dr. M.S. (Matthijs) Berends 2c98dac7ae Store all screening breakpoints under screening agents, and add these agents to antimicrobials (#328) ...

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

2026-11-02 17:31:46 +01:00

..

ab_from_text.Rd

(v3.0.1.9059) Fix WISCA in vignette

2026-06-23 14:38:59 +02:00

ab_property.Rd

(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

add_custom_antimicrobials.Rd

Add add_custom_antimicrobial_synonyms() (#307) (#311)

2026-10-10 09:14:07 +02:00

add_custom_microorganisms.Rd

(v2.1.1.9233) chore: make all argument texts full sentences

2025-03-31 14:53:24 +02:00

age_groups.Rd

(v3.0.1.9059) Fix WISCA in vignette

2026-06-23 14:38:59 +02:00

age.Rd

(v2.1.1.9233) chore: make all argument texts full sentences

2025-03-31 14:53:24 +02:00

amr_course.Rd

(v3.0.1.9088) add version number to intrinsic_resistant

2026-09-03 12:14:25 +02:00

AMR-deprecated.Rd

(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

AMR-options.Rd

Store all screening breakpoints under screening agents, and add these agents to antimicrobials (#328)

2026-11-02 17:31:46 +01:00

amr-tidymodels.Rd

(v3.1.0.9004) Document the columns argument of the tidymodels steps to fix the Rd usage warning in R CMD check

2026-10-17 18:23:06 +02:00

AMR.Rd

Store all screening breakpoints under screening agents, and add these agents to antimicrobials (#328)

2026-11-02 17:31:46 +01:00

antibiogram.Rd

(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

antimicrobial_selectors.Rd

(v3.0.1.9121) styler

2026-10-12 11:42:06 +02:00

antimicrobials.Rd

Store all screening breakpoints under screening agents, and add these agents to antimicrobials (#328)

2026-11-02 17:31:46 +01:00

as.ab.Rd

(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

as.av.Rd

(v3.0.1.9103) Replace dead EC Union Register URLs; URL check no longer includes closing braces

2026-10-04 19:53:40 +02:00

as.disk.Rd

(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

2026-10-15 17:05:41 +02:00

as.mic.Rd

(v3.0.1.9088) add version number to intrinsic_resistant

2026-09-03 12:14:25 +02:00

as.mo.Rd

Improve the session caches of as.ab(), as.mo() and all mo_*() functions (#313) (#314)

2026-10-07 14:29:48 +02:00

as.sir.Rd

Store all screening breakpoints under screening agents, and add these agents to antimicrobials (#328)

2026-11-02 17:31:46 +01:00

atc_online.Rd

(v3.0.1.9059) Fix WISCA in vignette

2026-06-23 14:38:59 +02:00

av_from_text.Rd

(v3.0.1.9059) Fix WISCA in vignette

2026-06-23 14:38:59 +02:00

av_property.Rd

(v3.0.1.9103) Replace dead EC Union Register URLs; URL check no longer includes closing braces

2026-10-04 19:53:40 +02:00

availability.Rd

(v2.1.1.9233) chore: make all argument texts full sentences

2025-03-31 14:53:24 +02:00

bug_drug_combinations.Rd

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

clinical_breakpoints.Rd

Leave EUCAST breakpoints in brackets out of clinical_breakpoints, and document where they are kept (#327)

2026-11-02 17:03:47 +01:00

count.Rd

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

custom_interpretive_rules.Rd

(v3.0.1.9109) Fix WHONET codes SUD and ROX in clinical_breakpoints, and add sulbactam/durlobactam (#308)

2026-10-10 09:42:25 +02:00

custom_mdro_guideline.Rd

(v3.0.1.9088) add version number to intrinsic_resistant

2026-09-03 12:14:25 +02:00

dosage.Rd

Add add_if_missing parameter to control NA handling in interpretive rules (#264)

2026-04-21 21:53:43 +02:00

esbl_isolates.Rd

(v3.0.1.9007) fix #246

2026-01-06 23:08:50 +01:00

example_isolates_unclean.Rd

(v2.1.1.9260) fix antibiogram

2025-04-29 16:15:18 +02:00

example_isolates.Rd

Add add_if_missing parameter to control NA handling in interpretive rules (#264)

2026-04-21 21:53:43 +02:00

export_ncbi_biosample.Rd

(v3.0.1.9059) Fix WISCA in vignette

2026-06-23 14:38:59 +02:00

first_isolate.Rd

(v3.0.1.9059) Fix WISCA in vignette

2026-06-23 14:38:59 +02:00

g.test.Rd

(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

2026-10-11 20:36:31 +02:00

get_episode.Rd

(v2.1.1.9233) chore: make all argument texts full sentences

2025-03-31 14:53:24 +02:00

ggplot_pca.Rd

(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

2026-10-11 20:36:31 +02:00

ggplot_sir.Rd

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

guess_ab_col.Rd

(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

interpretive_rules.Rd

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

intrinsic_resistant.Rd

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

italicise_taxonomy.Rd

(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

join.Rd

(v3.0.1.9059) Update taxonomy of microorganisms

2026-06-23 01:38:13 +02:00

key_antimicrobials.Rd

(v3.0.1.9059) Fix WISCA in vignette

2026-06-23 14:38:59 +02:00

kurtosis.Rd

(v2.1.1.9233) chore: make all argument texts full sentences

2025-03-31 14:53:24 +02:00

like.Rd

(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

mdro.Rd

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

mean_amr_distance.Rd

(v3.0.0.9007) allow any tidyselect language in as.sir()

2025-07-17 14:29:35 +02:00

microorganisms.codes.Rd

(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

2026-10-15 21:08:04 +02:00

microorganisms.groups.Rd

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

microorganisms.Rd

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

mo_matching_score.Rd

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

mo_property.Rd

(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

mo_source.Rd

(v3.0.1.9059) Fix WISCA in vignette

2026-06-23 14:38:59 +02:00

pca.Rd

(v3.0.1.9059) Fix WISCA in vignette

2026-06-23 14:38:59 +02:00

plot.Rd

(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

proportion.Rd

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

random.Rd

(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

resistance_predict.Rd

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

sir_combine.Rd

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

skewness.Rd

(v2.1.1.9233) chore: make all argument texts full sentences

2025-03-31 14:53:24 +02:00

top_n_microorganisms.Rd

improve top_n_microorganisms(): add property_for_each, fix property=NULL, enforce rank order (#297)

2026-06-26 21:40:11 +02:00

translate.Rd

(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

WHOCC.Rd

(v3.0.1.9059) Update taxonomy of microorganisms

2026-06-23 01:38:13 +02:00

WHONET.Rd

(v2.1.1.9260) fix antibiogram

2025-04-29 16:15:18 +02:00