dr. M.S. (Matthijs) Berends
844e2581ee
Test that Morganella is interpreted as reported, not as M. morganii ( #330 )
...
No code change was needed. Morganella follows Enterobacterales, except for imipenem and imipenem-relebactam, for which EUCAST gives rows for Morganellaceae or Morganella.
2026-11-02 16:55:36 +01:00
dr. M.S. (Matthijs) Berends
724a94a48f
Add a tool to compare as.sir() results between builds, and apply the Bacteroides extension to zone diameters
...
The new compare_clinical_breakpoints.R compares the interpretations of two builds, and fails on any change that is not explained. A rebuild of main with pinned WHONET files reproduces all rows of clinical_breakpoints and microorganisms.codes.
The filter on MIC rows in the scope extensions is removed, since these now join on the method of each statement. It kept the DISK rows of the Bacteroides statement from being copied.
2026-11-02 16:55:36 +01:00
Erwin Hassing
3132811fd2
Fix EUCAST bracket handling, redundant blockers and Bacteroides scope
2026-10-30 15:38:14 +01:00
Matthijs Berends
08e68037db
Merge pull request #333 from uzumakienes/uzumakienes-patch-1
...
Fix copyright link and add MycoBank to the welcome vignette
2026-10-23 19:42:19 +02:00
uzumakienes
904656241f
Bump version and add NEWS entry
2026-10-23 16:46:42 +03:00
uzumakienes
da44c3a569
Fix copyright link and add MycoBank in vignette
2026-10-23 16:46:27 +03:00
dr. M.S. (Matthijs) Berends
4e806b3d40
(v3.1.0.9005) Fix the CI check on R-oldrel-5 by letting pak ignore readxl on R versions older than 4.2, and by not forcing suggested packages in R CMD check
2026-10-23 14:15:49 +02:00
dr. M.S. (Matthijs) Berends and Claude Sonnet 5.5
5fc152ae94
(v3.1.0.9004) Document the columns argument of the tidymodels steps to fix the Rd usage warning in R CMD check
...
Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com >
2026-10-17 18:23:06 +02:00
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
52d9c4a9e7
(v3.1.0.9002) Add a release checklist (release.md) with all steps of a regular CRAN release
2026-10-16 14:23:01 +02:00
dr. M.S. (Matthijs) Berends
5a4387a141
(v3.1.0.9001) Update the MO code registry with the codes of release v3.1.0, and the versions in the bug report template
2026-10-16 14:19:48 +02:00
dr. M.S. (Matthijs) Berends
052edc4761
v3.1.0
2026-10-16 14:11:02 +02:00
dr. M.S. (Matthijs) Berends
6898472c8a
(v3.0.1.9154) Shorten an example comment of wisca() to fix the Rd line widths NOTE
2026-10-16 06:32:46 +02:00
dr. M.S. (Matthijs) Berends
30021a9831
(v3.0.1.9153) Speed up mdro(), as.sir(), wisca() and wisca_plot() and the binding of mo vectors, fix PDR in the CMI 2012 guideline of mdro() being assigned to the wrong rows, and limit the stratified WISCA example to the 5 most common species
2026-10-16 06:08:26 +02:00
dr. M.S. (Matthijs) Berends
08aa47842e
(v3.0.1.9152) Let a named colours_SIR without S, I or R use the default colours for these, which fixes the example of ggplot_sir() with colours = c(SI = "yellow"), let ggplot_sir() pass the facet as a value to facet_sir(), and make the test of the eucast_I default independent of the AMR_guideline option
2026-10-16 04:34:52 +02:00
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
b63263cc56
(v3.0.1.9150) Add the open issues found while correcting the WHONET codes to the taxonomy report
2026-10-15 21:31:28 +02:00
dr. M.S. (Matthijs) Berends
eb9a9c2fa5
(v3.0.1.9149) Fix WHONET codes in microorganisms.codes that referred to unrelated microorganisms, let codes refer to the name they were named after and add a source column, and replace the fuzzy matching of WHONET names by exact matching with a guard against unreviewed remaps
...
WHONET names are now matched exactly (also outdated names, after removing qualifiers), then on GBIF identifier, and fuzzy results are only kept if consistent with that; otherwise the genus or UNKNOWN is used. A code refers to the record of the name it was named after (e.g. EAE is Enterobacter aerogenes) if that name refers to the same taxon. Every remap of an existing code to another taxon must be listed in data-raw/whonet_remaps_reviewed.csv; the 198 remaps of this rebuild were reviewed.
2026-10-15 21:08:04 +02:00
dr. M.S. (Matthijs) Berends
179eec584f
(v3.0.1.9148) Store zone diameters without S category as blocking rows for EUCAST and as R-only rows for CLSI instead of capping them at 50 mm, let as.mo() return the complex for names such as 'Acinetobacter calcoaceticus-baumannii complex', make the breakpoint reproduction scripts stop on unchecked data defects and year-independent, and document that as.disk() returns NA above 50 mm
...
The full rebuild of clinical_breakpoints also assigns Salmonella serovars and the Bacteroides fragilis complex correctly and adds ECOFFs for Neocosmospora solani. The rebuilt microorganisms.codes is not included, since it remaps WHONET codes that need review first.
2026-10-15 17:05:41 +02:00
dr. M.S. (Matthijs) Berends
fcfaa87f5d
(v3.0.1.9147) Keep EUCAST blocking rows for infections other than UTI where EUCAST only gives a UTI breakpoint, e.g. breakpoints in brackets for aminoglycosides in Acinetobacter, and let as.sir() with unknown uti consistently prefer non-UTI breakpoints, use UTI breakpoints only if no others exist and note this in sir_interpretation_history() every time
...
The pruning of blocking rows in the EUCAST reproduction script now compares UTI status too, and the script is fixed for the renamed column of the as.ab() coercion cache. In clinical_breakpoints, only the blocking rows were replaced (356 organism/agent/method combinations newly blocked, none unblocked); other changes of a full rebuild, caused by taxonomy updates in the WHONET-based rows, are not included.
2026-10-15 14:55:57 +02:00
dr. M.S. (Matthijs) Berends
d69e7fa740
(v3.0.1.9146) Correct the comment in the EUCAST reproduction script stating that breakpoints in brackets are excluded from clinical_breakpoints: they are kept as blocking rows without values
2026-10-15 12:13:56 +02:00
Matthijs Berends
499b0396d9
Merge pull request #324 from msberends/guideline-aggregation
...
Let aggregated analyses follow the guideline for the 'I' category and deprecate `combine_SI`
2026-10-15 11:52:00 +02:00
dr. M.S. (Matthijs) Berends
38ae865a07
Document all values of rank_index in the clinical_breakpoints data set, including species groups, and the stored value of EUCAST's off-scale S breakpoint
2026-10-15 10:37:40 +02:00
dr. M.S. (Matthijs) Berends
859b99e596
Format the month of the taxonomy update in English regardless of the system locale
2026-10-15 10:34:06 +02:00
dr. M.S. (Matthijs) Berends
b3ecc01657
Show translated pathogen names instead of microorganism codes in grouped traditional antibiograms, including for unknown species
2026-10-15 10:31:07 +02:00
dr. M.S. (Matthijs) Berends
3db586a110
update logo to be perfect hexagon
2026-10-15 10:24:08 +02:00
dr. M.S. (Matthijs) Berends
eb6d07e1fe
Include isolates of unknown species in grouped antibiograms and in wisca(), which were silently excluded with the warning 'invalid microorganism code, NA generated'
2026-10-15 10:21:44 +02:00
dr. M.S. (Matthijs) Berends
3a87075ad3
Make the version formula for PRs in CLAUDE.md consistent with the pre-commit hook, which counts the commits before the new commit
2026-10-15 10:11:09 +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
46f5de1d36
(v3.0.1.9136) Fix the CI entry with a Dutch locale by using a UTF-8 locale that is installed on the runner, and skip the mo_source tests with skip_if() so that the tinytest harness for old R versions supports them
2026-10-15 00:11:07 +02:00
dr. M.S. (Matthijs) Berends
8b01bcb23c
(v3.0.1.9135) Fix get_mo_source() removing the mo_source file at the default location, returning the wrong mo_source, and throwing an error after the original file was moved, and run the unit tests in CI also in a real interactive session and with a user setup, a Dutch locale, and CLSI as default guideline, with tests that no longer assume an English locale or EUCAST
2026-10-14 23:34:45 +02:00
dr. M.S. (Matthijs) Berends
4be7352843
(v3.0.1.9134) Add session cache assertions for separate as.ab() and as.mo() calls, for get_mo_source() without a file, and for real cache hits, which detect the cache being emptied in interactive sessions
2026-10-14 22:49:00 +02:00
dr. M.S. (Matthijs) Berends
e88faf8d40
(v3.0.1.9133) Fix the as.mo() session cache being cleared on every call in interactive sessions without an mo_source file
2026-10-14 21:59:02 +02:00
dr. M.S. (Matthijs) Berends
1a1a3abed1
(v3.0.1.9132) Make translating around 50 times faster and coercion of unknown input in as.ab() up to 70 times faster with identical results, use DOIs instead of PubMed URLs, shorten an example line, and reword cran-comments.md
2026-10-14 20:17:28 +02:00
dr. M.S. (Matthijs) Berends
4115db67fa
(v3.0.1.9131) Remove the list of breaking changes from cran-comments.md
2026-10-13 22:30:31 +02:00
dr. M.S. (Matthijs) Berends
8b3bc220ed
(v3.0.1.9130) Add workflow to check reverse dependencies against the development version on every push to main, list WT/NWT for ECOFFs as breaking change, and update cran-comments.md for v3.1.0
2026-10-13 22:25:28 +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
c8f6cea0a7
(v3.0.1.9128) Revamp console output of interpretive_rules() with cli styling and guideline-dependent SIR colours, make it 11 to 18 times faster with identical results, and fix counts of values that were not actually written ( #259 )
2026-10-13 12:27:38 +02:00
dr. M.S. (Matthijs) Berends
bbfefe65ed
(v3.0.1.9127) update NEWS
2026-10-13 08:44:38 +02:00
dr. M.S. (Matthijs) Berends
32fc9bd689
(v3.0.1.9126) Improve translations of combination names and antimicrobial groups in 20 languages (not en, nl, uk, fr)
2026-10-12 22:56:12 +02:00
dr. M.S. (Matthijs) Berends
04a2f0b3ac
(v3.0.1.9125) Fix translations being translated again (e.g. Ticarcillinee, groupee) and untranslated parts of combination names, and let as.mo() recognise translated names in the set language, cached per language
2026-10-12 22:25:57 +02:00
dr. M.S. (Matthijs) Berends
d4ba5051e7
(v3.0.1.9124) Update French CoNS name in translation test after improved French translations ( #322 )
2026-10-12 21:39:36 +02:00
dr. M.S. (Matthijs) Berends
bf12e3abe7
(v3.0.1.9123) Add method argument to sir_combine() for resistance within a group (most_resistant), and restore the AMR 3.0.1 behaviour of count_*() and proportion_*() for multiple antimicrobials ( #321 )
2026-10-12 21:37:13 +02:00
dr. M.S. (Matthijs) Berends
239c5a87a8
(v3.0.1.9122) NEWS update
2026-10-12 12:55:27 +02:00
dr. M.S. (Matthijs) Berends
0293d296aa
(v3.0.1.9121) styler
2026-10-12 11:42:06 +02:00
Claude
c8cb36ddcf
(v3.0.1.9120) Improve French translations, fixes #322
...
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com >
Claude-Session: https://claude.ai/code/session_015b8mvB1tZ7LeCiLkwaBs5k
2026-10-12 07:55:34 +00:00
dr. M.S. (Matthijs) Berends
e19eabe828
(v3.0.1.9119) update doc
2026-10-11 23:03:06 +02:00
dr. M.S. (Matthijs) Berends
36e6388868
(v3.0.1.9118) update doc
2026-10-11 22:32:15 +02:00
dr. M.S. (Matthijs) Berends
10053d582e
(v3.0.1.9117) Fix static test in test-zzz.R to run without testthat (R 3.0/4.0 tinytest)
2026-10-11 22:15:43 +02:00
