proportion_SI()
our_data_1st %>% resistance(AMX) -#> ℹ `resistance()` assumes the EUCAST guideline and thus considers the 'I' -#> category susceptible. Set the `guideline` argument or the `AMR_guideline` -#> option to either "CLSI" or "EUCAST", see `?AMR-options`. -#> ℹ This message will be shown once per session. #> [1] 0.4203377
Or can be used in conjunction with group_by() and summarise(), both from the dplyr package:
group_by()
summarise()
dplyr
#> Groups (n=4, named as 'order'): diff --git a/articles/PCA.md b/articles/PCA.md index 879ba066a..cd1865196 100644 --- a/articles/PCA.md +++ b/articles/PCA.md @@ -80,10 +80,6 @@ resistance_data <- example_isolates %>% order, genus, AMC, CXM, CTX, CAZ, GEN, TOB, TMP, SXT ) # and select only relevant columns -#> ℹ `resistance()` assumes the EUCAST guideline and thus considers the 'I' -#> category susceptible. Set the `guideline` argument or the `AMR_guideline` -#> option to either "CLSI" or "EUCAST", see `?AMR-options`. -#> ℹ This message will be shown once per session. head(resistance_data) #> # A tibble: 6 × 10 @@ -123,7 +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 a34e707a9..e0cf60c31 100644 --- a/articles/WHONET.html +++ b/articles/WHONET.html @@ -30,7 +30,7 @@ AMR (for R) - 3.0.1.9077 + 3.0.1.9078 @@ -254,11 +254,7 @@ Longest: 40 # our transformed antibiotic columns # amoxicillin/clavulanic acid (J01CR02) as an example -data %>% freq(AMC_ND2) -#> ℹ `susceptibility()` assumes the EUCAST guideline and thus considers the 'I' -#> category susceptible. Set the `guideline` argument or the `AMR_guideline` -#> option to either "CLSI" or "EUCAST", see `?AMR-options`. -#> ℹ This message will be shown once per session. +data %>% freq(AMC_ND2)
# our transformed antibiotic columns # amoxicillin/clavulanic acid (J01CR02) as an example -data %>% freq(AMC_ND2) -#> ℹ `susceptibility()` assumes the EUCAST guideline and thus considers the 'I' -#> category susceptible. Set the `guideline` argument or the `AMR_guideline` -#> option to either "CLSI" or "EUCAST", see `?AMR-options`. -#> ℹ This message will be shown once per session.
Frequency table
Class: factor > ordered > sir (numeric) Length: 500 diff --git a/articles/WHONET.md b/articles/WHONET.md index e3e035082..d06e91e42 100644 --- a/articles/WHONET.md +++ b/articles/WHONET.md @@ -106,10 +106,6 @@ Longest: 40 # our transformed antibiotic columns # amoxicillin/clavulanic acid (J01CR02) as an example data %>% freq(AMC_ND2) -#> ℹ `susceptibility()` assumes the EUCAST guideline and thus considers the 'I' -#> category susceptible. Set the `guideline` argument or the `AMR_guideline` -#> option to either "CLSI" or "EUCAST", see `?AMR-options`. -#> ℹ This message will be shown once per session. ``` **Frequency table** diff --git a/articles/WISCA.html b/articles/WISCA.html index 75d8bcf74..0489f8b49 100644 --- a/articles/WISCA.html +++ b/articles/WISCA.html @@ -30,7 +30,7 @@ AMR (for R) - 3.0.1.9077 + 3.0.1.9078 diff --git a/articles/datasets.html b/articles/datasets.html index 95d8d0c88..85ae4b4ef 100644 --- a/articles/datasets.html +++ b/articles/datasets.html @@ -30,7 +30,7 @@ AMR (for R) - 3.0.1.9077 + 3.0.1.9078 @@ -80,7 +80,7 @@ Download data sets for download / own use - 26 June 2026 + 27 June 2026 Source: vignettes/datasets.Rmd datasets.Rmd diff --git a/articles/index.html b/articles/index.html index 79d7b1403..9a0b1ec88 100644 --- a/articles/index.html +++ b/articles/index.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9077 + 3.0.1.9078 diff --git a/authors.html b/authors.html index 6adc9ed4b..11b13a808 100644 --- a/authors.html +++ b/authors.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9077 + 3.0.1.9078 diff --git a/index.html b/index.html index 806619495..d8f5684a8 100644 --- a/index.html +++ b/index.html @@ -33,7 +33,7 @@ AMR (for R) - 3.0.1.9077 + 3.0.1.9078 diff --git a/news/index.html b/news/index.html index 86b9ff059..d25e5edfe 100644 --- a/news/index.html +++ b/news/index.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9077 + 3.0.1.9078 @@ -49,15 +49,15 @@ -AMR 3.0.1.9077 +AMR 3.0.1.9078 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) @@ -74,8 +74,9 @@ 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() On data frames: already-converted SIR columns no longer dropped on re-run (#278) Metadata columns (e.g. patient, ward) no longer misidentified as antibiotic columns @@ -101,7 +102,7 @@ -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 4be8e628c..d294fc321 100644 --- a/news/index.md +++ b/news/index.md @@ -1,6 +1,6 @@ # Changelog -## AMR 3.0.1.9077 +## AMR 3.0.1.9078 Planned as v3.1.0, end of June 2026. @@ -77,6 +77,15 @@ Planned as v3.1.0, end of June 2026. #### Fixed +- Setting `options(AMR_guideline = "EUCAST 2012")` or any year-qualified + value no longer causes errors or silent wrong behaviour in + [`interpretive_rules()`](https://amr-for-r.org/reference/interpretive_rules.md), + [`resistance()`](https://amr-for-r.org/reference/proportion.md), + [`susceptibility()`](https://amr-for-r.org/reference/proportion.md), + [`count_resistant()`](https://amr-for-r.org/reference/count.md), + [`count_susceptible()`](https://amr-for-r.org/reference/count.md), and + SIR plotting/printing functions + ([\#298](https://github.com/msberends/AMR/issues/298)) - [`as.sir()`](https://amr-for-r.org/reference/as.sir.md) - On data frames: already-converted SIR columns no longer dropped on re-run ([\#278](https://github.com/msberends/AMR/issues/278)) diff --git a/pkgdown.yml b/pkgdown.yml index 25d9340c4..94e9cdbbc 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -10,7 +10,7 @@ articles: PCA: PCA.html WHONET: WHONET.html WISCA: WISCA.html -last_built: 2026-06-26T19:42Z +last_built: 2026-06-27T11:56Z 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 994ec4a13..9a62fa243 100644 --- a/reference/AMR-deprecated.html +++ b/reference/AMR-deprecated.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9077 + 3.0.1.9078 diff --git a/reference/AMR-options.html b/reference/AMR-options.html index 12632a499..7ab46a832 100644 --- a/reference/AMR-options.html +++ b/reference/AMR-options.html @@ -9,7 +9,7 @@ options(AMR_guideline = "CLSI")'>AMR (for R) - 3.0.1.9077 + 3.0.1.9078 diff --git a/reference/AMR.html b/reference/AMR.html index 3ce9d81f5..ffa5083a8 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) - 3.0.1.9077 + 3.0.1.9078 diff --git a/reference/WHOCC.html b/reference/WHOCC.html index df53edfd8..3a7ae73e0 100644 --- a/reference/WHOCC.html +++ b/reference/WHOCC.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9077 + 3.0.1.9078 diff --git a/reference/WHONET.html b/reference/WHONET.html index c83c5ba15..5d7633552 100644 --- a/reference/WHONET.html +++ b/reference/WHONET.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9077 + 3.0.1.9078 diff --git a/reference/ab_from_text.html b/reference/ab_from_text.html index 5319d1381..07fbac33b 100644 --- a/reference/ab_from_text.html +++ b/reference/ab_from_text.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9077 + 3.0.1.9078 diff --git a/reference/ab_property.html b/reference/ab_property.html index d0e8d5912..b7b8a6d05 100644 --- a/reference/ab_property.html +++ b/reference/ab_property.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9077 + 3.0.1.9078 diff --git a/reference/add_custom_antimicrobials.html b/reference/add_custom_antimicrobials.html index a08318be0..7828f19df 100644 --- a/reference/add_custom_antimicrobials.html +++ b/reference/add_custom_antimicrobials.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9077 + 3.0.1.9078 diff --git a/reference/add_custom_microorganisms.html b/reference/add_custom_microorganisms.html index 325b18743..172f7ac28 100644 --- a/reference/add_custom_microorganisms.html +++ b/reference/add_custom_microorganisms.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9077 + 3.0.1.9078 diff --git a/reference/age.html b/reference/age.html index ea105eb09..6beb39711 100644 --- a/reference/age.html +++ b/reference/age.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9077 + 3.0.1.9078 @@ -112,16 +112,16 @@ df #> birth_date age age_exact age_at_y2k -#> 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 +#> 1 1999-06-30 26 26.99178 0 +#> 2 1968-01-29 58 58.40822 31 +#> 3 1965-12-05 60 60.55890 34 +#> 4 1980-03-01 46 46.32329 19 +#> 5 1949-11-01 76 76.65205 50 +#> 6 1947-02-14 79 79.36438 52 +#> 7 1940-02-19 86 86.35068 59 +#> 8 1988-01-10 38 38.46027 11 +#> 9 1997-08-27 28 28.83288 2 +#> 10 1978-01-26 48 48.41644 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()
options(AMR_guideline = "EUCAST 2012")
interpretive_rules()
resistance()
susceptibility()
count_resistant()
count_susceptible()
patient
ward
top_n_microorganisms()
property_for_each
property = NULL