dr. M.S. (Matthijs) Berends
bd208429cd
(v3.1.0.9003) Rewrite the manual index on the website for findability: sections ordered by task (cleaning data, interpreting results as SIR, analysing data), titles before function names, a filter field that also finds topics mentioning a term, and colours prepared for dark mode; also make the tidymodels extensions public in the manual and use consistent help page titles
2026-10-17 09:36:10 +02:00
dr. M.S. (Matthijs) Berends
53d0704271
(v3.0.1.9116) New sir_combine() for combination therapy as one engine for antibiogram(), wisca(), count_*() and proportion_*() ( #321 ), and make all suggested packages runtime-only with a new CI workflow without dplyr
...
- New sir_combine() to combine SIR results of multiple antimicrobials into one variable; antibiogram(), wisca() and the count/proportion functions now use the same engine (antibiogram() and wisca() output unchanged)
- With multiple antimicrobials, count_*() and proportion_*() now follow the documented combination therapy rules: resistance() is the proportion of failing combinations, count_all() excludes isolates with an unknown combination result, and WT/NWT/NS/NI are handled correctly
- where() is now decided at runtime instead of at installation, fixing antibiogram() and wisca() without tidyselect (e.g. CRAN binaries without dplyr)
- Imports from data.table and cli moved to .onLoad(); data.table functions are only used while it is loaded; the like() example no longer unloads data.table, which crashed R
- Static test that fails on code outside functions depending on suggested packages
- New check-without-dplyr workflow: installs AMR with all suggested packages, removes dplyr (and tidyselect), then runs all unit tests and examples against the installed package
- g.test() now returns the degrees of freedom as 'parameter', so they are printed
- Fix R CMD check NOTEs (hidden .claude folder, lost braces in inherited g.test and ggplot_pca docs)
2026-10-11 20:36:31 +02:00
Matthijs Berends
2c33297cf6
new eucast breakpoints parsing
2026-08-20 13:29:16 +01:00
dr. M.S. (Matthijs) Berends
bd63794136
(v3.0.1.9064) Documentation updates
2026-06-24 18:32:08 +02:00
dr. M.S. (Matthijs) Berends
0af3f84655
(v3.0.1.9057) website fix
2026-05-02 14:56:26 +02:00
dr. M.S. (Matthijs) Berends
4dc3ec0008
(v3.0.1.9034) Add amr_course()
2026-03-11 16:07:31 +01:00
dr. M.S. (Matthijs) Berends
f6e28ac95c
(v3.0.1.9006) Fix website
2025-12-21 12:29:46 +01:00
dr. M.S. (Matthijs) Berends
d2ced1db61
(v3.0.0.9024) fix todo tracker
2025-09-04 14:28:01 +02:00
Matthijs Berends
1013ef6086
Update _pkgdown.yml
2025-06-13 17:05:51 +02:00
dr. M.S. (Matthijs) Berends
26447fe29b
fix website
2025-05-16 17:53:21 +02:00
dr. M.S. (Matthijs) Berends
139f79d372
(v2.1.1.9278) support AMR selectors in custom MDRO guideline
2025-05-16 11:20:19 +02:00
dr. M.S. (Matthijs) Berends
d31371613e
(v2.1.1.9237) clean-up
2025-04-13 09:59:40 +02:00
dr. M.S. (Matthijs) Berends
40d7a971c3
(v2.1.1.9236) documentation
2025-04-12 11:46:42 +02:00
dr. M.S. (Matthijs) Berends
36fd99e1f4
(v2.1.1.9235) New website!
2025-04-08 15:54:30 +01:00
dr. M.S. (Matthijs) Berends
5f5b77bfaf
(v2.1.1.9231) Update EUCAST vignette
2025-03-29 18:03:31 +01:00
dr. M.S. (Matthijs) Berends
b972bbb96f
(v2.1.1.9230) deprecated resistance_predict(), data set folder name without space
2025-03-28 16:48:56 +01:00
dr. M.S. (Matthijs) Berends
7f1ae1f474
(v2.1.1.9203) unit tests
2025-03-15 13:25:23 +01:00
dr. M.S. (Matthijs) Berends
72f2e723fb
(v2.1.1.9200) new argument capped_mic_handling, add Search to website
2025-03-14 17:01:50 +01:00
dr. M.S. (Matthijs) Berends
58d7aa8790
(v2.1.1.9199) fix eucast
2025-03-14 13:43:22 +01:00
dr. M.S. (Matthijs) Berends
f7938289eb
(v2.1.1.9186) replace antibiotics with antimicrobials!
2025-03-07 20:43:26 +01:00
dr. M.S. (Matthijs) Berends
ef02f4a7f2
(v2.1.1.9151) update readme
2025-02-15 20:53:12 +01:00
dr. M.S. (Matthijs) Berends
2561494e06
(v2.1.1.9133) update math formulae
2025-01-27 22:43:35 +01:00
dr. M.S. (Matthijs) Berends
9520977a10
(v2.1.1.9133) (v2.1.1.9132) unit test, final fixes
2025-01-27 22:09:16 +01:00
dr. M.S. (Matthijs) Berends
66833b4f5a
(v2.1.1.9126) implemented WISCA! Also added top_n_microorganisms() and fixed Python wrapper
2025-01-26 23:01:17 +01:00
dr. M.S. (Matthijs) Berends
92c4fc0f94
(v2.1.1.9125) replace 'antibiotic selectors' with 'antimicrobial selectors'
2025-01-17 12:09:39 +01:00
dr. M.S. (Matthijs) Berends
15fc72fc66
(v2.1.1.9121) support tidymodels
2024-12-19 20:17:15 +01:00
dr. M.S. (Matthijs) Berends
c588902f4c
(v2.1.1.9092) Fix website
2024-10-06 16:25:31 +02:00
Matthijs Berends
3dd3b6292a
Update _pkgdown.yml
2024-10-04 16:49:55 +02:00
dr. M.S. (Matthijs) Berends
325664f5aa
(v2.1.1.9090) website error
2024-10-04 16:08:41 +02:00
dr. M.S. (Matthijs) Berends
0736ac7a7e
(v2.1.1.9089) website update
2024-10-04 15:44:05 +02:00
dr. M.S. (Matthijs) Berends
91415462c0
(v2.1.1.9084) add vignette about Python
2024-09-30 22:04:44 +02:00
dr. M.S. (Matthijs) Berends
ac1c40d8bb
(v2.1.1.9081) HUGE microorganisms update for fungi!
2024-09-29 22:17:56 +02:00
dr. M.S. (Matthijs) Berends
28bf91cbf5
(v2.1.1.9077) fix logos
2024-09-19 14:40:19 +02:00
dr. M.S. (Matthijs) Berends
640888f408
(v2.1.1.9064) update all microbial taxonomy, add mycobank, big documentation update
2024-07-16 14:53:17 +02:00
dr. M.S. (Matthijs) Berends
a4dc37a4e4
(v2.1.1.9057) fix for missing breakpoints
2024-06-17 16:52:12 +02:00
dr. M.S. (Matthijs) Berends
31207952d3
(v2.1.1.9043) fix sir translation with as.double
2024-06-10 10:34:45 +02:00
dr. M.S. (Matthijs) Berends
94e9a4d99b
update MIC implementation
2024-04-07 20:22:59 +02:00
dr. M.S. (Matthijs) Berends
46634bfcaa
navbar colour
2024-02-25 16:48:04 +01:00
Matthijs Berends
8b43fed94d
Update _pkgdown.yml
2024-02-25 14:40:19 +01:00
dr. M.S. (Matthijs) Berends
8d077149fa
new logo
2024-02-25 14:20:43 +01:00
dr. M.S. (Matthijs) Berends
c7461766ce
Remove RSI from package, add extra MIC scale functions
2023-12-03 11:34:48 +01:00
dr. M.S. (Matthijs) Berends
4c11a7bd9c
v2.1.1
2023-10-22 15:51:27 +02:00
dr. M.S. (Matthijs) Berends
3829311dd3
random() fix
2023-07-08 21:00:49 +02:00
dr. M.S. (Matthijs) Berends
acb534102b
new species groups, updated clinical breakpoints
2023-07-08 17:30:05 +02:00
dr. M.S. (Matthijs) Berends
9591688811
documentation update
2023-05-27 10:39:22 +02:00
dr. M.S. (Matthijs) Berends
c6135d2082
updated microorganism codes
2023-05-26 16:10:01 +02:00
dr. M.S. (Matthijs) Berends
0bcf55d3b6
improve as.mo()
2023-05-24 15:55:53 +02:00
dr. M.S. (Matthijs) Berends
4416394e10
website update
2023-02-26 21:26:58 +01:00
dr. M.S. (Matthijs) Berends
e890360986
website syntax update
2023-02-17 11:39:00 +01:00
dr. M.S. (Matthijs) Berends
9e99e66f01
use dplyr where available, new antibiogram() for WISCA, fixed Salmonella Typhi/Paratyphi
2023-02-06 11:57:22 +01:00
