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
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
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
49da312506
(v2.1.1.9228) repo cleaning
2025-03-28 11:17:49 +01:00
969a42cc8c
(v2.1.1.9226) update intrinsic_resistant, unit test fixes
2025-03-27 15:20:22 +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
681fe011fe
(v2.1.1.9082) algorithm updates
2024-09-30 18:46:55 +02:00
ac1c40d8bb
(v2.1.1.9081) HUGE microorganisms update for fungi!
2024-09-29 22:17:56 +02:00
ddb23b6e73
(v2.1.1.9071) update veterinary SIR interpretation, add only_fungi
2024-09-19 11:44:56 +02:00
573c0346ed
(v2.1.1.9070) fix for mo_current mo (no-verify)
2024-07-19 18:05:49 +02:00
7258a491b9
(v2.1.1.9068) fix for mo_url() and as.mo() for synonyms
2024-07-17 14:29:55 +02:00
640888f408
(v2.1.1.9064) update all microbial taxonomy, add mycobank, big documentation update
2024-07-16 14:53:17 +02:00
2899b3c840
new mo_group_members()
2024-04-19 10:18:21 +02:00
7be4dabbc0
support veterinary MIC/disk translation
2024-02-24 15:16:52 +01:00
a4e2e25e3f
reftbl in plots, speedup for as.sir() and mo_validate
2023-07-10 16:43:46 +02:00
70c601ca11
breakpoints UTI interpretation fix
2023-07-10 13:41:52 +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
91fa73dedf
add oxygen tolerance
2023-05-11 21:56:27 +02:00
cabffb22fd
anaerobic codes
2023-04-17 11:26:19 +02:00
262598b8d7
support for old rsi arguments
2023-03-11 14:24:34 +01:00
dad25302f2
make rsi work in more cases, documentation update
2023-02-22 14:38:57 +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
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
593d740b84
documentation, file permissions
2023-01-19 12:54:53 +01:00
ca79068604
Fix for adding MO's
2023-01-14 17:10:10 +01:00
1029aa2fdc
algorithm improvement
2023-01-07 14:53:14 +01:00
2375bfdcb5
documentation
2023-01-07 01:51:19 +01:00
84ed8c32bb
documentation
2023-01-06 19:21:04 +01:00
86e28bafce
add mo_pathogenicity
2023-01-06 13:35:37 +01:00
f619fb683b
support new mo codes
2022-12-27 15:16:15 +01:00
6f4bb603ec
unit tests
2022-12-20 22:18:50 +01:00
f0a2cdbf5e
update mo algorithm
2022-12-20 16:14:04 +01:00
56dad34e68
update prevalence with new phyla
2022-12-09 13:37:08 +01:00
510140fc55
Updated mo_gramstain() to reflect current taxonomy, fixes #83
2022-12-09 10:30:25 +01:00
7ca44fb756
cleanup and new intro logo
2022-11-13 13:44:25 +01:00
9444ed6d1d
fix antibiotics error
2022-10-30 21:05:46 +01:00
d40e0ef20b
completely updated antibiotics
2022-10-30 14:31:45 +01:00
6ad7857d39
fix missing R breakpoints
2022-10-29 14:15:23 +02:00
85e2fbe4a3
remove warnings from unit tests
2022-10-19 11:47:57 +02:00
43c638d122
add mo_current()
2022-10-10 10:12:08 +02:00
b753b84128
fix for mo type translation
2022-10-06 12:11:51 +02:00
