#> Groups (n=4, named as 'order'): diff --git a/articles/PCA.md b/articles/PCA.md index 5b9e7f33d..cd1865196 100644 --- a/articles/PCA.md +++ b/articles/PCA.md @@ -119,7 +119,7 @@ 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 1.232e-16 +#> Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 9.577e-17 #> 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 2539880fd..6e5799ec3 100644 --- a/articles/WHONET.html +++ b/articles/WHONET.html @@ -30,7 +30,7 @@ AMR (for R) - 3.0.1.9089 + 3.0.1.9090 diff --git a/articles/WISCA.html b/articles/WISCA.html index cc3ab9ffd..6690eb566 100644 --- a/articles/WISCA.html +++ b/articles/WISCA.html @@ -30,7 +30,7 @@ AMR (for R) - 3.0.1.9089 + 3.0.1.9090 diff --git a/articles/datasets.html b/articles/datasets.html index a445e46b5..05bdca2f2 100644 --- a/articles/datasets.html +++ b/articles/datasets.html @@ -30,7 +30,7 @@ AMR (for R) - 3.0.1.9089 + 3.0.1.9090 @@ -80,7 +80,7 @@ Download data sets for download / own use - 03 September 2026 + 04 September 2026 Source: vignettes/datasets.Rmd datasets.Rmd diff --git a/articles/index.html b/articles/index.html index bce1f79d8..317b5e939 100644 --- a/articles/index.html +++ b/articles/index.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9089 + 3.0.1.9090 diff --git a/authors.html b/authors.html index cade3efd1..ca37a9ca9 100644 --- a/authors.html +++ b/authors.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9089 + 3.0.1.9090 diff --git a/index.html b/index.html index 4086e19a6..a920c65b8 100644 --- a/index.html +++ b/index.html @@ -33,7 +33,7 @@ AMR (for R) - 3.0.1.9089 + 3.0.1.9090 diff --git a/news/index.html b/news/index.html index eb40f9030..64136f60c 100644 --- a/news/index.html +++ b/news/index.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9089 + 3.0.1.9090 @@ -49,10 +49,10 @@ -AMR 3.0.1.9089 +AMR 3.0.1.9090 Planned as v3.1.0, end of September 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. @@ -105,7 +105,7 @@ 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) @@ -122,7 +122,7 @@ New wisca_plot() to assess the susceptibility and incidence distributions from the Monte Carlo simulations -Fixed +Fixed Setting options(AMR_guideline = "EUCAST 2012") or any year-qualified value no longer causes errors or silent wrong behaviour in interpretive_rules(), resistance(), susceptibility(), count_resistant(), count_susceptible(), and SIR plotting/printing functions (#298) as.sir() @@ -151,7 +151,7 @@ -Updated +Updated top_n_microorganisms(): new property_for_each argument for sub-grouping within top n groups; rank ordering enforced (only lower taxonomic ranks allowed); fixed property = NULL not being accepted; inner filter now tracks original row indices to prevent cross-group contamination Taxonomic update for all microorganisms, now updated to June 2026 diff --git a/news/index.md b/news/index.md index 2b01f0428..7a0a2c7dc 100644 --- a/news/index.md +++ b/news/index.md @@ -1,6 +1,6 @@ # Changelog -## AMR 3.0.1.9089 +## AMR 3.0.1.9090 Planned as v3.1.0, end of September 2026. diff --git a/pkgdown.yml b/pkgdown.yml index 249ea8e69..c5bbaa4cf 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -10,7 +10,7 @@ articles: PCA: PCA.html WHONET: WHONET.html WISCA: WISCA.html -last_built: 2026-09-03T14:05Z +last_built: 2026-09-04T17:51Z 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 6638979b2..97592b537 100644 --- a/reference/AMR-deprecated.html +++ b/reference/AMR-deprecated.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9089 + 3.0.1.9090 diff --git a/reference/AMR-options.html b/reference/AMR-options.html index 4e0a569bd..5aa05ba50 100644 --- a/reference/AMR-options.html +++ b/reference/AMR-options.html @@ -9,7 +9,7 @@ options(AMR_guideline = "CLSI")'>AMR (for R) - 3.0.1.9089 + 3.0.1.9090 diff --git a/reference/AMR.html b/reference/AMR.html index 5cd0013b1..d78d9bbc0 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) - 3.0.1.9089 + 3.0.1.9090 diff --git a/reference/WHOCC.html b/reference/WHOCC.html index 3f301a9a5..588f08874 100644 --- a/reference/WHOCC.html +++ b/reference/WHOCC.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9089 + 3.0.1.9090 diff --git a/reference/WHONET.html b/reference/WHONET.html index e1aeed3b8..427115da9 100644 --- a/reference/WHONET.html +++ b/reference/WHONET.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9089 + 3.0.1.9090 diff --git a/reference/ab_from_text.html b/reference/ab_from_text.html index e99c3068e..0dc649bd3 100644 --- a/reference/ab_from_text.html +++ b/reference/ab_from_text.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9089 + 3.0.1.9090 diff --git a/reference/ab_property.html b/reference/ab_property.html index 81ae57686..b46d0fc96 100644 --- a/reference/ab_property.html +++ b/reference/ab_property.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9089 + 3.0.1.9090 diff --git a/reference/add_custom_antimicrobials.html b/reference/add_custom_antimicrobials.html index 5e4468715..4568c5b2e 100644 --- a/reference/add_custom_antimicrobials.html +++ b/reference/add_custom_antimicrobials.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9089 + 3.0.1.9090 diff --git a/reference/add_custom_microorganisms.html b/reference/add_custom_microorganisms.html index a1790e146..d17241a86 100644 --- a/reference/add_custom_microorganisms.html +++ b/reference/add_custom_microorganisms.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9089 + 3.0.1.9090 diff --git a/reference/age.html b/reference/age.html index 5042160b5..547c59986 100644 --- a/reference/age.html +++ b/reference/age.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9089 + 3.0.1.9090 @@ -112,16 +112,16 @@ df #> birth_date age age_exact age_at_y2k -#> 1 1999-06-30 27 27.17808 0 -#> 2 1968-01-29 58 58.59452 31 -#> 3 1965-12-05 60 60.74521 34 -#> 4 1980-03-01 46 46.50959 19 -#> 5 1949-11-01 76 76.83836 50 -#> 6 1947-02-14 79 79.55068 52 -#> 7 1940-02-19 86 86.53699 59 -#> 8 1988-01-10 38 38.64658 11 -#> 9 1997-08-27 29 29.01918 2 -#> 10 1978-01-26 48 48.60274 21 +#> 1 1999-06-30 27 27.18082 0 +#> 2 1968-01-29 58 58.59726 31 +#> 3 1965-12-05 60 60.74795 34 +#> 4 1980-03-01 46 46.51233 19 +#> 5 1949-11-01 76 76.84110 50 +#> 6 1947-02-14 79 79.55342 52 +#> 7 1940-02-19 86 86.53973 59 +#> 8 1988-01-10 38 38.64932 11 +#> 9 1997-08-27 29 29.02192 2 +#> 10 1978-01-26 48 48.60548 21
vignettes/datasets.Rmd
datasets.Rmd
Planned as v3.1.0, end of September 2026.
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.
domain
microorganisms
mo_kingdom()
"Pseudomonadati"
"Bacteria"
mo_domain()
kingdom
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.
future
as.sir()
wisca()
future::plan(future::multisession)
parallel = TRUE
clinical_breakpoints
breakpoint_type = "ECOFF"
wisca_plot()
options(AMR_guideline = "EUCAST 2012")
interpretive_rules()
resistance()
susceptibility()
count_resistant()
count_susceptible()
top_n_microorganisms()
property_for_each
property = NULL