Claude
d23004641f
Revert mo_matching_score.R; fix #288 in mo.R pre-filter instead
...
Issue #288 : when the abbreviated-genus pre-filter (≤3 char genus) yields
exactly one candidate whose species (and subspecies) word(s) exactly match
the input, narrow filtr to that single candidate and set
minimum_matching_score = 0. This bypasses the automatic 0.55 cutoff that
only runs in the is.null() branch, so "S. apiospermum" resolves to
Scedosporium apiospermum without touching the validated scoring formula.
https://claude.ai/code/session_01VH4Ju4Xq9aW1AHuoVbjGEo
2026-05-06 18:07:37 +00:00
Claude
b3b8d301ff
Fix #287 (complex fallback) and #288 (species epithet scoring bias)
...
#287 : as.mo() now strips " complex" from input when that exact complex
is not in the taxonomy and retries with the bare name, so inputs like
"Proteus vulgaris complex" no longer return NA.
#288 : mo_matching_score() applies a ×2 bonus when the input has an
abbreviated genus (≤3 chars) and the candidate's species epithet exactly
matches the input species epithet. This ensures "S. apiospermum" resolves
to Scedosporium apiospermum rather than Staphylococcus aureus, overcoming
the kingdom/prevalence denominator bias in favour of common bacteria.
https://claude.ai/code/session_01VH4Ju4Xq9aW1AHuoVbjGEo
2026-05-06 15:11:31 +00:00
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
1fdab84103
(v2.1.1.9233) chore: make all argument texts full sentences
2025-03-31 14:53:24 +02:00
49da312506
(v2.1.1.9228) repo cleaning
2025-03-28 11:17:49 +01:00
2561494e06
(v2.1.1.9133) update math formulae
2025-01-27 22:43:35 +01:00
681fe011fe
(v2.1.1.9082) algorithm updates
2024-09-30 18:46:55 +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
acb534102b
new species groups, updated clinical breakpoints
2023-07-08 17:30:05 +02:00
9591688811
documentation update
2023-05-27 10:39:22 +02:00
19fd0ef121
sort sir history
2023-01-23 15:01:21 +01:00
Dr. Matthijs Berends
98e62c9af2
Replace RSI with SIR
2023-01-21 23:47:20 +01:00
ca79068604
Fix for adding MO's
2023-01-14 17:10:10 +01:00
08fe5a88c0
documentation
2023-01-07 01:54:46 +01:00
2375bfdcb5
documentation
2023-01-07 01:51:19 +01:00
84ed8c32bb
documentation
2023-01-06 19:21:04 +01:00
f619fb683b
support new mo codes
2022-12-27 15:16:15 +01:00
f0a2cdbf5e
update mo algorithm
2022-12-20 16:14:04 +01:00
b1b7534c78
incorporate Bartlett et al (2022)
2022-12-19 15:32:41 +01:00
eed1c14b96
website update
2022-12-11 11:44:29 +01:00
76bcd3528c
move object assignment to AMR_env
2022-10-14 13:02:50 +02:00
Dr. Matthijs Berends
cd2acc4a29
New mo algorithm, prepare for 2.0
2022-10-05 09:12:22 +02:00
e7af5fc716
fix AMR vignette
2022-08-28 22:38:08 +02:00
4d050aef7c
styled, unit test fix
2022-08-28 10:31:50 +02:00
952d16de33
new, automated website
2022-08-21 16:37:20 +02:00
18e8525d10
(v1.8.0.9001) as.mo improvement, fixes #52
2022-02-26 21:58:23 +01:00
25cef46c59
(v1.8.0) prerelease 1.8.0
2021-12-23 18:56:28 +01:00
e18c49ed93
(v1.7.1.9063) not_intrinsic_resistant
2021-12-09 10:48:25 +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
00d3e437a8
(v1.6.0.9003) like() fix
2021-04-16 11:41:05 +02:00
4e0a9533ad
(v1.5.0.9041) SNOMED update
2021-03-11 21:42:30 +01:00
2eca8c3f01
(v1.5.0.9014) only_rsi_columns, is.rsi.eligible improvement
2021-02-02 23:57:35 +01:00
4eab095306
(v1.5.0.9006) major documentation update
2021-01-18 16:57:56 +01:00
d014955ce0
(v.1.5.0.9000) implementation of EUCAST rules v11 (2021)
2021-01-12 22:08:04 +01:00
8b52f9b1be
(v1.4.0.9047) unit tests
2020-12-27 00:30:28 +01:00
423879c034
(v1.4.0.9012) reference_df fix
2020-11-05 01:11:49 +01:00
4e9ccb4435
(v1.4.0.9001) is_gram_positive(), is_gram_negative(), parameter hardening
2020-10-19 17:09:19 +02:00
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
36ec8b0d81
(v1.3.0.9033) skimr fix
2020-09-28 11:00:59 +02:00
22f6ceb3e4
(v1.3.0.9031) matching score update
2020-09-26 16:51:17 +02:00
050a9a04fb
(v1.3.0.9030) matching score update
2020-09-26 16:26:01 +02:00
c19095a3d5
(v1.3.0.9026) eucast expert rules 3.2
2020-09-24 00:30:11 +02:00
2f0186ace2
(v1.3.0.9024) optimalisation
2020-09-19 12:57:51 +02:00
d049cce69b
(v1.3.0.9023) optimalisation
2020-09-19 11:54:01 +02:00
4e40e42011
(v1.3.0.9022) mo_matching_score(), poorman update, as.rsi() fix
2020-09-18 16:05:53 +02:00
