head(my_TB_data) #> rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin -#> 1 S R I I S I -#> 2 I I S S S S -#> 3 S I S R I R -#> 4 S R I S I R -#> 5 S R R I R S -#> 6 S R R S S S +#> 1 I S S S S R +#> 2 I S R R S S +#> 3 R I R R S I +#> 4 R R S S R I +#> 5 R R I S R I +#> 6 R R R S R S #> kanamycin -#> 1 R -#> 2 I -#> 3 I +#> 1 S +#> 2 S +#> 3 R #> 4 I -#> 5 S -#> 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 -3255 -65.10% -3255 -65.10% +3232 +64.64% +3232 +64.64% 2 Negative -961 -19.22% -4216 -84.32% +991 +19.82% +4223 +84.46% 3 Multi-drug-resistant -454 -9.08% -4670 -93.40% +441 +8.82% +4664 +93.28% 4 Poly-resistant -245 -4.90% -4915 -98.30% +246 +4.92% +4910 +98.20% 5 Extensively drug-resistant -85 -1.70% +90 +1.80% 5000 100.00% diff --git a/articles/PCA.html b/articles/PCA.html index f46ad1c2..80763886 100644 --- a/articles/PCA.html +++ b/articles/PCA.html @@ -39,7 +39,7 @@ AMR (for R) - 2.1.1.9012 + 2.1.1.9013 diff --git a/articles/PCA_files/figure-html/unnamed-chunk-6-1.png b/articles/PCA_files/figure-html/unnamed-chunk-6-1.png index a5668a59..d3186e87 100644 Binary files a/articles/PCA_files/figure-html/unnamed-chunk-6-1.png and b/articles/PCA_files/figure-html/unnamed-chunk-6-1.png differ diff --git a/articles/PCA_files/figure-html/unnamed-chunk-7-1.png b/articles/PCA_files/figure-html/unnamed-chunk-7-1.png index 6e5b7b3f..70ea4c5d 100644 Binary files a/articles/PCA_files/figure-html/unnamed-chunk-7-1.png and b/articles/PCA_files/figure-html/unnamed-chunk-7-1.png differ diff --git a/articles/WHONET.html b/articles/WHONET.html index df24cdee..c06c4bb1 100644 --- a/articles/WHONET.html +++ b/articles/WHONET.html @@ -39,7 +39,7 @@ AMR (for R) - 2.1.1.9012 + 2.1.1.9013 diff --git a/articles/datasets.html b/articles/datasets.html index 743ec237..5b665dd2 100644 --- a/articles/datasets.html +++ b/articles/datasets.html @@ -39,7 +39,7 @@ AMR (for R) - 2.1.1.9012 + 2.1.1.9013 @@ -194,7 +194,7 @@ Data sets for download / own use - 25 February 2024 + 03 March 2024 Source: vignettes/datasets.Rmd datasets.Rmd diff --git a/articles/index.html b/articles/index.html index 8604c456..f912828b 100644 --- a/articles/index.html +++ b/articles/index.html @@ -10,7 +10,7 @@ AMR (for R) - 2.1.1.9012 + 2.1.1.9013 diff --git a/articles/other_pkg.html b/articles/other_pkg.html index 85d02f28..9916e001 100644 --- a/articles/other_pkg.html +++ b/articles/other_pkg.html @@ -39,7 +39,7 @@ AMR (for R) - 2.1.1.9012 + 2.1.1.9013 diff --git a/articles/resistance_predict.html b/articles/resistance_predict.html index dafb5bb9..1973d213 100644 --- a/articles/resistance_predict.html +++ b/articles/resistance_predict.html @@ -39,7 +39,7 @@ AMR (for R) - 2.1.1.9012 + 2.1.1.9013 diff --git a/articles/welcome_to_AMR.html b/articles/welcome_to_AMR.html index 01c25316..a089001e 100644 --- a/articles/welcome_to_AMR.html +++ b/articles/welcome_to_AMR.html @@ -39,7 +39,7 @@ AMR (for R) - 2.1.1.9012 + 2.1.1.9013 diff --git a/authors.html b/authors.html index 560010a2..2c26670a 100644 --- a/authors.html +++ b/authors.html @@ -10,7 +10,7 @@ AMR (for R) - 2.1.1.9012 + 2.1.1.9013 diff --git a/extra.css b/extra.css index a50028c3..8eae06b3 100644 --- a/extra.css +++ b/extra.css @@ -29,18 +29,30 @@ # ==================================================================== # */ -:root { - --bs-primary: #128F76 !important; - --bs-primary-color: #128F76 !important; - --bs-primary-rgb: 18, 143, 118 !important; - - --bs-secondary: #a7dbc3 !important; - --bs-secondary-color: #a7dbc3 !important; - --bs-secondary-rgb: 167, 219, 195 !important; - +:root, .navbar * { + --bs-primary: #a7dbc3 !important; + --bs-primary-color: #a7dbc3 !important; + --bs-primary-rgb: 167, 219, 195 !important; + --bs-secondary: #ffffff !important; + --bs-secondary-color: #ffffff !important; + --bs-secondary-rgb: 255, 255, 255 !important; + --bs-navbar-brand-color: var(--bs-body-color) !important; + --bs-navbar-brand-color-hover: var(--bs-body-color) !important; + --bs-nav-link-color: var(--bs-body-color) !important; --bs-bg-opacity: 1 !important; } +.nav-text.text-muted { + color: var(--bs-success) !important; +} +.template-home img.logo { + width: 200px; +} +@media (max-width: 575.98px) { + .template-home img.logo { + width: 140px; + } +} /* fix some footer issues with the logos */ @media (min-width: 576px) { footer .pkgdown-footer-right { diff --git a/index.html b/index.html index 01b90db9..5f869bd0 100644 --- a/index.html +++ b/index.html @@ -43,7 +43,7 @@ AMR (for R) - 2.1.1.9012 + 2.1.1.9013 @@ -781,7 +781,7 @@ Manually, using: install.packages("remotes") # if you haven't already -remotes::install_github("msberends/AMR") +remotes::install_github("msberends/AMR") Automatically, using the rOpenSci R-universe platform, by adding our R-universe address to your list of repositories (‘repos’): diff --git a/news/index.html b/news/index.html index e224d6e5..1518e2a1 100644 --- a/news/index.html +++ b/news/index.html @@ -10,7 +10,7 @@ AMR (for R) - 2.1.1.9012 + 2.1.1.9013 @@ -159,18 +159,18 @@
vignettes/datasets.Rmd
datasets.Rmd
Manually, using:
install.packages("remotes") # if you haven't already -remotes::install_github("msberends/AMR")
Automatically, using the rOpenSci R-universe platform, by adding our R-universe address to your list of repositories (‘repos’):
(this beta version will eventually become v3.0. We’re happy to reach a new major milestone soon, which will be all about the new One Health support!)
This package now supports not only tools for AMR data analysis in clinical settings, but also for veterinary and environmental microbiology. This was made possible through a collaboration with the University of Prince Edward Island, Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change.
rsi
sir
scale_*_mic()
scale_x_mic()
scale_y_mic()
scale_colour_mic()
scale_fill_mic()
limit_mic_range()
keep_operators
as.mic()
"all"
"none"
"edges"
The new function add_custom_antimicrobials() allows users to add custom antimicrobial codes and names to the AMR package.
add_custom_antimicrobials()
AMR
The antibiotics data set was greatly updated:
antibiotics
We now added extensive support for antiviral agents! For the first time, the AMR package has extensive support for antiviral drugs and to work with their names, codes and other data in any way.
antivirals
av
ab
as.av()
av_name()
av_atc()
av_synonyms()
av_from_text()
ab_*()