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43accd35d1794da89018d074bc103fbe68266cf3
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Author SHA1 Message Date
dr. M.S. (Matthijs) Berends 43accd35d1 (v3.0.1.9151) Fix inconsistencies in the plotting functions and correct the translations of the interpretation categories 
Plotting:
- Base colours and legends of interpreted MIC and disk values on the interpretation itself instead of matching colours
- Fix SDD in autoplot() for disks, the colours of barplot() for SIR values, and barplot() for MICs ignoring language and expand
- Match a named colours_SIR by name; let keep_operators = TRUE/FALSE in scale_*_mic() behave as "all"/"none"
- Let a named values in scale_*_sir() replace the colours it names, warn in scale_x_sir(), and pass other arguments on
- Let the default of eucast_I follow the guideline option, also for EUCAST before 2019
- Support unquoted column names in facet_sir() without evaluating them
- Correct the documentation and examples

Translations:
- Add SDD, NS, WT and NWT, and correct S, I, R and NI in 18 languages
- Sources of the terms for 'I': NAK via German laboratories (de), SZU national reference laboratory (cs), lex.dk (da), Karolinska University Hospital (sv), COESANT (es), Nordlab (fi), CA-SFM (fr); no by analogy with da and sv
- Not verified against an official source: ar, bn, el, hi, id, ja, ko, pl, ro, ru, sw, tr, uk, ur, vi, zh

Tests:
- Let the grouped antibiogram test use English so it passes in other locales
 2026-10-15 22:25:20 +02:00
dr. M.S. (Matthijs) Berends 0efc8826c8 Let aggregated analyses follow the guideline for the 'I' category in count_df(), proportion_df(), sir_df(), the plotting functions, antibiogram(), wisca(), and bug_drug_combinations(), deprecate combine_SI in favour of guideline, fix format() on bug_drug_combinations() counting I as resistant, and add a shared section 'Interpretation of SIR' 2026-10-15 09:58:21 +02:00
dr. M.S. (Matthijs) Berends dbd95ffa46 (v3.0.1.9137) Add the guideline argument to count_df(), proportion_df(), sir_df(), ggplot_sir(), geom_sir(), and labels_sir_count(), so that with CLSI the 'I' category is merged with R, and describe in the documentation of get_AMR_locale() that LANG takes precedence over LANGUAGE 2026-10-15 08:25:37 +02:00
dr. M.S. (Matthijs) Berends 9ebc33a59d (v3.0.1.9129) Add guideline argument to random_mic() and random_disk() so that values are based on one guideline version, make guideline years in examples, vignettes and website always the latest, and reword NEWS 2026-10-13 21:43:19 +02:00
dr. M.S. (Matthijs) Berends bbdd3a92e2 (v3.0.1.9088) add version number to intrinsic_resistant 2026-09-03 12:14:25 +02:00
Matthijs BerendsandClaude Sonnet 4.6 03be4b87fc (v3.0.1.9079) docs: rename remaining 'antibiotic selectors'/'AB selectors' to 'antimicrobial selectors'/'AMR selectors' 
* docs: rename remaining 'antibiotic selectors'/'AB selectors' to 'antimicrobial selectors'/'AMR selectors'

Five leftover occurrences of the old terminology updated in the AMR
vignette (section heading + code comment), the amr_selectors test file,
and two roxygen example comments in amr_selectors.R. The auto-generated
man/antimicrobial_selectors.Rd will update on the next devtools::document() run.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_0169LucQ7SHDLHdTnDs1ENhd

* fix

---------

Co-authored-by: Claude <noreply@anthropic.com>
 2026-06-27 14:31:58 +02:00
dr. M.S. (Matthijs) Berends 9898b5df4b (v3.0.1.9059) Fix WISCA in vignette 2026-06-23 14:38:59 +02:00
dr. M.S. (Matthijs) Berends e0f8cf0882 (v3.0.1.9047) fix #272 2026-04-21 22:11:40 +02:00
Matthijs Berends 8ff5d4472a Add add_if_missing parameter to control NA handling in interpretive rules (#264) 2026-04-21 21:53:43 +02:00
dr. M.S. (Matthijs) Berends 26613d774b (v3.0.1.9042) add EUCAST breakpoint table v16 to interpretive_rules() 2026-04-02 11:42:19 +02:00
dr. M.S. (Matthijs) Berends 3a736bc484 (v3.0.1.9041) add breakpoints 2026 2026-03-30 10:01:49 +02:00
dr. M.S. (Matthijs) Berends 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
dr. M.S. (Matthijs) Berends 0b24967b23 (v3.0.1.9001) fix antibiogram 2025-09-30 10:54:07 +02:00
dr. M.S. (Matthijs) Berends adee419f1c v3.0.1 2025-09-20 17:14:07 +01:00
dr. M.S. (Matthijs) Berends 49274f010b (v3.0.0.9014) fix plot colours 2025-07-18 15:57:48 +02:00
dr. M.S. (Matthijs) Berends d94bdd2c6a (v3.0.0.9008) fix ggplot_sir(), support lighter green for SDD 2025-07-17 17:05:41 +02:00
dr. M.S. (Matthijs) Berends dc5559a2c4 (v2.1.1.9270) Add support for Korean, fix ATCs 2025-05-04 14:24:43 +02:00
dr. M.S. (Matthijs) Berends b8f0f64287 (v2.1.1.9269) Support 7 new languages 2025-05-02 19:25:19 +02:00
dr. M.S. (Matthijs) Berends ea443f7483 (v2.1.1.9247) CLSI/EUCAST 2025! 2025-04-20 12:55:31 +02:00
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 f7938289eb (v2.1.1.9186) replace antibiotics with antimicrobials! 2025-03-07 20:43:26 +01:00
dr. M.S. (Matthijs) Berends 07efc292bc (v2.1.1.9163) cleanup 2025-02-27 14:04:29 +01:00
dr. M.S. (Matthijs) Berends aa8f6af185 (v2.1.1.9155) new mic_p50() and mic_p90() - updated AMR intro 2025-02-23 11:18:08 +01:00
dr. M.S. (Matthijs) Berends 226d10f546 (v2.1.1.9154) documentation fix 2025-02-22 22:07:56 +01:00
dr. M.S. (Matthijs) Berends abb5602532 (v2.1.1.9153) mic plot fix 2025-02-22 21:26:38 +01:00
dr. M.S. (Matthijs) Berends 883fbe7cfe (v2.1.1.9149) doc fix 2025-02-15 12:46:48 +01:00
dr. M.S. (Matthijs) Berends d94efb0f5e (v2.1.1.9147) scale fixes and WISCA update, fix conserved capped values 2025-02-14 14:16:46 +01:00
dr. M.S. (Matthijs) Berends bd2887bcd4 (v2.1.1.9146) new scale_*_sir() functions 2025-02-13 19:47:57 +01:00
Matthijs Berends 5ff9210c12 Update plot.Rd 2025-02-11 17:23:34 +01:00
dr. M.S. (Matthijs) Berends 07757c933c (v2.1.1.9144) new MIC scales and fix for rescale_mic() 2025-02-11 08:48:37 +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 2e31ec19c3 (v2.1.1.9122) fix documentation 2024-12-20 10:52:44 +01:00
dr. M.S. (Matthijs) Berends d7de1bc33d (v2.1.1.9118) move ggplot2 plotting functions to general 'plotting' man page 2024-12-14 19:41:15 +01:00
dr. M.S. (Matthijs) Berends a558f4c121 (v2.1.1.9080) fix rescale_mic() for an outside MIC range 2024-09-24 22:39:40 +02:00
dr. M.S. (Matthijs) Berends 1ca40e8d67 (v2.1.1.9079) fix for uti in as.sir() 2024-09-24 15:34:12 +02:00
dr. M.S. (Matthijs) Berends 9bf7584d58 (v2.1.1.9049) new 2024 breakpoints, add AMO, set NI instead of N 2024-06-14 22:39:01 +02:00
dr. M.S. (Matthijs) Berends 7be4dabbc0 support veterinary MIC/disk translation 2024-02-24 15:16:52 +01:00
dr. M.S. (Matthijs) Berends 83e92fd88c docu fix 2023-12-04 08:19:02 +01:00
dr. M.S. (Matthijs) Berends 7059568581 fix scale functions 2023-12-03 16:51:54 +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 6f417d0ef2 add scale_x_mic() 2023-12-03 01:06:00 +01:00
dr. M.S. (Matthijs) Berends 4c11a7bd9c v2.1.1 2023-10-22 15:51:27 +02:00
dr. M.S. (Matthijs) Berends a4e2e25e3f reftbl in plots, speedup for as.sir() and mo_validate 2023-07-10 16:43:46 +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
dr. M.S. (Matthijs) Berends 262598b8d7 support for old rsi arguments 2023-03-11 14:24:34 +01:00
dr. M.S. (Matthijs) Berends dad25302f2 make rsi work in more cases, documentation update 2023-02-22 14:38:57 +01:00
dr. M.S. (Matthijs) Berends 830c67f1bf documentation, unit tests 2023-01-24 10:20:27 +01:00
dr. M.S. (Matthijs) Berends eef00069fd add all options to documentation 2023-01-23 20:07:57 +01:00
Dr. Matthijs Berends 98e62c9af2 Replace RSI with SIR 2023-01-21 23:47:20 +01:00