Claude
3e4983ff93
Replace single-quoted literals in messaging calls with cli markup
...
Converted bare 'value' strings inside stop_(), warning_(), message_()
to appropriate cli markup:
- {.val}: option values ('drug', 'dose', 'administration', 'SDD', 'logbook')
- {.cls}: class names ('sir', 'mo')
- {.field}: column names ('mo' in mo_source)
- {.code}: object/dataset names ('clinical_breakpoints')
Files changed: ab_from_text.R, av_from_text.R, sir.R, sir_calc.R, mo_source.R
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
2026-03-18 23:36:53 +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
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
65ec098acf
(v3.0.0.9010) in as.sir(), add note when higher taxonomic levels are used
2025-07-17 19:06:12 +02:00
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
a2c2be23c1
(v2.1.1.9190) antibiotics deprecation in antibiogram()
2025-03-09 10:41:11 +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
5c4d8fcd2a
(v2.1.1.9095) Python support
2024-10-15 17:12:55 +02:00
640888f408
(v2.1.1.9064) update all microbial taxonomy, add mycobank, big documentation update
2024-07-16 14:53:17 +02:00
9bf7584d58
(v2.1.1.9049) new 2024 breakpoints, add AMO, set NI instead of N
2024-06-14 22:39:01 +02:00
31207952d3
(v2.1.1.9043) fix sir translation with as.double
2024-06-10 10:34:45 +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
c7461766ce
Remove RSI from package, add extra MIC scale functions
2023-12-03 11:34:48 +01:00
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
dad25302f2
make rsi work in more cases, documentation update
2023-02-22 14:38:57 +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
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
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
