From the shell:
# CRAN check from parent directory R CMD check AMR
#> Groups (n=4, named as 'order'): diff --git a/articles/PCA.md b/articles/PCA.md index 79cec35ca..879ba066a 100644 --- a/articles/PCA.md +++ b/articles/PCA.md @@ -123,7 +123,7 @@ summary(pca_result) #> [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales" #> Importance of components: #> PC1 PC2 PC3 PC4 PC5 PC6 PC7 -#> Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 9.577e-17 +#> Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 1.232e-16 #> Proportion of Variance 0.5799 0.3531 0.0471 0.01435 0.00541 0.00012 0.000e+00 #> Cumulative Proportion 0.5799 0.9330 0.9801 0.99446 0.99988 1.00000 1.000e+00 ``` diff --git a/articles/WHONET.html b/articles/WHONET.html index a3755f5e1..2f634491c 100644 --- a/articles/WHONET.html +++ b/articles/WHONET.html @@ -30,7 +30,7 @@ AMR (for R) - 3.0.1.9069 + 3.0.1.9070 diff --git a/articles/WISCA.html b/articles/WISCA.html index 4cdb97e43..cf9dac0ba 100644 --- a/articles/WISCA.html +++ b/articles/WISCA.html @@ -30,7 +30,7 @@ AMR (for R) - 3.0.1.9069 + 3.0.1.9070 diff --git a/articles/datasets.html b/articles/datasets.html index 6fc0111ed..85278cb4a 100644 --- a/articles/datasets.html +++ b/articles/datasets.html @@ -30,7 +30,7 @@ AMR (for R) - 3.0.1.9069 + 3.0.1.9070 @@ -80,7 +80,7 @@ Download data sets for download / own use - 24 June 2026 + 26 June 2026 Source: vignettes/datasets.Rmd datasets.Rmd diff --git a/articles/index.html b/articles/index.html index 0f6c39d85..684f7d994 100644 --- a/articles/index.html +++ b/articles/index.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9069 + 3.0.1.9070 diff --git a/authors.html b/authors.html index c0fd918b6..eacc7aeef 100644 --- a/authors.html +++ b/authors.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9069 + 3.0.1.9070 diff --git a/index.html b/index.html index fab8ad6bc..e220f19fb 100644 --- a/index.html +++ b/index.html @@ -33,7 +33,7 @@ AMR (for R) - 3.0.1.9069 + 3.0.1.9070 diff --git a/news/index.html b/news/index.html index 3efbf5852..bae40f19f 100644 --- a/news/index.html +++ b/news/index.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9069 + 3.0.1.9070 @@ -49,15 +49,15 @@ -AMR 3.0.1.9069 +AMR 3.0.1.9070 Planned as v3.1.0, end of June 2026. -Breaking Changes +Breaking Changes The former kingdoms Bacteria and Archaea are now each divided into four kingdoms with new top-level domains ‘Bacteria’ and ‘Archaea’ (Göker and Oren, 2024, DOI: 10.1099/ijsem.0.006242). Following this, a new domain column in the microorganisms data set was added, and more importantly, mo_kingdom() now returns the formal kingdom (e.g. "Pseudomonadati" instead of "Bacteria"). Use mo_domain() for the old behaviour. For non-prokaryotic kingdoms (Fungi, Protozoa, etc.), kingdom and domain are identical. Faster parallel computing via the future package for as.sir() and wisca(): a non-sequential plan (e.g. future::plan(future::multisession)) must be active before using parallel = TRUE. -New +New EUCAST 2026 and CLSI 2026 breakpoints: over 5,700 new breakpoints added to the clinical_breakpoints data set; EUCAST 2026 is now the default for all MIC and disk diffusion interpretations Wildtype/Non-wildtype (WT/NWT) output when using ECOFF-based interpretation, by setting breakpoint_type = "ECOFF" in as.sir(); WT/NWT results are fully supported in all resistance/susceptibility functions and plots (#254) @@ -74,7 +74,7 @@ New wisca_plot() to assess the susceptibility and incidence distributions from the Monte Carlo simulations -Fixed +Fixed as.sir() On data frames: already-converted SIR columns no longer dropped on re-run (#278) @@ -101,7 +101,7 @@ -Updated +Updated Taxonomic update for all microorganisms, now updated to June 2026 mo_kingdom() now returns the formal taxonomic kingdom; a one-time note per session explains the change when querying bacterial or archaeal records. @@ -125,6 +125,8 @@ Improved console messages with clickable links throughout, powered by cli if it is installed (#191, #265) as.disk(): input validation is now more strict, rejecting values that are not recognisable as a numeric disk zone diameter + +as.sir() gains an enforce_method argument ("auto", "mic", or "disk") to force the interpretation method when S3 class information is lost, e.g. when called from Python (#291) diff --git a/news/index.md b/news/index.md index 089430a81..51b0cf0b2 100644 --- a/news/index.md +++ b/news/index.md @@ -1,6 +1,6 @@ # Changelog -## AMR 3.0.1.9069 +## AMR 3.0.1.9070 Planned as v3.1.0, end of June 2026. @@ -175,6 +175,11 @@ Planned as v3.1.0, end of June 2026. - [`as.disk()`](https://amr-for-r.org/reference/as.disk.md): input validation is now more strict, rejecting values that are not recognisable as a numeric disk zone diameter +- [`as.sir()`](https://amr-for-r.org/reference/as.sir.md) gains an + `enforce_method` argument (`"auto"`, `"mic"`, or `"disk"`) to force + the interpretation method when S3 class information is lost, e.g. when + called from Python + ([\#291](https://github.com/msberends/AMR/issues/291)) ## AMR 3.0.1 diff --git a/pkgdown.yml b/pkgdown.yml index 65aa65b9f..3d46139a4 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -10,7 +10,7 @@ articles: PCA: PCA.html WHONET: WHONET.html WISCA: WISCA.html -last_built: 2026-06-24T18:32Z +last_built: 2026-06-26T07:29Z urls: reference: https://amr-for-r.org/reference article: https://amr-for-r.org/articles diff --git a/reference/AMR-deprecated.html b/reference/AMR-deprecated.html index 0e031d84f..1365b428b 100644 --- a/reference/AMR-deprecated.html +++ b/reference/AMR-deprecated.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9069 + 3.0.1.9070 diff --git a/reference/AMR-options.html b/reference/AMR-options.html index 2907c3f6b..15383bebd 100644 --- a/reference/AMR-options.html +++ b/reference/AMR-options.html @@ -9,7 +9,7 @@ options(AMR_guideline = "CLSI")'>AMR (for R) - 3.0.1.9069 + 3.0.1.9070 diff --git a/reference/AMR.html b/reference/AMR.html index b2e54d8ed..7af5366c8 100644 --- a/reference/AMR.html +++ b/reference/AMR.html @@ -21,7 +21,7 @@ The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish AMR (for R) - 3.0.1.9069 + 3.0.1.9070 diff --git a/reference/WHOCC.html b/reference/WHOCC.html index ba75ead20..da108f1a1 100644 --- a/reference/WHOCC.html +++ b/reference/WHOCC.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9069 + 3.0.1.9070 diff --git a/reference/WHONET.html b/reference/WHONET.html index 19b7e6381..6d9eb6210 100644 --- a/reference/WHONET.html +++ b/reference/WHONET.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9069 + 3.0.1.9070 diff --git a/reference/ab_from_text.html b/reference/ab_from_text.html index 929136f5a..0f52e09ed 100644 --- a/reference/ab_from_text.html +++ b/reference/ab_from_text.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9069 + 3.0.1.9070 diff --git a/reference/ab_property.html b/reference/ab_property.html index a76d4cb6d..0049cdb7f 100644 --- a/reference/ab_property.html +++ b/reference/ab_property.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9069 + 3.0.1.9070 diff --git a/reference/add_custom_antimicrobials.html b/reference/add_custom_antimicrobials.html index 14299564c..bf7792852 100644 --- a/reference/add_custom_antimicrobials.html +++ b/reference/add_custom_antimicrobials.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9069 + 3.0.1.9070 diff --git a/reference/add_custom_microorganisms.html b/reference/add_custom_microorganisms.html index a7007b9ad..19ee0e1c4 100644 --- a/reference/add_custom_microorganisms.html +++ b/reference/add_custom_microorganisms.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9069 + 3.0.1.9070 diff --git a/reference/age.html b/reference/age.html index 541cfa8cd..84af2ecd7 100644 --- a/reference/age.html +++ b/reference/age.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9069 + 3.0.1.9070 @@ -112,16 +112,16 @@ df #> birth_date age age_exact age_at_y2k -#> 1 1999-06-30 26 26.98356 0 -#> 2 1968-01-29 58 58.40000 31 -#> 3 1965-12-05 60 60.55068 34 -#> 4 1980-03-01 46 46.31507 19 -#> 5 1949-11-01 76 76.64384 50 -#> 6 1947-02-14 79 79.35616 52 -#> 7 1940-02-19 86 86.34247 59 -#> 8 1988-01-10 38 38.45205 11 -#> 9 1997-08-27 28 28.82466 2 -#> 10 1978-01-26 48 48.40822 21 +#> 1 1999-06-30 26 26.98904 0 +#> 2 1968-01-29 58 58.40548 31 +#> 3 1965-12-05 60 60.55616 34 +#> 4 1980-03-01 46 46.32055 19 +#> 5 1949-11-01 76 76.64932 50 +#> 6 1947-02-14 79 79.36164 52 +#> 7 1940-02-19 86 86.34795 59 +#> 8 1988-01-10 38 38.45753 11 +#> 9 1997-08-27 28 28.83014 2 +#> 10 1978-01-26 48 48.41370 21
vignettes/datasets.Rmd
datasets.Rmd
Planned as v3.1.0, end of June 2026.
domain
microorganisms
mo_kingdom()
"Pseudomonadati"
"Bacteria"
mo_domain()
kingdom
future
as.sir()
wisca()
future::plan(future::multisession)
parallel = TRUE
clinical_breakpoints
breakpoint_type = "ECOFF"
wisca_plot()
cli
as.disk()
enforce_method
"auto"
"mic"
"disk"