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
d384b492cf
(v2.1.1.9289) unit test fix
2025-06-01 16:00:12 +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
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
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
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
f03933940c
(v2.1.1.9131) implement testthat
2025-01-27 21:43:10 +01:00
d8c91d5876
(v1.6.0.9031) tinytest unit tests
2021-05-15 21:36:22 +02:00
9a381c8d18
(v1.6.0.9030) new unit test flow
2021-05-13 23:07:31 +02:00
9ed2f6490f
(v1.6.0.9028) new unit test flow
2021-05-13 22:44:11 +02:00
aeea00881e
(v1.6.0.9023) new unit test flow
2021-05-13 19:31:47 +02:00
7a3139f7cc
(v1.6.0.9000) custom EUCAST rules
2021-04-07 08:37:42 +02:00
cb404492b2
(v1.5.0.9017) unit testing
2021-02-08 21:09:36 +01:00
2eca8c3f01
(v1.5.0.9014) only_rsi_columns, is.rsi.eligible improvement
2021-02-02 23:57:35 +01:00
27f084d819
(v1.5.0.9007) updated unit tests
2021-01-18 18:45:43 +01:00
4eab095306
(v1.5.0.9006) major documentation update
2021-01-18 16:57:56 +01:00
e699de955c
(v1.5.0.9004) custom MDRO guideline
2021-01-17 00:26:48 +01:00
8b52f9b1be
(v1.4.0.9047) unit tests
2020-12-27 00:30:28 +01:00
68ac39aa7f
(v1.4.0.9016) as.rsi() older R versions
2020-11-10 19:59:14 +01:00
28e77680c5
(v1.4.0) matching score update
2020-10-08 11:16:03 +02:00
4e0374af29
(v1.3.0.9035) mdro() for EUCAST 3.2, examples cleanup
2020-09-29 23:35:46 +02:00
76fc8e1b14
(v1.2.0.9026) move to github
2020-07-08 14:48:06 +02:00
5216d2b520
(v1.1.0.9014) lose dependencies
2020-05-19 14:16:45 +02:00
7f3da74b17
(v1.1.0.9004) lose dependencies
2020-05-16 13:05:47 +02:00
ced1a7b7fa
(v0.9.0.9008) Happy new year! Add lifecycles
2020-01-05 17:22:09 +01:00
1c4f91ab74
ci fix
2019-11-06 16:08:58 +01:00
5345d2759a
(v0.8.0.9012) mdro improvement
2019-11-05 11:28:52 +01:00
29e448883d
(v0.8.0.9008) new verbose mode for MDROs
2019-11-03 22:24:42 +01:00
412077a6f2
(v0.8.0.9005) fix unit tests
2019-10-26 22:21:26 +02:00
d2e8249edd
(v0.8.0.9004) added MDR guideline by Magiorakos et al.
2019-10-26 21:56:41 +02:00
3e5ab53209
(v0.8.0.9002) eucast_rules() fix for S. maltophilia
2019-10-23 14:48:25 +02:00
10e6b225e7
(v0.7.1.9107) v0.8.0
2019-10-15 14:35:23 +02:00
00cdb498a0
(v0.7.1.9102) lintr
2019-10-11 17:21:02 +02:00
5dbff3e170
(v0.7.1.9098) mdro() unit test fix
2019-10-07 15:12:42 +02:00
4e9c4c1b4e
(v0.7.1.9096) German guideline for mdro()
2019-10-07 14:32:06 +02:00
e2aa4f996b
(v0.7.1.9075) new microorganism codes
2019-09-18 15:46:09 +02:00
93be16484b
(v0.7.1.9063) septic_patients -> example_isolates
2019-08-27 16:45:42 +02:00
c57ad26c5b
(v0.7.1.9007) mdro update
2019-07-04 15:26:07 +02:00
270aa0dd33
v0.7.0
2019-06-03 17:45:22 +02:00
60983a1640
added mdr_tb()
2019-05-23 16:58:59 +02:00
07d26cd485
faster determination of abx
2019-05-20 19:12:41 +02:00
461eec9bac
cfta streptococci, codecov.yml
2019-04-09 14:59:17 +02:00
fbc9191b13
new EUCAST rules algorithm
2019-04-05 18:47:39 +02:00
80ea555663
guess_ab
2019-01-03 23:56:19 +01:00
6b2d464f8c
big website update, licence txt update
2019-01-02 23:24:07 +01:00
