Claude
6912c9deee
Reproduce clinical breakpoints from latest WHONET/AMRIE data
...
- Ran reproduction_of_microorganisms.groups.R and reproduction_of_clinical_breakpoints.R
against the latest WHONET/AMRIE source (includes EUCAST 2026, CLSI 2025)
- Updated data/clinical_breakpoints.rda, microorganisms.codes.rda, microorganisms.groups.rda,
and data-raw/organisms.rds
- Fixed reproduction_of_microorganisms.groups.R: replaced base ifelse() with dplyr::if_else()
to preserve the <mo> S3 class; base ifelse() strips class attributes, causing
bind_rows() to fail with strict vctrs type checking in dplyr >= 1.1.0
- Added data-raw/_run_reproduction.R: non-interactive wrapper that overrides View(),
sets UTF-8 locale, and sources both scripts in the correct order
https://claude.ai/code/session_01S5vMqfsiJb59RN2Gyz1tDY
2026-03-26 06:01:17 +00:00
fcd8b95e51
(v2.1.1.9272) mo codes sensititre
2025-05-04 18:50:25 +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
ac1c40d8bb
(v2.1.1.9081) HUGE microorganisms update for fungi!
2024-09-29 22:17:56 +02:00
640888f408
(v2.1.1.9064) update all microbial taxonomy, add mycobank, big documentation update
2024-07-16 14:53:17 +02:00
4ffac7e22d
(v2.1.1.9051) fix VGS mo code
2024-06-16 11:28:56 +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
3179216c81
(v2.1.1.9047) unit test and index
2024-06-13 07:37:53 +02:00
acb534102b
new species groups, updated clinical breakpoints
2023-07-08 17:30:05 +02:00
Dr. Matthijs Berends
f065945d7b
Update clinical breakpoints and fix some as.mo() bugs ( #117 )
...
* Updates clinical breakpoints EUCAST/CLSI 2023, fixes #102 , fixes #112 , fixes #113 , fixes #114 , fixes #115
* docs
* implement ecoffs
* unit tests
2023-06-22 15:10:59 +02:00
c6135d2082
updated microorganism codes
2023-05-26 16:10:01 +02:00
ed70f95380
Fix clinical breakpoints
2023-04-14 23:14:34 +02:00
147f9112e9
Fix some WHONET codes
2023-04-14 11:12:26 +02:00
5f3a7694aa
microorganisms update, added Salmonella groups
2022-12-16 16:10:43 +01:00
8da2467209
updated taxonomy
2022-12-12 00:14:56 +01:00
c2801ba7a1
new rsi_translation
2022-10-22 22:00:15 +02:00
Dr. Matthijs Berends
cd2acc4a29
New mo algorithm, prepare for 2.0
2022-10-05 09:12:22 +02:00
71db246d5c
unit test fix
2022-08-28 19:17:12 +02:00
303d61b473
new tibble export
2022-08-27 20:49:37 +02:00
37e6e35ec4
(v1.7.1.9051) updated taxonomy, updated git branch name
2021-10-06 13:23:57 +02:00
8f5e5a3fc2
(v1.7.1.9050) fix for as.mo
2021-10-05 14:00:35 +02:00
5679ccdaf9
(v1.6.0.9017) extra system codes
2021-05-04 12:47:33 +02:00
ddf88345f1
(v1.5.0.9028) Updated taxonomy until March 2021
2021-03-04 23:28:32 +01:00
d014955ce0
(v.1.5.0.9000) implementation of EUCAST rules v11 (2021)
2021-01-12 22:08:04 +01:00
5e45fdcf2a
(v1.3.0.9007) tibble printing
2020-08-26 11:33:54 +02:00
86d44054f0
(v1.1.0.9020) updated taxonomy
2020-05-27 16:37:49 +02:00
19703eb5d3
(v1.1.0.9012) lose dependencies
2020-05-19 12:08:49 +02:00
d1cb7d3b6f
(v1.0.1.9005) as.mo() improvements
2020-04-13 21:09:56 +02:00
c7a76ba713
(v0.9.0.9020) as.mo() improvement
2020-02-09 22:04:29 +01:00
9a3891efe4
(v0.9.0.9014) Machine reading guidelines
2020-01-27 11:05:39 +01:00
7c28b392b1
(v0.8.0.9035) add more mo codes
2019-11-24 22:48:56 +01:00
3e5ab53209
(v0.8.0.9002) eucast_rules() fix for S. maltophilia
2019-10-23 14:48:25 +02:00
8ce252fbc5
(v0.7.1.9083) LIS code improvement
2019-09-23 17:32:05 +02:00
66d405ff57
(v0.7.1.9080) new LIS codes
2019-09-22 17:19:59 +02:00
3596adb295
(v0.7.1.9076) mo codes
2019-09-20 12:33:05 +02:00
e2aa4f996b
(v0.7.1.9075) new microorganism codes
2019-09-18 15:46:09 +02:00
3f5828e74a
(v0.7.1.9034) mo.codes fix for Dracunculus spp.
2019-08-09 23:45:26 +02:00
9ac5a34b36
(v0.7.1.9014) MO codes update
2019-07-16 16:14:11 +02:00
254745061c
(v0.7.0.9008) T. vaginalis, rsi_df
2019-06-13 14:28:46 +02:00
27380fa021
fixes for microorganisms.codes
2019-05-28 16:50:40 +02:00
4c3cf85a65
ab_info, other bug fixes
2019-05-16 21:20:00 +02:00
68cc7ef0d0
new antibiotics
2019-05-10 16:44:59 +02:00
c6a12266e7
DSMZ data
2019-03-18 14:29:41 +01:00
504a042fba
uncertainty levels, new WHONET codes
2019-03-12 12:19:27 +01:00
54f8258f8c
Catalogue of Life, replaces ITIS
2019-02-18 02:33:37 +01:00
efb2af9e3a
benchmarks plots
2019-02-14 10:23:51 +01:00
ed30312048
mo codes for WHONET
2019-02-08 16:06:54 +01:00
46dcc7e2e8
set_mo_source
2019-01-21 15:53:01 +01:00
