#> Groups (n=4, named as 'order'): diff --git a/articles/PCA.md b/articles/PCA.md index fb76acece..21efe5903 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 5a953a47b..3be340d4e 100644 --- a/articles/WHONET.html +++ b/articles/WHONET.html @@ -30,7 +30,7 @@ AMR (for R) - 3.0.1.9043 + 3.0.1.9044 diff --git a/articles/WISCA.html b/articles/WISCA.html index e97008910..6a32c50f2 100644 --- a/articles/WISCA.html +++ b/articles/WISCA.html @@ -30,7 +30,7 @@ AMR (for R) - 3.0.1.9043 + 3.0.1.9044 diff --git a/articles/datasets.html b/articles/datasets.html index b85dab458..b97cf35a7 100644 --- a/articles/datasets.html +++ b/articles/datasets.html @@ -30,7 +30,7 @@ AMR (for R) - 3.0.1.9043 + 3.0.1.9044 @@ -80,7 +80,7 @@ Download data sets for download / own use - 02 April 2026 + 04 April 2026 Source: vignettes/datasets.Rmd datasets.Rmd @@ -424,7 +424,7 @@ column names:ab, cid, name, group, a iv_ddd, iv_units, and loinc. This data set is in R available as antimicrobials, after you load the AMR package. -It was last updated on 23 March 2026 09:38:28 UTC. Find more info +It was last updated on 4 April 2026 09:51:50 UTC. Find more info about the contents, (scientific) source, and structure of this data set here. Direct download links: diff --git a/articles/datasets.md b/articles/datasets.md index f0256e45d..a3cdf3349 100644 --- a/articles/datasets.md +++ b/articles/datasets.md @@ -100,7 +100,7 @@ names: This data set is in R available as `antimicrobials`, after you load the `AMR` package. -It was last updated on 23 March 2026 09:38:28 UTC. Find more info about +It was last updated on 4 April 2026 09:51:50 UTC. Find more info about the contents, (scientific) source, and structure of this [data set here](https://amr-for-r.org/reference/antimicrobials.html). diff --git a/articles/index.html b/articles/index.html index 9fc03e145..e1df56c3c 100644 --- a/articles/index.html +++ b/articles/index.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9043 + 3.0.1.9044 diff --git a/authors.html b/authors.html index 48ee42577..740474458 100644 --- a/authors.html +++ b/authors.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9043 + 3.0.1.9044 diff --git a/index.html b/index.html index a5a85ede5..65c00fbe3 100644 --- a/index.html +++ b/index.html @@ -33,7 +33,7 @@ AMR (for R) - 3.0.1.9043 + 3.0.1.9044 diff --git a/news/index.html b/news/index.html index 796aa18e9..652b6671c 100644 --- a/news/index.html +++ b/news/index.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9043 + 3.0.1.9044 @@ -49,9 +49,9 @@ -AMR 3.0.1.9043 +AMR 3.0.1.9044 -New +New Support for clinical breakpoints of 2026 of both CLSI and EUCAST, by adding all of their over 5,700 new clinical breakpoints to the clinical_breakpoints data set for usage in as.sir(). EUCAST 2026 is now the new default guideline for all MIC and disk diffusion interpretations. Integration with the tidymodels framework to allow seamless use of SIR, MIC and disk data in modelling pipelines via recipes @@ -84,7 +84,7 @@ Function amr_course(), which allows for automated download and unpacking of a GitHub repository for e.g. webinar use -Fixes +Fixes Fixed a bug in as.sir() where values that were purely numeric (e.g., "1") and matched the broad SIR-matching regex would be incorrectly stripped of all content by the Unicode letter filter Fixed a bug in as.mic() where MIC values in scientific notation (e.g., "1e-3") were incorrectly handled because the letter e was removed along with other Unicode letters; scientific notation e is now preserved Fixed a bug in as.ab() where certain AB codes containing “PH” or “TH” (such as ETH, MTH, PHE, PHN, STH, THA, THI1) would incorrectly return NA when combined in a vector with any untranslatable value (#245) @@ -99,7 +99,7 @@ Fixed SIR and MIC coercion of combined values, e.g. as.sir("<= 0.002; S") or as.mic("S; 0.002") (#252) -Updates +Updates Extensive cli integration for better message handling and clickable links in messages and warnings (#191, #265) mdro() now infers resistance for a missing base drug column from an available corresponding drug+inhibitor combination showing resistance (e.g., piperacillin is absent but required, while piperacillin/tazobactam available and resistant). Can be set with the new argument infer_from_combinations, which defaults to TRUE (#209). Note that this can yield a higher MDRO detection (which is a good thing as it has become more reliable). diff --git a/news/index.md b/news/index.md index 2e67c2ae2..30f22f826 100644 --- a/news/index.md +++ b/news/index.md @@ -1,6 +1,6 @@ # Changelog -## AMR 3.0.1.9043 +## AMR 3.0.1.9044 #### New diff --git a/pkgdown.yml b/pkgdown.yml index d3682b439..3116a1e8e 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -10,7 +10,7 @@ articles: PCA: PCA.html WHONET: WHONET.html WISCA: WISCA.html -last_built: 2026-04-02T10:27Z +last_built: 2026-04-04T09:58Z 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 5af7c01a3..2cc11cfa9 100644 --- a/reference/AMR-deprecated.html +++ b/reference/AMR-deprecated.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9043 + 3.0.1.9044 diff --git a/reference/AMR-options.html b/reference/AMR-options.html index a2309f804..b8eabdc3b 100644 --- a/reference/AMR-options.html +++ b/reference/AMR-options.html @@ -9,7 +9,7 @@ options(AMR_guideline = "CLSI")'>AMR (for R) - 3.0.1.9043 + 3.0.1.9044 diff --git a/reference/AMR.html b/reference/AMR.html index b2520d1b4..468acbea0 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) - 3.0.1.9043 + 3.0.1.9044 diff --git a/reference/WHOCC.html b/reference/WHOCC.html index a3bec4004..fc345e802 100644 --- a/reference/WHOCC.html +++ b/reference/WHOCC.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9043 + 3.0.1.9044 diff --git a/reference/WHONET.html b/reference/WHONET.html index 227e9915a..2a150ad74 100644 --- a/reference/WHONET.html +++ b/reference/WHONET.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9043 + 3.0.1.9044 diff --git a/reference/ab_from_text.html b/reference/ab_from_text.html index 9d52f985f..38b0fc3dd 100644 --- a/reference/ab_from_text.html +++ b/reference/ab_from_text.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9043 + 3.0.1.9044 diff --git a/reference/ab_property.html b/reference/ab_property.html index 5bd986b71..52072cecc 100644 --- a/reference/ab_property.html +++ b/reference/ab_property.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9043 + 3.0.1.9044 diff --git a/reference/add_custom_antimicrobials.html b/reference/add_custom_antimicrobials.html index e0ff9eb06..7c9dd564a 100644 --- a/reference/add_custom_antimicrobials.html +++ b/reference/add_custom_antimicrobials.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9043 + 3.0.1.9044 diff --git a/reference/add_custom_microorganisms.html b/reference/add_custom_microorganisms.html index e7fc363d0..dcfb73b3e 100644 --- a/reference/add_custom_microorganisms.html +++ b/reference/add_custom_microorganisms.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9043 + 3.0.1.9044 diff --git a/reference/age.html b/reference/age.html index 9f66f9b34..764d6b056 100644 --- a/reference/age.html +++ b/reference/age.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9043 + 3.0.1.9044 @@ -112,16 +112,16 @@ df #> birth_date age age_exact age_at_y2k -#> 1 1999-06-30 26 26.75616 0 -#> 2 1968-01-29 58 58.17260 31 -#> 3 1965-12-05 60 60.32329 34 -#> 4 1980-03-01 46 46.08767 19 -#> 5 1949-11-01 76 76.41644 50 -#> 6 1947-02-14 79 79.12877 52 -#> 7 1940-02-19 86 86.11507 59 -#> 8 1988-01-10 38 38.22466 11 -#> 9 1997-08-27 28 28.59726 2 -#> 10 1978-01-26 48 48.18082 21 +#> 1 1999-06-30 26 26.76164 0 +#> 2 1968-01-29 58 58.17808 31 +#> 3 1965-12-05 60 60.32877 34 +#> 4 1980-03-01 46 46.09315 19 +#> 5 1949-11-01 76 76.42192 50 +#> 6 1947-02-14 79 79.13425 52 +#> 7 1940-02-19 86 86.12055 59 +#> 8 1988-01-10 38 38.23014 11 +#> 9 1997-08-27 28 28.60274 2 +#> 10 1978-01-26 48 48.18630 21
vignettes/datasets.Rmd
datasets.Rmd
This data set is in R available as antimicrobials, after you load the AMR package.
antimicrobials
AMR
It was last updated on 23 March 2026 09:38:28 UTC. Find more info +
It was last updated on 4 April 2026 09:51:50 UTC. Find more info about the contents, (scientific) source, and structure of this data set here.
Direct download links:
clinical_breakpoints
as.sir()
recipes
amr_course()
"1"
as.mic()
"1e-3"
e
as.ab()
ETH
MTH
PHE
PHN
STH
THA
THI1
NA
as.sir("<= 0.002; S")
as.mic("S; 0.002")
cli
mdro()
infer_from_combinations
TRUE