#> Groups (n=4, named as 'order'): diff --git a/articles/PCA.md b/articles/PCA.md index 741cc4899..7cbb2cf45 100644 --- a/articles/PCA.md +++ b/articles/PCA.md @@ -113,7 +113,7 @@ 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 107815e95..5448d1a79 100644 --- a/articles/WHONET.html +++ b/articles/WHONET.html @@ -30,7 +30,7 @@ AMR (for R) - 3.0.1.9008 + 3.0.1.9012 diff --git a/articles/WISCA.html b/articles/WISCA.html index 45af45bec..88b89154d 100644 --- a/articles/WISCA.html +++ b/articles/WISCA.html @@ -30,7 +30,7 @@ AMR (for R) - 3.0.1.9008 + 3.0.1.9012 @@ -368,9 +368,9 @@ all be used for the wisca() Grupo sindrómico -Amoxicillin ácido clavulánico -Amoxicillin ácido clavulánico + Ciprofloxacin -Amoxicillin ácido clavulánico + Gentamicina +Amoxicillin/ácido clavulánico +Amoxicillin/ácido clavulánico + Ciprofloxacin +Amoxicillin/ácido clavulánico + Gentamicina diff --git a/articles/WISCA.md b/articles/WISCA.md index c74757d49..543985664 100644 --- a/articles/WISCA.md +++ b/articles/WISCA.md @@ -207,7 +207,7 @@ wisca(data, language = "Spanish") ``` -| Grupo sindrómico | Amoxicillin ácido clavulánico | Amoxicillin ácido clavulánico + Ciprofloxacin | Amoxicillin ácido clavulánico + Gentamicina | +| Grupo sindrómico | Amoxicillin/ácido clavulánico | Amoxicillin/ácido clavulánico + Ciprofloxacin | Amoxicillin/ácido clavulánico + Gentamicina | |:-----------------|:------------------------------|:----------------------------------------------|:--------------------------------------------| | No UCI | 70% (67.8-72.4%) | 85.3% (83.3-87.2%) | 87% (85.3-88.8%) | | UCI | 80.9% (77.7-83.9%) | 88.2% (85.5-90.6%) | 90.9% (88.7-93%) | diff --git a/articles/datasets.html b/articles/datasets.html index 0c09f7d3c..6f56dbc71 100644 --- a/articles/datasets.html +++ b/articles/datasets.html @@ -30,7 +30,7 @@ AMR (for R) - 3.0.1.9008 + 3.0.1.9012 @@ -80,7 +80,7 @@ Download data sets for download / own use - 06 January 2026 + 07 January 2026 Source: vignettes/datasets.Rmd datasets.Rmd diff --git a/articles/index.html b/articles/index.html index 5d1cc3ee4..e1be814c8 100644 --- a/articles/index.html +++ b/articles/index.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9008 + 3.0.1.9012 diff --git a/authors.html b/authors.html index 211299372..df06a8fea 100644 --- a/authors.html +++ b/authors.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9008 + 3.0.1.9012 diff --git a/index.html b/index.html index 76e513d13..343f6ebe8 100644 --- a/index.html +++ b/index.html @@ -33,7 +33,7 @@ AMR (for R) - 3.0.1.9008 + 3.0.1.9012 diff --git a/news/index.html b/news/index.html index 66cbe36a9..9fa87f8b3 100644 --- a/news/index.html +++ b/news/index.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9008 + 3.0.1.9012 @@ -49,9 +49,9 @@ -AMR 3.0.1.9008 +AMR 3.0.1.9012 -New +New Integration with the tidymodels framework to allow seamless use of SIR, MIC and disk data in modelling pipelines via recipes step_mic_log2() to transform <mic> columns with log2, and step_sir_numeric() to convert <sir> columns to numeric @@ -74,7 +74,7 @@ ab_group() gained an argument all_groups to return all groups the antimicrobial drug is in (#246) -Changed +Changed Fixed a bug in antibiogram() for when no antimicrobials are set Added taniborbactam (TAN) and cefepime/taniborbactam (FTA) to the antimicrobials data set Fixed a bug in as.sir() where for numeric input the arguments S, i, and R would not be considered (#244) diff --git a/news/index.md b/news/index.md index bfd1ba62c..8057761a7 100644 --- a/news/index.md +++ b/news/index.md @@ -1,6 +1,6 @@ # Changelog -## AMR 3.0.1.9008 +## AMR 3.0.1.9012 #### New diff --git a/pkgdown.yml b/pkgdown.yml index 4a43f2d67..c7dcdeda7 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -10,7 +10,7 @@ articles: PCA: PCA.html WHONET: WHONET.html WISCA: WISCA.html -last_built: 2026-01-06T22:17Z +last_built: 2026-01-07T10:04Z 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 33b033ede..b604a6f49 100644 --- a/reference/AMR-deprecated.html +++ b/reference/AMR-deprecated.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9008 + 3.0.1.9012 diff --git a/reference/AMR-options.html b/reference/AMR-options.html index e9a67e638..e57c1185a 100644 --- a/reference/AMR-options.html +++ b/reference/AMR-options.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9008 + 3.0.1.9012 diff --git a/reference/AMR.html b/reference/AMR.html index 9b713f0eb..7c9c4f9d5 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) - 3.0.1.9008 + 3.0.1.9012 diff --git a/reference/WHOCC.html b/reference/WHOCC.html index d9aafcc25..bfbff50f5 100644 --- a/reference/WHOCC.html +++ b/reference/WHOCC.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9008 + 3.0.1.9012 diff --git a/reference/WHONET.html b/reference/WHONET.html index 743dd33a2..7730eee84 100644 --- a/reference/WHONET.html +++ b/reference/WHONET.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9008 + 3.0.1.9012 diff --git a/reference/ab_from_text.html b/reference/ab_from_text.html index baa9604ac..838ba0c1b 100644 --- a/reference/ab_from_text.html +++ b/reference/ab_from_text.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9008 + 3.0.1.9012 diff --git a/reference/ab_property.html b/reference/ab_property.html index 136fe70e0..c4ab926ce 100644 --- a/reference/ab_property.html +++ b/reference/ab_property.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9008 + 3.0.1.9012 @@ -262,7 +262,7 @@ #> [1] "Amoxicillin" #> #> $group -#> [1] "Aminopenicillins" +#> [1] "Aminopenicillins" "Penicillins" "Beta-lactams" #> #> $atc #> [1] "J01CA04" "QG51AA03" "QJ01CA04" diff --git a/reference/ab_property.md b/reference/ab_property.md index fe35c6e72..0db802a4d 100644 --- a/reference/ab_property.md +++ b/reference/ab_property.md @@ -264,7 +264,7 @@ ab_info("AMX") # all properties as a list #> [1] "Amoxicillin" #> #> $group -#> [1] "Aminopenicillins" +#> [1] "Aminopenicillins" "Penicillins" "Beta-lactams" #> #> $atc #> [1] "J01CA04" "QG51AA03" "QJ01CA04" diff --git a/reference/add_custom_antimicrobials.html b/reference/add_custom_antimicrobials.html index 16d64c76c..110bedb36 100644 --- a/reference/add_custom_antimicrobials.html +++ b/reference/add_custom_antimicrobials.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9008 + 3.0.1.9012 diff --git a/reference/add_custom_microorganisms.html b/reference/add_custom_microorganisms.html index cc4609a1f..8a985505f 100644 --- a/reference/add_custom_microorganisms.html +++ b/reference/add_custom_microorganisms.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9008 + 3.0.1.9012 diff --git a/reference/age.html b/reference/age.html index 8977aff5c..b0050f9c7 100644 --- a/reference/age.html +++ b/reference/age.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9008 + 3.0.1.9012 @@ -112,16 +112,16 @@ df #> birth_date age age_exact age_at_y2k -#> 1 1980-02-27 45 45.85753 19 -#> 2 1953-07-26 72 72.44932 46 -#> 3 1949-09-02 76 76.34521 50 -#> 4 1986-08-03 39 39.42740 13 -#> 5 1932-11-19 93 93.13151 67 -#> 6 1949-03-30 76 76.77260 50 -#> 7 1996-06-23 29 29.53973 3 -#> 8 1963-09-16 62 62.30685 36 -#> 9 1952-05-16 73 73.64384 47 -#> 10 1952-11-14 73 73.14521 47 +#> 1 1980-02-27 45 45.86027 19 +#> 2 1953-07-26 72 72.45205 46 +#> 3 1949-09-02 76 76.34795 50 +#> 4 1986-08-03 39 39.43014 13 +#> 5 1932-11-19 93 93.13425 67 +#> 6 1949-03-30 76 76.77534 50 +#> 7 1996-06-23 29 29.54247 3 +#> 8 1963-09-16 62 62.30959 36 +#> 9 1952-05-16 73 73.64658 47 +#> 10 1952-11-14 73 73.14795 47
wisca() Grupo sindrómico -Amoxicillin ácido clavulánico -Amoxicillin ácido clavulánico + Ciprofloxacin -Amoxicillin ácido clavulánico + Gentamicina +Amoxicillin/ácido clavulánico +Amoxicillin/ácido clavulánico + Ciprofloxacin +Amoxicillin/ácido clavulánico + Gentamicina diff --git a/articles/WISCA.md b/articles/WISCA.md index c74757d49..543985664 100644 --- a/articles/WISCA.md +++ b/articles/WISCA.md @@ -207,7 +207,7 @@ wisca(data, language = "Spanish") ``` -| Grupo sindrómico | Amoxicillin ácido clavulánico | Amoxicillin ácido clavulánico + Ciprofloxacin | Amoxicillin ácido clavulánico + Gentamicina | +| Grupo sindrómico | Amoxicillin/ácido clavulánico | Amoxicillin/ácido clavulánico + Ciprofloxacin | Amoxicillin/ácido clavulánico + Gentamicina | |:-----------------|:------------------------------|:----------------------------------------------|:--------------------------------------------| | No UCI | 70% (67.8-72.4%) | 85.3% (83.3-87.2%) | 87% (85.3-88.8%) | | UCI | 80.9% (77.7-83.9%) | 88.2% (85.5-90.6%) | 90.9% (88.7-93%) | diff --git a/articles/datasets.html b/articles/datasets.html index 0c09f7d3c..6f56dbc71 100644 --- a/articles/datasets.html +++ b/articles/datasets.html @@ -30,7 +30,7 @@ AMR (for R) - 3.0.1.9008 + 3.0.1.9012 @@ -80,7 +80,7 @@ Download data sets for download / own use - 06 January 2026 + 07 January 2026 Source: vignettes/datasets.Rmd datasets.Rmd diff --git a/articles/index.html b/articles/index.html index 5d1cc3ee4..e1be814c8 100644 --- a/articles/index.html +++ b/articles/index.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9008 + 3.0.1.9012 diff --git a/authors.html b/authors.html index 211299372..df06a8fea 100644 --- a/authors.html +++ b/authors.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9008 + 3.0.1.9012 diff --git a/index.html b/index.html index 76e513d13..343f6ebe8 100644 --- a/index.html +++ b/index.html @@ -33,7 +33,7 @@ AMR (for R) - 3.0.1.9008 + 3.0.1.9012 diff --git a/news/index.html b/news/index.html index 66cbe36a9..9fa87f8b3 100644 --- a/news/index.html +++ b/news/index.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9008 + 3.0.1.9012 @@ -49,9 +49,9 @@ -AMR 3.0.1.9008 +AMR 3.0.1.9012 -New +New Integration with the tidymodels framework to allow seamless use of SIR, MIC and disk data in modelling pipelines via recipes step_mic_log2() to transform <mic> columns with log2, and step_sir_numeric() to convert <sir> columns to numeric @@ -74,7 +74,7 @@ ab_group() gained an argument all_groups to return all groups the antimicrobial drug is in (#246) -Changed +Changed Fixed a bug in antibiogram() for when no antimicrobials are set Added taniborbactam (TAN) and cefepime/taniborbactam (FTA) to the antimicrobials data set Fixed a bug in as.sir() where for numeric input the arguments S, i, and R would not be considered (#244) diff --git a/news/index.md b/news/index.md index bfd1ba62c..8057761a7 100644 --- a/news/index.md +++ b/news/index.md @@ -1,6 +1,6 @@ # Changelog -## AMR 3.0.1.9008 +## AMR 3.0.1.9012 #### New diff --git a/pkgdown.yml b/pkgdown.yml index 4a43f2d67..c7dcdeda7 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -10,7 +10,7 @@ articles: PCA: PCA.html WHONET: WHONET.html WISCA: WISCA.html -last_built: 2026-01-06T22:17Z +last_built: 2026-01-07T10:04Z 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 33b033ede..b604a6f49 100644 --- a/reference/AMR-deprecated.html +++ b/reference/AMR-deprecated.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9008 + 3.0.1.9012 diff --git a/reference/AMR-options.html b/reference/AMR-options.html index e9a67e638..e57c1185a 100644 --- a/reference/AMR-options.html +++ b/reference/AMR-options.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9008 + 3.0.1.9012 diff --git a/reference/AMR.html b/reference/AMR.html index 9b713f0eb..7c9c4f9d5 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) - 3.0.1.9008 + 3.0.1.9012 diff --git a/reference/WHOCC.html b/reference/WHOCC.html index d9aafcc25..bfbff50f5 100644 --- a/reference/WHOCC.html +++ b/reference/WHOCC.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9008 + 3.0.1.9012 diff --git a/reference/WHONET.html b/reference/WHONET.html index 743dd33a2..7730eee84 100644 --- a/reference/WHONET.html +++ b/reference/WHONET.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9008 + 3.0.1.9012 diff --git a/reference/ab_from_text.html b/reference/ab_from_text.html index baa9604ac..838ba0c1b 100644 --- a/reference/ab_from_text.html +++ b/reference/ab_from_text.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9008 + 3.0.1.9012 diff --git a/reference/ab_property.html b/reference/ab_property.html index 136fe70e0..c4ab926ce 100644 --- a/reference/ab_property.html +++ b/reference/ab_property.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9008 + 3.0.1.9012 @@ -262,7 +262,7 @@ #> [1] "Amoxicillin" #> #> $group -#> [1] "Aminopenicillins" +#> [1] "Aminopenicillins" "Penicillins" "Beta-lactams" #> #> $atc #> [1] "J01CA04" "QG51AA03" "QJ01CA04" diff --git a/reference/ab_property.md b/reference/ab_property.md index fe35c6e72..0db802a4d 100644 --- a/reference/ab_property.md +++ b/reference/ab_property.md @@ -264,7 +264,7 @@ ab_info("AMX") # all properties as a list #> [1] "Amoxicillin" #> #> $group -#> [1] "Aminopenicillins" +#> [1] "Aminopenicillins" "Penicillins" "Beta-lactams" #> #> $atc #> [1] "J01CA04" "QG51AA03" "QJ01CA04" diff --git a/reference/add_custom_antimicrobials.html b/reference/add_custom_antimicrobials.html index 16d64c76c..110bedb36 100644 --- a/reference/add_custom_antimicrobials.html +++ b/reference/add_custom_antimicrobials.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9008 + 3.0.1.9012 diff --git a/reference/add_custom_microorganisms.html b/reference/add_custom_microorganisms.html index cc4609a1f..8a985505f 100644 --- a/reference/add_custom_microorganisms.html +++ b/reference/add_custom_microorganisms.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9008 + 3.0.1.9012 diff --git a/reference/age.html b/reference/age.html index 8977aff5c..b0050f9c7 100644 --- a/reference/age.html +++ b/reference/age.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9008 + 3.0.1.9012 @@ -112,16 +112,16 @@ df #> birth_date age age_exact age_at_y2k -#> 1 1980-02-27 45 45.85753 19 -#> 2 1953-07-26 72 72.44932 46 -#> 3 1949-09-02 76 76.34521 50 -#> 4 1986-08-03 39 39.42740 13 -#> 5 1932-11-19 93 93.13151 67 -#> 6 1949-03-30 76 76.77260 50 -#> 7 1996-06-23 29 29.53973 3 -#> 8 1963-09-16 62 62.30685 36 -#> 9 1952-05-16 73 73.64384 47 -#> 10 1952-11-14 73 73.14521 47 +#> 1 1980-02-27 45 45.86027 19 +#> 2 1953-07-26 72 72.45205 46 +#> 3 1949-09-02 76 76.34795 50 +#> 4 1986-08-03 39 39.43014 13 +#> 5 1932-11-19 93 93.13425 67 +#> 6 1949-03-30 76 76.77534 50 +#> 7 1996-06-23 29 29.54247 3 +#> 8 1963-09-16 62 62.30959 36 +#> 9 1952-05-16 73 73.64658 47 +#> 10 1952-11-14 73 73.14795 47
vignettes/datasets.Rmd
datasets.Rmd
recipes
step_mic_log2()
<mic>
step_sir_numeric()
<sir>
ab_group()
all_groups
antibiogram()
TAN
FTA
antimicrobials
as.sir()
S
i
R