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
daab605ca4
(v3.0.1.9028) fix unique CIDs
2026-03-06 18:53:42 +01:00
12cf144b19
(v3.0.1.9021) add guideline to resistance() and susceptibility()
2026-02-12 20:34:06 +01:00
499c830ee7
(v3.0.1.9020) unit test fixes
2026-02-09 13:16:36 +01:00
fd50c51543
(v3.0.1.9017) fix documentation
2026-01-08 14:03:02 +01:00
cfd1922dd9
(v3.0.1.9016) fix unit test
2026-01-08 12:29:08 +01:00
cfbbfb4fa5
(v3.0.1.9007) fix #246
2026-01-06 23:08:50 +01:00
151af21f38
(v3.0.1.9005) re-add tidymodels implementation
2025-12-21 12:19:43 +01:00
225c73f7e7
(v3.0.1.9004) Revamp as.sir() interpretation for capped MICs
...
Fixes #243
Fixes #244
2025-12-15 13:18:13 +01:00
0b24967b23
(v3.0.1.9001) fix antibiogram
2025-09-30 10:54:07 +02:00
13f2a864da
(v3.0.0.9035) fix mo_pathogenicity unit test following MycoBank bugfix
2025-09-18 14:22:52 +01:00
e8c99f2775
(v3.0.0.9031) fix for ggplot2
2025-09-12 16:52:59 +02:00
c7b2acbeb6
(v3.0.0.9029) fix for vignette and envir data
2025-09-10 16:19:30 +02:00
4d7c4ca52c
(v3.0.0.9027) skimr update and as.ab warning - fixes #234 , fixes #232
2025-09-10 13:32:52 +02:00
8dab0a3730
(v3.0.0.9007) allow any tidyselect language in as.sir()
2025-07-17 14:29:35 +02:00
72db2b2562
(v3.0.0.9003) eucast_rules fix, new tidymodels integration
2025-06-13 14:03:21 +02:00
d384b492cf
(v2.1.1.9289) unit test fix
2025-06-01 16:00:12 +02:00
46f80b1378
(v2.1.1.9288) mdro fix
2025-06-01 15:35:04 +02:00
4b171745de
(v2.1.1.9276) mdro() fix
2025-05-15 10:39:48 +02:00
48a59ee31a
(v2.1.1.9275) include guideline name in MDRO verbose output
2025-05-13 18:56:12 +02:00
7d45ca9fbf
(v2.1.1.9274) Improve is_sir_eligible, rename verbose MDRO output
2025-05-12 12:35:11 +02:00
2461631bce
(v2.1.1.9268) WISCA vignette, antibiogram sorting, fix translations
2025-05-01 14:45:21 +02:00
5e6bbdf3d1
(v2.1.1.9267) update ATCs
2025-05-01 11:48:49 +02:00
d2b3937a90
(v2.1.1.9257) adjust unit tests
2025-04-27 09:58:19 +02:00
f340e257fa
(v2.1.1.9256) unit tests
2025-04-26 21:29:50 +02:00
4e7fca3b38
(v2.1.1.9253) parallel computing
2025-04-26 15:47:00 +02:00
be13934fe7
(v2.1.1.9249) unit test
2025-04-20 17:49:47 +02:00
492fe6872f
(v2.1.1.9244) automated GPT training data
2025-04-19 15:57:12 +02:00
579025f678
(v2.1.1.9241) fix sir
2025-04-18 13:25:59 +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
b972bbb96f
(v2.1.1.9230) deprecated resistance_predict(), data set folder name without space
2025-03-28 16:48:56 +01:00
bd873ac1bc
(v2.1.1.9229) unit tests
2025-03-28 11:40:09 +01:00
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
8deaf2c8eb
(v2.1.1.9224) skip tests on cran
2025-03-20 23:29:21 +01:00
58d7aa8790
(v2.1.1.9199) fix eucast
2025-03-14 13:43:22 +01:00
861331b1df
(v2.1.1.9196) fix eucast, unit tests
2025-03-13 15:38:39 +01:00
9aab129ea6
(v2.1.1.9195) add BTL-S, fix ranks in unknown microorganisms
2025-03-13 14:30:14 +01:00
a7ef22a21e
(v2.1.1.9194) new argument for missing R breakpoints - updated from WHONET
2025-03-12 16:24:38 +01:00
067a8aca66
(v2.1.1.9192) fix fluoroquinolones and add bleomycin
2025-03-10 17:04:35 +01:00
32024e597a
(v2.1.1.9191) unit tests
2025-03-10 12:16:45 +01:00
245483e41c
(v2.1.1.9188) fix antibiogram plot
2025-03-07 23:01:25 +01:00
f7938289eb
(v2.1.1.9186) replace antibiotics with antimicrobials!
2025-03-07 20:43:26 +01:00
e28dd86c43
(v2.1.1.9183) unit test for older R versions
2025-03-03 14:54:42 +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
Matthijs Berends
68efddab3d
unit tests
2025-02-26 22:26:42 +01:00
1a43882583
ab fix
2025-02-26 21:34:07 +01:00
22e66741cc
(v2.1.1.9160) cleanup
2025-02-26 20:28:33 +01:00
