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
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
1fdab84103
(v2.1.1.9233) chore: make all argument texts full sentences
2025-03-31 14:53:24 +02:00
dr. M.S. (Matthijs) Berends
63099cd81e
(v2.1.1.9232) is.mic() iteration, documentation cleanup
2025-03-31 10:51:31 +02:00
dr. M.S. (Matthijs) Berends
f03933940c
(v2.1.1.9131) implement testthat
2025-01-27 21:43:10 +01:00
dr. M.S. (Matthijs) Berends
1149360b27
(v2.1.1.9129) unit test fix
2025-01-27 16:17:03 +01:00
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
c7461766ce
Remove RSI from package, add extra MIC scale functions
2023-12-03 11:34:48 +01:00
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
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
dr. M.S. (Matthijs) Berends
f619fb683b
support new mo codes
2022-12-27 15:16:15 +01:00
dr. M.S. (Matthijs) Berends
7ca44fb756
cleanup and new intro logo
2022-11-13 13:44:25 +01:00
dr. M.S. (Matthijs) Berends
8dc94a9eda
documentation fix
2022-11-05 09:31:19 +01:00
Dr. Matthijs Berends
cd2acc4a29
New mo algorithm, prepare for 2.0
2022-10-05 09:12:22 +02:00
dr. M.S. (Matthijs) Berends
4d050aef7c
styled, unit test fix
2022-08-28 10:31:50 +02:00
dr. M.S. (Matthijs) Berends
952d16de33
new, automated website
2022-08-21 16:37:20 +02:00
dr. M.S. (Matthijs) Berends
25cef46c59
(v1.8.0) prerelease 1.8.0
2021-12-23 18:56:28 +01:00
dr. M.S. (Matthijs) Berends
a13fd98e8b
(v1.6.0.9063) prepare new release
2021-05-24 09:00:11 +02:00
dr. M.S. (Matthijs) Berends
29dbfa2f49
(v1.6.0.9021) join functions update
2021-05-12 18:15:03 +02:00
dr. M.S. (Matthijs) Berends
a9fd4aa49f
(v1.6.0.9013) website update
2021-04-29 17:16:30 +02:00
dr. M.S. (Matthijs) Berends
551f99dc8f
v1.6.0
2021-03-15 07:23:21 +01:00
dr. M.S. (Matthijs) Berends
850c123de7
(v1.5.0.9032) All group generics for MICs
2021-03-07 13:52:39 +01:00
dr. M.S. (Matthijs) Berends
2eca8c3f01
(v1.5.0.9014) only_rsi_columns, is.rsi.eligible improvement
2021-02-02 23:57:35 +01:00
dr. M.S. (Matthijs) Berends
286eaa9699
(v1.5.0.9010) MDRO vignette update, get_episode for < day
2021-01-24 14:48:56 +01:00
dr. M.S. (Matthijs) Berends
4eab095306
(v1.5.0.9006) major documentation update
2021-01-18 16:57:56 +01:00
dr. M.S. (Matthijs) Berends
526f8afb08
(v1.4.0.9052) replaced all sapply's with type-safe vapply's
2020-12-28 22:24:33 +01:00
dr. M.S. (Matthijs) Berends
8b52f9b1be
(v1.4.0.9047) unit tests
2020-12-27 00:30:28 +01:00
dr. M.S. (Matthijs) Berends
128ebcfd62
(v1.4.0.9043) documentation update
2020-12-22 00:51:17 +01:00
dr. M.S. (Matthijs) Berends
01d9522434
(v1.4.0.9017) stringsAsFactors definitions
2020-11-11 16:49:27 +01:00
dr. M.S. (Matthijs) Berends
4e9ccb4435
(v1.4.0.9001) is_gram_positive(), is_gram_negative(), parameter hardening
2020-10-19 17:09:19 +02:00
dr. M.S. (Matthijs) Berends
28e77680c5
(v1.4.0) matching score update
2020-10-08 11:16:03 +02:00
dr. M.S. (Matthijs) Berends
4e0374af29
(v1.3.0.9035) mdro() for EUCAST 3.2, examples cleanup
2020-09-29 23:35:46 +02:00
dr. M.S. (Matthijs) Berends
c5f7294381
(v1.3.0) skip more CRAN tests
2020-07-31 10:50:08 +02:00
dr. M.S. (Matthijs) Berends
1b65d76cfb
(v1.2.0.9037) survey on website
2020-07-28 18:39:57 +02:00
dr. M.S. (Matthijs) Berends
76fc8e1b14
(v1.2.0.9026) move to github
2020-07-08 14:48:06 +02:00
dr. M.S. (Matthijs) Berends
93a158aebd
(v1.2.0.9011) mo_domain(), improved error handling
2020-06-22 11:18:40 +02:00
dr. M.S. (Matthijs) Berends
df2456b91f
(v1.1.0.9005) lose dependencies
2020-05-16 20:08:21 +02:00
dr. M.S. (Matthijs) Berends
7f3da74b17
(v1.1.0.9004) lose dependencies
2020-05-16 13:05:47 +02:00
dr. M.S. (Matthijs) Berends
d1cb7d3b6f
(v1.0.1.9005) as.mo() improvements
2020-04-13 21:09:56 +02:00
dr. M.S. (Matthijs) Berends
77656a676c
(v1.0.1.9002) PCA unit tests
2020-03-08 11:18:59 +01:00
dr. M.S. (Matthijs) Berends
9fc858f208
(v1.0.1.9001) PCA unit tests
2020-03-08 09:12:11 +01:00
dr. M.S. (Matthijs) Berends
fa0d9c58d9
(v1.0.1.9000) first PCA implementation
2020-03-07 21:48:21 +01:00
