Claude
c500fdb645
Add sir.R/mic.R fixes and mdro() unit tests; bump to 3.0.1.9030
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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
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()
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Fixes #246
Fixes #254
Fixes #255
Fixes #256
2026-02-08 23:15:40 +01:00
2df2911cf4
(v3.0.1.9018) fixes #249
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updates AB groups
2026-01-16 10:57:03 +01:00
225c73f7e7
(v3.0.1.9004) Revamp as.sir() interpretation for capped MICs
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Fixes #243
Fixes #244
2025-12-15 13:18:13 +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
65ec098acf
(v3.0.0.9010) in as.sir(), add note when higher taxonomic levels are used
2025-07-17 19:06:12 +02:00
Nick Thomson
e9e3de4469
(v3.0.0.9009) fix as.sir when uti = FALSE
2025-07-17 17:15:52 +02:00
d94bdd2c6a
(v3.0.0.9008) fix ggplot_sir(), support lighter green for SDD
2025-07-17 17:05:41 +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
a94452b9be
(v2.1.1.9281) speed improvement is_sir_eligible
2025-05-20 11:31:42 +02:00
38cebc1541
(v2.1.1.9279) fix documentation, add foreign S3 exports to functions
2025-05-16 16:55:29 +02:00
139f79d372
(v2.1.1.9278) support AMR selectors in custom MDRO guideline
2025-05-16 11:20:19 +02:00
7d45ca9fbf
(v2.1.1.9274) Improve is_sir_eligible, rename verbose MDRO output
2025-05-12 12:35:11 +02:00
a778eb9bcf
(v2.1.1.9272) (v2.1.1.9271) add sensititre AB and animal codes
2025-05-04 16:40:08 +02:00
5e6bbdf3d1
(v2.1.1.9267) update ATCs
2025-05-01 11:48:49 +02:00
407bc17311
(v2.1.1.9263) small as.sir fix
2025-04-29 16:51:29 +02:00
faa9ae0d85
(v2.1.1.9260) fix antibiogram
2025-04-29 16:15:18 +02:00
6819473457
(v2.1.1.9259) Parallel computing for R < 4
2025-04-27 20:25:39 +02:00
52cd3e88cd
(v2.1.1.9258) fix for R <= 3.6
2025-04-27 17:53:13 +02:00
f340e257fa
(v2.1.1.9256) unit tests
2025-04-26 21:29:50 +02:00
d166aa2c1d
(v2.1.1.9255) fix examples
2025-04-26 16:35:14 +02:00
92316d5ddc
(v2.1.1.9254) fix antimicrobial synonyms
2025-04-26 16:23:14 +02:00
4e7fca3b38
(v2.1.1.9253) parallel computing
2025-04-26 15:47:00 +02:00
abee2a954e
(v2.1.1.9252) fix MIC for >= and <=
2025-04-25 10:19:40 +02:00
be13934fe7
(v2.1.1.9249) unit test
2025-04-20 17:49:47 +02:00
9e64d7708e
(v2.1.1.9248) unit test fix
2025-04-20 15:27:36 +02:00
ea443f7483
(v2.1.1.9247) CLSI/EUCAST 2025!
2025-04-20 12:55:31 +02:00
ca00ed468e
(v2.1.1.9243) fix sir documentation
2025-04-18 16:32:45 +02:00
29b0ef1089
(v2.1.1.9242) sir log
2025-04-18 16:03:50 +02:00
579025f678
(v2.1.1.9241) fix sir
2025-04-18 13:25:59 +02:00
cf91e677c6
(v2.1.1.9240) fix sir interpretation
2025-04-16 15:22:12 +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
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
d77ad6bd6e
(v2.1.1.9227) unit test fixes
2025-03-27 15:36:27 +01:00
969a42cc8c
(v2.1.1.9226) update intrinsic_resistant, unit test fixes
2025-03-27 15:20:22 +01:00
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
287e361a54
(v2.1.1.9218) Fix unit tests
2025-03-19 16:05:24 +01:00
7f1ae1f474
(v2.1.1.9203) unit tests
2025-03-15 13:25:23 +01:00
f758ab60f3
run MICs and disks if detected
2025-03-14 17:23:24 +01:00
6cc273bbc7
(v2.1.1.9201) oops
2025-03-14 17:12:12 +01:00
72f2e723fb
(v2.1.1.9200) new argument capped_mic_handling, add Search to website
2025-03-14 17:01:50 +01:00
eafe9bd113
(v2.1.1.9197) Final fixes for vetmed
2025-03-13 15:51:58 +01:00
861331b1df
(v2.1.1.9196) fix eucast, unit tests
2025-03-13 15:38:39 +01:00
