head(my_TB_data) #> rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin -#> 1 R I S R R S -#> 2 I I R S R S -#> 3 S R R I S S -#> 4 S I R S S R -#> 5 S R R I R R -#> 6 S R S S I S +#> 1 R R S R S I +#> 2 I I S R I R +#> 3 R R R R S I +#> 4 S S I R R R +#> 5 I R R R I I +#> 6 I R I R R R #> kanamycin -#> 1 S -#> 2 S -#> 3 I -#> 4 I -#> 5 R -#> 6 R
We can now add the interpretation of MDR-TB to our data set. You can use:
@@ -455,40 +455,40 @@ Unique: 5 1 Mono-resistant -3307 -66.14% -3307 -66.14% +3234 +64.68% +3234 +64.68% 2 Negative -934 -18.68% -4241 -84.82% +943 +18.86% +4177 +83.54% 3 Multi-drug-resistant -436 -8.72% -4677 -93.54% +475 +9.50% +4652 +93.04% 4 Poly-resistant -235 -4.70% -4912 -98.24% +262 +5.24% +4914 +98.28% 5 Extensively drug-resistant -88 -1.76% +86 +1.72% 5000 100.00% diff --git a/articles/PCA.html b/articles/PCA.html index e36e32da..0e188750 100644 --- a/articles/PCA.html +++ b/articles/PCA.html @@ -15,7 +15,7 @@ - + @@ -38,7 +38,7 @@ AMR (for R) - 2.1.0 + 2.1.0.9001 @@ -307,7 +307,7 @@ function: #> [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
#> Groups (n=4, named as 'order'): diff --git a/articles/WHONET.html b/articles/WHONET.html index 86bf5fb0..78c0a7fe 100644 --- a/articles/WHONET.html +++ b/articles/WHONET.html @@ -15,7 +15,7 @@ - + @@ -38,7 +38,7 @@ AMR (for R) - 2.1.0 + 2.1.0.9001 diff --git a/articles/datasets.html b/articles/datasets.html index 2be5624d..0bdaa9d8 100644 --- a/articles/datasets.html +++ b/articles/datasets.html @@ -15,7 +15,7 @@ - + @@ -38,7 +38,7 @@ AMR (for R) - 2.1.0 + 2.1.0.9001 @@ -193,7 +193,7 @@ Data sets for download / own use - 16 July 2023 + 20 July 2023 Source: vignettes/datasets.Rmd datasets.Rmd diff --git a/articles/index.html b/articles/index.html index 8f7cdb87..f2d97327 100644 --- a/articles/index.html +++ b/articles/index.html @@ -1,5 +1,5 @@ -Articles • AMR (for R)Articles • AMR (for R) @@ -10,7 +10,7 @@ AMR (for R) - 2.1.0 + 2.1.0.9001 diff --git a/articles/other_pkg.html b/articles/other_pkg.html index 9a748d75..25d8685f 100644 --- a/articles/other_pkg.html +++ b/articles/other_pkg.html @@ -15,7 +15,7 @@ - + @@ -38,7 +38,7 @@ AMR (for R) - 2.1.0 + 2.1.0.9001 diff --git a/articles/resistance_predict.html b/articles/resistance_predict.html index 32bf5619..3e8d006c 100644 --- a/articles/resistance_predict.html +++ b/articles/resistance_predict.html @@ -15,7 +15,7 @@ - + @@ -38,7 +38,7 @@ AMR (for R) - 2.1.0 + 2.1.0.9001 diff --git a/articles/welcome_to_AMR.html b/articles/welcome_to_AMR.html index 3ac20e01..15414cf2 100644 --- a/articles/welcome_to_AMR.html +++ b/articles/welcome_to_AMR.html @@ -15,7 +15,7 @@ - + @@ -38,7 +38,7 @@ AMR (for R) - 2.1.0 + 2.1.0.9001 diff --git a/authors.html b/authors.html index 33af07ad..729535e1 100644 --- a/authors.html +++ b/authors.html @@ -1,5 +1,5 @@ -Authors and Citation • AMR (for R)Authors and Citation • AMR (for R) @@ -10,7 +10,7 @@ AMR (for R) - 2.1.0 + 2.1.0.9001 diff --git a/deps/Fira_Code-0.4.6/font.css b/deps/Fira_Code-0.4.7/font.css similarity index 100% rename from deps/Fira_Code-0.4.6/font.css rename to deps/Fira_Code-0.4.7/font.css diff --git a/deps/Fira_Code-0.4.6/uU9eCBsR6Z2vfE9aq3bL0fxyUs4tcw4W_D1sFVQ.woff b/deps/Fira_Code-0.4.7/uU9eCBsR6Z2vfE9aq3bL0fxyUs4tcw4W_D1sFVQ.woff similarity index 100% rename from deps/Fira_Code-0.4.6/uU9eCBsR6Z2vfE9aq3bL0fxyUs4tcw4W_D1sFVQ.woff rename to deps/Fira_Code-0.4.7/uU9eCBsR6Z2vfE9aq3bL0fxyUs4tcw4W_D1sFVQ.woff diff --git a/deps/data-deps.txt b/deps/data-deps.txt index 80fdf793..dcc2b743 100644 --- a/deps/data-deps.txt +++ b/deps/data-deps.txt @@ -2,4 +2,4 @@ - + diff --git a/index.html b/index.html index 8601bb85..2a5420d3 100644 --- a/index.html +++ b/index.html @@ -17,7 +17,7 @@ - + @@ -42,7 +42,7 @@ AMR (for R) - 2.1.0 + 2.1.0.9001 diff --git a/news/index.html b/news/index.html index bc62dc26..c87f5bca 100644 --- a/news/index.html +++ b/news/index.html @@ -1,5 +1,5 @@ -Changelog • AMR (for R)Changelog • AMR (for R) @@ -10,7 +10,7 @@ AMR (for R) - 2.1.0 + 2.1.0.9001 @@ -159,7 +159,11 @@ -AMR 2.1.0 +AMR 2.1.0.9001 +Fix rounding MICs on latest R beta (‘R-devel’) + + +AMR 2.1.0CRAN release: 2023-07-16 New Regarding clinical breakpoints: diff --git a/pkgdown.yml b/pkgdown.yml index efea05d9..2fa4a097 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -11,7 +11,7 @@ articles: other_pkg: other_pkg.html resistance_predict: resistance_predict.html welcome_to_AMR: welcome_to_AMR.html -last_built: 2023-07-16T14:22Z +last_built: 2023-07-20T06:28Z urls: reference: https://msberends.github.io/AMR/reference article: https://msberends.github.io/AMR/articles diff --git a/reference/AMR-deprecated.html b/reference/AMR-deprecated.html index 69985981..44c70e07 100644 --- a/reference/AMR-deprecated.html +++ b/reference/AMR-deprecated.html @@ -1,5 +1,5 @@ -Deprecated Functions — AMR-deprecated • AMR (for R)Deprecated Functions — AMR-deprecated • AMR (for R) @@ -10,7 +10,7 @@ AMR (for R) - 2.1.0 + 2.1.0.9001 diff --git a/reference/AMR-options.html b/reference/AMR-options.html index 604f2b6d..2c41d8c1 100644 --- a/reference/AMR-options.html +++ b/reference/AMR-options.html @@ -1,5 +1,5 @@ -Options for the AMR package — AMR-options • AMR (for R)Options for the AMR package — AMR-options • AMR (for R) @@ -10,7 +10,7 @@ AMR (for R) - 2.1.0 + 2.1.0.9001 diff --git a/reference/AMR.html b/reference/AMR.html index 34d61489..3b2a0daf 100644 --- a/reference/AMR.html +++ b/reference/AMR.html @@ -6,7 +6,7 @@ This work was published in the Journal of Statistical Software (Volume 104(3); d and doi:10.33612/diss.192486375 ). After installing this package, R knows ~52 000 microorganisms (updated December 2022) and all ~600 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice Foundation and University Medical Center Groningen. -The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish, Turkish, and Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.">The AMR Package — AMR • AMR (for R)The AMR Package — AMR • AMR (for R)AMR (for R) - 2.1.0 + 2.1.0.9001 diff --git a/reference/WHOCC.html b/reference/WHOCC.html index eae2ba92..ac5323af 100644 --- a/reference/WHOCC.html +++ b/reference/WHOCC.html @@ -1,5 +1,5 @@ -WHOCC: WHO Collaborating Centre for Drug Statistics Methodology — WHOCC • AMR (for R)WHOCC: WHO Collaborating Centre for Drug Statistics Methodology — WHOCC • AMR (for R) @@ -10,7 +10,7 @@ AMR (for R) - 2.1.0 + 2.1.0.9001 diff --git a/reference/WHONET.html b/reference/WHONET.html index b8e46a70..957c5ccf 100644 --- a/reference/WHONET.html +++ b/reference/WHONET.html @@ -1,5 +1,5 @@ -Data Set with 500 Isolates - WHONET Example — WHONET • AMR (for R)Data Set with 500 Isolates - WHONET Example — WHONET • AMR (for R) @@ -10,7 +10,7 @@ AMR (for R) - 2.1.0 + 2.1.0.9001 diff --git a/reference/ab_from_text.html b/reference/ab_from_text.html index 0c142e60..e527603e 100644 --- a/reference/ab_from_text.html +++ b/reference/ab_from_text.html @@ -1,5 +1,5 @@ -Retrieve Antimicrobial Drug Names and Doses from Clinical Text — ab_from_text • AMR (for R)Retrieve Antimicrobial Drug Names and Doses from Clinical Text — ab_from_text • AMR (for R) @@ -10,7 +10,7 @@ AMR (for R) - 2.1.0 + 2.1.0.9001 diff --git a/reference/ab_property.html b/reference/ab_property.html index a12cb07b..5464b386 100644 --- a/reference/ab_property.html +++ b/reference/ab_property.html @@ -1,5 +1,5 @@ -Get Properties of an Antibiotic — ab_property • AMR (for R)Get Properties of an Antibiotic — ab_property • AMR (for R) @@ -10,7 +10,7 @@ AMR (for R) - 2.1.0 + 2.1.0.9001 diff --git a/reference/add_custom_antimicrobials.html b/reference/add_custom_antimicrobials.html index 810d71f7..3e23cfd5 100644 --- a/reference/add_custom_antimicrobials.html +++ b/reference/add_custom_antimicrobials.html @@ -1,5 +1,5 @@ -Add Custom Antimicrobials — add_custom_antimicrobials • AMR (for R)Add Custom Antimicrobials — add_custom_antimicrobials • AMR (for R) @@ -10,7 +10,7 @@ AMR (for R) - 2.1.0 + 2.1.0.9001 diff --git a/reference/add_custom_microorganisms.html b/reference/add_custom_microorganisms.html index 475d9256..de668aed 100644 --- a/reference/add_custom_microorganisms.html +++ b/reference/add_custom_microorganisms.html @@ -1,5 +1,5 @@ -Add Custom Microorganisms — add_custom_microorganisms • AMR (for R)Add Custom Microorganisms — add_custom_microorganisms • AMR (for R) @@ -10,7 +10,7 @@ AMR (for R) - 2.1.0 + 2.1.0.9001 diff --git a/reference/age.html b/reference/age.html index 2ddc011e..479e49d6 100644 --- a/reference/age.html +++ b/reference/age.html @@ -1,5 +1,5 @@ -Age in Years of Individuals — age • AMR (for R)Age in Years of Individuals — age • AMR (for R) @@ -10,7 +10,7 @@ AMR (for R) - 2.1.0 + 2.1.0.9001 @@ -222,16 +222,16 @@ df #> birth_date age age_exact age_at_y2k -#> 1 1967-02-24 56 56.38904 32 -#> 2 1989-12-18 33 33.57534 10 -#> 3 1981-03-15 42 42.33699 18 -#> 4 1935-10-19 87 87.73973 64 -#> 5 1987-11-07 35 35.68767 12 -#> 6 1995-11-05 27 27.69315 4 -#> 7 1953-11-09 69 69.68219 46 -#> 8 1970-04-17 53 53.24658 29 -#> 9 1950-04-25 73 73.22466 49 -#> 10 1937-07-08 86 86.02192 62 +#> 1 1957-11-17 65 65.67123 42 +#> 2 1983-08-04 39 39.95890 16 +#> 3 1942-11-16 80 80.67397 57 +#> 4 1948-11-24 74 74.65205 51 +#> 5 1976-01-30 47 47.46849 23 +#> 6 1958-02-28 65 65.38904 41 +#> 7 1993-05-18 30 30.17260 6 +#> 8 1942-08-16 80 80.92603 57 +#> 9 1994-05-24 29 29.15616 5 +#> 10 1977-08-28 45 45.89315 22
vignettes/datasets.Rmd
datasets.Rmd
CRAN release: 2023-07-16
kurtosis(rnorm(10000)) -#> [1] 3.031459 +#> [1] 3.004586 kurtosis(rnorm(10000), excess = TRUE) -#> [1] -0.01139673 +#> [1] 0.0308963