extract the display text from the [text](topic) markdown link format,
so that non-cli environments show just the function name (e.g. `fn()`),
not the raw link markup.
Dynamic cases in amr_selectors.R and mo_property.R also updated.
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
2026-03-18 22:37:46 +00:00
Claude
10c00ff606
Implement cli::code_highlight() for R code examples in messages (issue #191 )
...
Add highlight_code() helper that wraps cli::code_highlight() when cli >= 3.0.0
is available, falling back to plain code otherwise. Apply it to all inline
R code examples embedded in message/warning/stop strings across the package.
Also convert remaining backtick-quoted function and argument references in
messaging calls to proper cli markup: {.help AMR::fn}(), {.arg arg},
{.code expr}, and {.pkg pkg} throughout ab.R, ab_from_text.R, av_from_text.R,
amr_selectors.R, count.R, custom_antimicrobials.R, custom_microorganisms.R,
interpretive_rules.R, mo.R, mo_property.R, sir.R, sir_calc.R.
Fixes #191
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
2026-03-18 22:23:39 +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
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
9bf7584d58
(v2.1.1.9049) new 2024 breakpoints, add AMO, set NI instead of N
2024-06-14 22:39:01 +02:00
d214f74e25
allow column name for ab in as.sir()
2024-05-20 21:29:13 +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
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
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
4e1efd902c
(v1.7.1.9022) rely on vctrs for ab selectors
2021-07-23 21:42:11 +02:00
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
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
df37584189
(v1.4.0.9044) mo tibble printing, mo_shortname() fix
2020-12-24 23:29:10 +01:00
15c732703d
(v1.4.0.9015) bugfix
2020-11-10 16:35:56 +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
4e40e42011
(v1.3.0.9022) mo_matching_score(), poorman update, as.rsi() fix
2020-09-18 16:05:53 +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
f68d71a5e0
(v1.1.0.9007) lose dependencies
2020-05-16 21:40:50 +02:00
df2456b91f
(v1.1.0.9005) lose dependencies
2020-05-16 20:08:21 +02:00
7f3da74b17
(v1.1.0.9004) lose dependencies
2020-05-16 13:05:47 +02:00
ced1a7b7fa
(v0.9.0.9008) Happy new year! Add lifecycles
2020-01-05 17:22:09 +01:00
bb2ed55842
(v0.9.0) v0.9.0
2019-11-29 19:43:23 +01:00
c5f00f4a9f
(v0.8.0.9036) complete documentation rewrite
2019-11-28 22:32:17 +01:00
d22834c5b8
(v0.8.0.9029) cleanup
2019-11-10 15:50:18 +01:00
59ededa8dc
(v0.8.0.9027) adding susceptibility() and resistance()
2019-11-10 12:16:56 +01:00
e2d05cb1b0
(v0.8.0.9017) keywords update
2019-11-06 14:43:23 +01:00
00cdb498a0
(v0.7.1.9102) lintr
2019-10-11 17:21:02 +02:00
93be16484b
(v0.7.1.9063) septic_patients -> example_isolates
2019-08-27 16:45:42 +02:00
