Claude
c500fdb645
Add sir.R/mic.R fixes and mdro() unit tests; bump to 3.0.1.9030
...
R/sir.R (line 571):
Guard purely numeric strings (e.g. "1", "8") from the Unicode letter
filter. Values matching the broad SIR regex but consisting only of digits
must not be stripped; add `x %unlike% "^[0-9+]$"` predicate.
R/mic.R (lines 220-222):
Preserve the letter 'e' during Unicode-letter removal so that MIC values
in scientific notation (e.g. "1e-3", "2.5e-2") survive the cleaning step.
- Line 220: [\\p{L}] → [^e\\P{L}] (remove all letters except 'e')
- Line 222: [^0-9.><= -]+ → [^0-9e.><= -]+ (allow 'e' in whitelist)
tests/testthat/test-mdro.R:
New tests for the drug+inhibitor inference added in the previous commit
(issue #209 ):
- TZP=R with no PIP column → PIP inferred R → MDRO class elevated
- TZP=S with no PIP column → proxy col is NA (not S) → class lower
- verbose mode emits "Inferring resistance" message
- AMC=R with no AMX column runs without error (Enterococcus faecium)
https://claude.ai/code/session_01Cp154UtssHg84bw38xiiTG
2026-03-07 13:43:21 +00:00
c0a394008e
(v3.0.1.9027) Fixes #252 and add documentation update regarding #253
2026-03-06 13:10:33 +01:00
b6211931f8
(v3.0.1.9022) add ceftibuten/avibactam (CTA), kasugamycin (KAS), ostreogrycin (OST), thiostrepton (THS), xeruborbactam (XER), zorbamycin (ZOR)
2026-03-03 15:41:08 +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
2df2911cf4
(v3.0.1.9018) fixes #249
...
updates AB groups
2026-01-16 10:57:03 +01:00
4d7c4ca52c
(v3.0.0.9027) skimr update and as.ab warning - fixes #234 , fixes #232
2025-09-10 13:32:52 +02:00
72db2b2562
(v3.0.0.9003) eucast_rules fix, new tidymodels integration
2025-06-13 14:03:21 +02:00
38cebc1541
(v2.1.1.9279) fix documentation, add foreign S3 exports to functions
2025-05-16 16:55:29 +02:00
ea443f7483
(v2.1.1.9247) CLSI/EUCAST 2025!
2025-04-20 12:55:31 +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
e6f88241b2
(v2.1.1.9225) fix geom_hline()/_vline() in MIC plotting, add EUCAT 1.2 in full, add London contribs, fix mo codes, add Kleb pneu complex
2025-03-26 17:19:17 +01:00
43660f2b18
(v2.1.1.9221) allow combined numeric MIC values
2025-03-20 21:47:45 +01:00
a7ef22a21e
(v2.1.1.9194) new argument for missing R breakpoints - updated from WHONET
2025-03-12 16:24:38 +01:00
9a9468fa84
(v2.1.1.9182) fix AMR selectors for tidymodels, add unit tests
2025-03-03 12:59:27 +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
abb5602532
(v2.1.1.9153) mic plot fix
2025-02-22 21:26:38 +01:00
671d657fd8
(v2.1.1.9152) MIC plot fix
2025-02-18 08:07:02 +01:00
07757c933c
(v2.1.1.9144) new MIC scales and fix for rescale_mic()
2025-02-11 08:48:37 +01:00
Edwin van Leeuwen
1697ad37ce
feat: Remove leading equal signs before mic levels ( #181 )
2025-01-16 11:57:25 +01:00
a558f4c121
(v2.1.1.9080) fix rescale_mic() for an outside MIC range
2024-09-24 22:39:40 +02:00
640888f408
(v2.1.1.9064) update all microbial taxonomy, add mycobank, big documentation update
2024-07-16 14:53:17 +02:00
af74e1d4f2
(v2.1.1.9041) antibiotics update
2024-06-08 17:35:25 +02:00
d4490c7f25
fix sorting of MICs, MIC autoplot titles
2024-05-30 15:50:17 +02:00
c3ce1b551d
rename limit_mic_range() to rescale_mic()
2024-05-24 15:07:41 +02:00
2899b3c840
new mo_group_members()
2024-04-19 10:18:21 +02:00
94e9a4d99b
update MIC implementation
2024-04-07 20:22:59 +02:00
0039cb05d6
update MIC comparisons
2024-04-05 16:44:43 +02:00
7be4dabbc0
support veterinary MIC/disk translation
2024-02-24 15:16:52 +01:00
83e92fd88c
docu fix
2023-12-04 08:19:02 +01:00
c7461766ce
Remove RSI from package, add extra MIC scale functions
2023-12-03 11:34:48 +01:00
6f417d0ef2
add scale_x_mic()
2023-12-03 01:06:00 +01:00
4c11a7bd9c
v2.1.1
2023-10-22 15:51:27 +02:00
ca72a646d0
scientific notation for MICs
2023-10-20 15:45:00 +02:00
7cda9e575b
prepare for CRAN
2023-10-20 14:51:48 +02:00
7dc96794be
fix rounding MICs on R-devel
2023-07-20 08:24:27 +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
dad25302f2
make rsi work in more cases, documentation update
2023-02-22 14:38:57 +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
ba51c2d92f
add column to as.mic() and as.disk() warnings
2022-11-28 19:39:52 +01:00
f6862a139d
expert rules 12.0
2022-11-14 15:20:39 +01:00
85e2fbe4a3
remove warnings from unit tests
2022-10-19 11:47:57 +02:00
