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Implements the decisions ticked in #328, and the behaviour specified in https://github.com/msberends/AMR/pull/339#issuecomment-6577438074: `include_screening` now defaults to NULL, using screening breakpoints for screening agents only. With TRUE, a regular agent also takes these breakpoints, and with FALSE a screening agent gives NA with a note.
- antimicrobials gains 13 screening agents, e.g. GEN-S, ERY-S and STR1-S
- GEH and STH rows move to GEN-S and STR1-S, and as.sir() keeps accepting both codes
- Topical cut-off values move to -S agents with site "Topical"
- WHONET-based rows move as ticked, including CLSI cefoxitin for staphylococci and pefloxacin for Salmonella, and EUCAST 2012-2018 cefoxitin MIC
- Clinical breakpoints that EUCAST also allows as a screening test get a copy under the -S agent
as.sir() treats them as absent, so it can use PK/PD breakpoints or, for unknown `uti`, UTI breakpoints. The values stay available in data-raw/breakpoints_eucast_raw.csv, to which the manual now points. Organisms that a table excludes stay excluded, since these have their own blocking rows.
This also fixes the change for unknown `uti` of the previous commit: a blocking row only gives way to an actual UTI breakpoint, not to a UTI row without breakpoints.
`site` takes fixed codes, e.g. "meningitis" or "iv", and can be a column. With `site = NA`, any fitting breakpoint can apply, from most to least systemic. With a site set, breakpoints for contradicting sites are left out, while a breakpoint without a site still applies, and the result is NA if only contradicting sites exist, without falling back to PK/PD. `uti = TRUE` stays available and equals `site = "uti"`. Every choice is noted in sir_interpretation_history(), including the site that was used.
For unknown `uti`, a blocking row without a UTI status no longer overrides a UTI breakpoint at the same taxonomic level. A `uti` vector mixing NA with TRUE or FALSE no longer gives an error.
Veterinary sites are not part of the fixed codes yet, and are treated as breakpoints without a site.
The reproduction script no longer maps MIC breakpoints to AMR:::COMMON_MIC_VALUES, and also keeps the off-scale S breakpoint of 0.001 mg/L. as.sir() compares through the new internal mic_dilution_level(), so that e.g. an MIC of 0.032 and a breakpoint of 0.03 are the same dilution, and shows the published breakpoints in sir_interpretation_history().
Every parsed breakpoint now holds the address of its workbook cell in breakpoints_eucast_raw, and the script stops if a second reading of the workbooks with readxl does not find the value in that cell.
The data sets are rebuilt once, at the end of this PR.
No code change was needed. Morganella follows Enterobacterales, except for imipenem and imipenem-relebactam, for which EUCAST gives rows for Morganellaceae or Morganella.
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.
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
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.
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.
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.
