Claude
b1cf7a94ad
Migrate parallel computing in as.sir() from parallel:: to future/future.apply
...
Replace parallel::mclapply() and parallel::parLapply() with
future.apply::future_lapply(), enabling transparent support for any
future backend (multisession, multicore, mirai_multisession, cluster)
on all platforms including Windows.
When parallel = TRUE the function now: (1) respects an active
future::plan() set by the user without overriding it on exit, or
(2) sets a temporary multisession plan with parallelly::availableCores()
and tears it down on exit. The max_cores argument controls worker count
only when no user plan is active.
future and future.apply are added to Suggests in DESCRIPTION.
https://claude.ai/code/session_01M1Jvf2Miu6JL4TQrEh1wS8
2026-04-27 12:21:48 +00:00
Matthijs Berends
8ff5d4472a
Add add_if_missing parameter to control NA handling in interpretive rules ( #264 )
2026-04-21 21:53:43 +02:00
353eaa3f38
(v3.0.1.9033) add ionophores(), clorobiocin, aminocoumarins group
2026-03-09 11:57:36 +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
cfbbfb4fa5
(v3.0.1.9007) fix #246
2026-01-06 23:08:50 +01:00
ba30b08f76
(v3.0.1.9003) Add taniborbactam and cefepime/taniborbactam
2025-11-24 11:24:02 +01:00
60bd631e1a
(v3.0.0.9019) Fixes #229 , #230 , #227 , #225
2025-09-01 16:56:55 +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
ea443f7483
(v2.1.1.9247) CLSI/EUCAST 2025!
2025-04-20 12:55:31 +02:00
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
e134e01418
(v2.1.1.9198) support eucast expert rules 14 and 13.1
2025-03-14 10:10:35 +01:00
e1b7252ff6
(v2.1.1.9193) new antimicrobials for screening
2025-03-12 15:09:28 +01:00
067a8aca66
(v2.1.1.9192) fix fluoroquinolones and add bleomycin
2025-03-10 17:04:35 +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
8ba2e4ed94
(v2.1.1.9141) new AMR selectors, eucast overwrite arg
2025-02-07 18:01:22 +01:00
08ddbaa930
(v2.1.1.9123) add EFF code to antibiotics data set
2025-01-15 16:14:09 +01:00
0488d00f20
(v2.1.1.9111) add betalactams_with_inhibitor(), fixes #175
2024-12-06 15:44:20 +01:00
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
9bf7584d58
(v2.1.1.9049) new 2024 breakpoints, add AMO, set NI instead of N
2024-06-14 22:39:01 +02:00
de17de1be9
(v2.1.1.9048) vctrs update for sir
2024-06-13 20:55:17 +02:00
af74e1d4f2
(v2.1.1.9041) antibiotics update
2024-06-08 17:35:25 +02:00
60c6c21e45
fix SIR interpretation
2024-05-31 09:50:54 +02:00
91fa73dedf
add oxygen tolerance
2023-05-11 21:56:27 +02:00
dad25302f2
make rsi work in more cases, documentation update
2023-02-22 14:38:57 +01:00
830c67f1bf
documentation, unit tests
2023-01-24 10:20:27 +01:00
Dr. Matthijs Berends
98e62c9af2
Replace RSI with SIR
2023-01-21 23:47:20 +01:00
593d740b84
documentation, file permissions
2023-01-19 12:54:53 +01:00
a98d0d75ea
styler dep
2023-01-05 14:46:44 +01:00
7ca44fb756
cleanup and new intro logo
2022-11-13 13:44:25 +01:00
d40e0ef20b
completely updated antibiotics
2022-10-30 14:31:45 +01:00
Dr. Matthijs Berends
cd2acc4a29
New mo algorithm, prepare for 2.0
2022-10-05 09:12:22 +02:00
63fe160322
new rsi_interpretation_history
2022-09-01 15:20:57 +02:00
4d050aef7c
styled, unit test fix
2022-08-28 10:31:50 +02:00
303d61b473
new tibble export
2022-08-27 20:49:37 +02:00
952d16de33
new, automated website
2022-08-21 16:37:20 +02:00
b84d647cac
(v1.8.1.9012) update prevalence of some genera
2022-06-03 13:28:55 +02:00
1b84564d36
(v1.8.1.9011) update prevalence of some genera
2022-06-03 12:43:25 +02:00
08d387b5ce
(v1.8.0.9005) as.rsi() fix
2022-03-10 19:33:25 +01:00
18e8525d10
(v1.8.0.9001) as.mo improvement, fixes #52
2022-02-26 21:58:23 +01:00
578e7dfee9
(v1.7.1.9070) Better WHONET support
2021-12-13 10:18:28 +01:00
7965468ccd
(v1.7.1.9058) vars selection for set_ab_names()
2021-12-05 22:06:45 +01:00
694cf5ba77
(v1.7.1.9054) mdro() update - fixes #49 , first_isolate() speedup
2021-11-28 23:01:26 +01:00
a2d249962f
(v1.7.1.9023) Removed filter_ functions, new set_ab_names(), ATC code update, ab selector update, fixes #46 and fixed #47
2021-08-16 21:54:34 +02:00
