head(my_TB_data) #> rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin -#> 1 I R I S S I -#> 2 I S I I S R -#> 3 I R S I R I -#> 4 I S R S R I -#> 5 R R I S I I -#> 6 S S R I I S +#> 1 R I S I S I +#> 2 S R R R I R +#> 3 R R I I S R +#> 4 I R S I R R +#> 5 R S S S R R +#> 6 R S R R R R #> kanamycin -#> 1 I -#> 2 I -#> 3 S -#> 4 I -#> 5 I -#> 6 R
We can now add the interpretation of MDR-TB to our data set. You can use:
@@ -438,40 +438,40 @@ Unique: 5 1 Mono-resistant -3243 -64.86% -3243 -64.86% +3238 +64.76% +3238 +64.76% 2 Negative -937 -18.74% -4180 -83.60% +1002 +20.04% +4240 +84.80% 3 Multi-drug-resistant -463 -9.26% -4643 -92.86% +408 +8.16% +4648 +92.96% 4 Poly-resistant -257 -5.14% -4900 -98.00% +244 +4.88% +4892 +97.84% 5 Extensively drug-resistant -100 -2.00% +108 +2.16% 5000 100.00% diff --git a/articles/PCA.html b/articles/PCA.html index cdb6efb8..a5ef02a7 100644 --- a/articles/PCA.html +++ b/articles/PCA.html @@ -38,7 +38,7 @@ AMR (for R) - 2.0.0.9008 + 2.0.0.9009 @@ -290,7 +290,7 @@ 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/SPSS.html b/articles/SPSS.html index 1b49ff5e..5afd4aa6 100644 --- a/articles/SPSS.html +++ b/articles/SPSS.html @@ -38,7 +38,7 @@ AMR (for R) - 2.0.0.9008 + 2.0.0.9009 @@ -178,7 +178,7 @@ Dr. Matthijs Berends - 15 April 2023 + 17 April 2023 Source: vignettes/SPSS.Rmd SPSS.Rmd @@ -257,7 +257,7 @@ data using a custom made website. The webdesign knowledge needed R has a huge community. Many R users just ask questions on websites like StackOverflow.com, the largest -online community for programmers. At the time of writing, 486 808 +online community for programmers. At the time of writing, 487 449 R-related questions have already been asked on this platform (that covers questions and answers for any programming language). In my own experience, most questions are answered within a couple of diff --git a/articles/WHONET.html b/articles/WHONET.html index 864dfe84..8dd4c2e1 100644 --- a/articles/WHONET.html +++ b/articles/WHONET.html @@ -38,7 +38,7 @@ AMR (for R) - 2.0.0.9008 + 2.0.0.9009 diff --git a/articles/datasets.html b/articles/datasets.html index 0e60b784..6d0e19d7 100644 --- a/articles/datasets.html +++ b/articles/datasets.html @@ -38,7 +38,7 @@ AMR (for R) - 2.0.0.9008 + 2.0.0.9009 @@ -176,7 +176,7 @@ Data sets for download / own use - 15 April 2023 + 17 April 2023 Source: vignettes/datasets.Rmd datasets.Rmd diff --git a/articles/index.html b/articles/index.html index c74066d8..128f4631 100644 --- a/articles/index.html +++ b/articles/index.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9008 + 2.0.0.9009 diff --git a/articles/resistance_predict.html b/articles/resistance_predict.html index 90cd6374..c2e6edcf 100644 --- a/articles/resistance_predict.html +++ b/articles/resistance_predict.html @@ -38,7 +38,7 @@ AMR (for R) - 2.0.0.9008 + 2.0.0.9009 diff --git a/articles/welcome_to_AMR.html b/articles/welcome_to_AMR.html index 5fee48ac..28d585ae 100644 --- a/articles/welcome_to_AMR.html +++ b/articles/welcome_to_AMR.html @@ -38,7 +38,7 @@ AMR (for R) - 2.0.0.9008 + 2.0.0.9009 diff --git a/authors.html b/authors.html index 23d97110..1b648cde 100644 --- a/authors.html +++ b/authors.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9008 + 2.0.0.9009 diff --git a/index.html b/index.html index 9aafedeb..e991a159 100644 --- a/index.html +++ b/index.html @@ -42,7 +42,7 @@ AMR (for R) - 2.0.0.9008 + 2.0.0.9009 diff --git a/news/index.html b/news/index.html index c207376a..5547432f 100644 --- a/news/index.html +++ b/news/index.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9008 + 2.0.0.9009 @@ -142,13 +142,14 @@ -AMR 2.0.0.9008 +AMR 2.0.0.9009 -Changed +Changed formatting fix for sir_interpretation_history() Fixed some WHONET codes for microorganisms and consequently a couple of entries in clinical_breakpoints +Added microbial codes for Gram-negative/positive anaerobic bacteria diff --git a/pkgdown.yml b/pkgdown.yml index c4641a84..07f450d4 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -11,7 +11,7 @@ articles: datasets: datasets.html resistance_predict: resistance_predict.html welcome_to_AMR: welcome_to_AMR.html -last_built: 2023-04-15T08:38Z +last_built: 2023-04-17T09:33Z 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 88e27c95..cbdff312 100644 --- a/reference/AMR-deprecated.html +++ b/reference/AMR-deprecated.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9008 + 2.0.0.9009 diff --git a/reference/AMR-options.html b/reference/AMR-options.html index 4cf99743..ceb6618b 100644 --- a/reference/AMR-options.html +++ b/reference/AMR-options.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9008 + 2.0.0.9009 diff --git a/reference/AMR.html b/reference/AMR.html index 9e545ad8..50ee66c8 100644 --- a/reference/AMR.html +++ b/reference/AMR.html @@ -24,7 +24,7 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish, AMR (for R) - 2.0.0.9008 + 2.0.0.9009 diff --git a/reference/Rplot005.png b/reference/Rplot005.png index cbf0ff4e..f1448ef2 100644 Binary files a/reference/Rplot005.png and b/reference/Rplot005.png differ diff --git a/reference/Rplot006.png b/reference/Rplot006.png index 6c26182d..e082f83b 100644 Binary files a/reference/Rplot006.png and b/reference/Rplot006.png differ diff --git a/reference/Rplot007.png b/reference/Rplot007.png index d73c0681..a5959145 100644 Binary files a/reference/Rplot007.png and b/reference/Rplot007.png differ diff --git a/reference/Rplot008.png b/reference/Rplot008.png index fecbc15e..9bc62c9c 100644 Binary files a/reference/Rplot008.png and b/reference/Rplot008.png differ diff --git a/reference/Rplot009.png b/reference/Rplot009.png index 2095e86f..23ccfdd5 100644 Binary files a/reference/Rplot009.png and b/reference/Rplot009.png differ diff --git a/reference/WHOCC.html b/reference/WHOCC.html index 83a8a688..70eb8f95 100644 --- a/reference/WHOCC.html +++ b/reference/WHOCC.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9008 + 2.0.0.9009 diff --git a/reference/WHONET.html b/reference/WHONET.html index 453c92bf..3ed6da8a 100644 --- a/reference/WHONET.html +++ b/reference/WHONET.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9008 + 2.0.0.9009 diff --git a/reference/ab_from_text.html b/reference/ab_from_text.html index 501f5f4c..e3a6b3ad 100644 --- a/reference/ab_from_text.html +++ b/reference/ab_from_text.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9008 + 2.0.0.9009 diff --git a/reference/ab_property.html b/reference/ab_property.html index 27951d8a..3f542140 100644 --- a/reference/ab_property.html +++ b/reference/ab_property.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9008 + 2.0.0.9009 diff --git a/reference/add_custom_antimicrobials.html b/reference/add_custom_antimicrobials.html index 3ef2ad59..e338eb19 100644 --- a/reference/add_custom_antimicrobials.html +++ b/reference/add_custom_antimicrobials.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9008 + 2.0.0.9009 diff --git a/reference/add_custom_microorganisms.html b/reference/add_custom_microorganisms.html index 6d76e4c6..a45ac088 100644 --- a/reference/add_custom_microorganisms.html +++ b/reference/add_custom_microorganisms.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9008 + 2.0.0.9009 diff --git a/reference/age.html b/reference/age.html index 643db3bb..aaffab62 100644 --- a/reference/age.html +++ b/reference/age.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9008 + 2.0.0.9009 @@ -205,16 +205,16 @@ df #> birth_date age age_exact age_at_y2k -#> 1 1948-03-22 75 75.06575 51 -#> 2 1971-11-19 51 51.40274 28 -#> 3 1988-03-07 35 35.10685 11 -#> 4 1999-11-11 23 23.42466 0 -#> 5 1946-07-04 76 76.78082 53 -#> 6 1974-10-29 48 48.46027 25 -#> 7 1969-12-08 53 53.35068 30 -#> 8 1969-04-23 53 53.97808 30 -#> 9 1954-03-03 69 69.11781 45 -#> 10 1966-11-10 56 56.42740 33 +#> 1 1948-06-20 74 74.82466 51 +#> 2 1965-01-08 58 58.27123 34 +#> 3 1970-04-04 53 53.03562 29 +#> 4 1995-07-29 27 27.71781 4 +#> 5 1998-11-21 24 24.40274 1 +#> 6 1990-11-23 32 32.39726 9 +#> 7 1934-09-09 88 88.60274 65 +#> 8 1982-09-28 40 40.55068 17 +#> 9 1963-06-12 59 59.84658 36 +#> 10 1953-05-04 69 69.95342 46
vignettes/SPSS.Rmd
SPSS.Rmd
R has a huge community.
Many R users just ask questions on websites like StackOverflow.com, the largest -online community for programmers. At the time of writing, 486 808 +online community for programmers. At the time of writing, 487 449 R-related questions have already been asked on this platform (that covers questions and answers for any programming language). In my own experience, most questions are answered within a couple of diff --git a/articles/WHONET.html b/articles/WHONET.html index 864dfe84..8dd4c2e1 100644 --- a/articles/WHONET.html +++ b/articles/WHONET.html @@ -38,7 +38,7 @@ AMR (for R) - 2.0.0.9008 + 2.0.0.9009 diff --git a/articles/datasets.html b/articles/datasets.html index 0e60b784..6d0e19d7 100644 --- a/articles/datasets.html +++ b/articles/datasets.html @@ -38,7 +38,7 @@ AMR (for R) - 2.0.0.9008 + 2.0.0.9009 @@ -176,7 +176,7 @@ Data sets for download / own use - 15 April 2023 + 17 April 2023 Source: vignettes/datasets.Rmd datasets.Rmd diff --git a/articles/index.html b/articles/index.html index c74066d8..128f4631 100644 --- a/articles/index.html +++ b/articles/index.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9008 + 2.0.0.9009 diff --git a/articles/resistance_predict.html b/articles/resistance_predict.html index 90cd6374..c2e6edcf 100644 --- a/articles/resistance_predict.html +++ b/articles/resistance_predict.html @@ -38,7 +38,7 @@ AMR (for R) - 2.0.0.9008 + 2.0.0.9009 diff --git a/articles/welcome_to_AMR.html b/articles/welcome_to_AMR.html index 5fee48ac..28d585ae 100644 --- a/articles/welcome_to_AMR.html +++ b/articles/welcome_to_AMR.html @@ -38,7 +38,7 @@ AMR (for R) - 2.0.0.9008 + 2.0.0.9009 diff --git a/authors.html b/authors.html index 23d97110..1b648cde 100644 --- a/authors.html +++ b/authors.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9008 + 2.0.0.9009 diff --git a/index.html b/index.html index 9aafedeb..e991a159 100644 --- a/index.html +++ b/index.html @@ -42,7 +42,7 @@ AMR (for R) - 2.0.0.9008 + 2.0.0.9009 diff --git a/news/index.html b/news/index.html index c207376a..5547432f 100644 --- a/news/index.html +++ b/news/index.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9008 + 2.0.0.9009 @@ -142,13 +142,14 @@ -AMR 2.0.0.9008 +AMR 2.0.0.9009 -Changed +Changed formatting fix for sir_interpretation_history() Fixed some WHONET codes for microorganisms and consequently a couple of entries in clinical_breakpoints +Added microbial codes for Gram-negative/positive anaerobic bacteria diff --git a/pkgdown.yml b/pkgdown.yml index c4641a84..07f450d4 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -11,7 +11,7 @@ articles: datasets: datasets.html resistance_predict: resistance_predict.html welcome_to_AMR: welcome_to_AMR.html -last_built: 2023-04-15T08:38Z +last_built: 2023-04-17T09:33Z 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 88e27c95..cbdff312 100644 --- a/reference/AMR-deprecated.html +++ b/reference/AMR-deprecated.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9008 + 2.0.0.9009 diff --git a/reference/AMR-options.html b/reference/AMR-options.html index 4cf99743..ceb6618b 100644 --- a/reference/AMR-options.html +++ b/reference/AMR-options.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9008 + 2.0.0.9009 diff --git a/reference/AMR.html b/reference/AMR.html index 9e545ad8..50ee66c8 100644 --- a/reference/AMR.html +++ b/reference/AMR.html @@ -24,7 +24,7 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish, AMR (for R) - 2.0.0.9008 + 2.0.0.9009 diff --git a/reference/Rplot005.png b/reference/Rplot005.png index cbf0ff4e..f1448ef2 100644 Binary files a/reference/Rplot005.png and b/reference/Rplot005.png differ diff --git a/reference/Rplot006.png b/reference/Rplot006.png index 6c26182d..e082f83b 100644 Binary files a/reference/Rplot006.png and b/reference/Rplot006.png differ diff --git a/reference/Rplot007.png b/reference/Rplot007.png index d73c0681..a5959145 100644 Binary files a/reference/Rplot007.png and b/reference/Rplot007.png differ diff --git a/reference/Rplot008.png b/reference/Rplot008.png index fecbc15e..9bc62c9c 100644 Binary files a/reference/Rplot008.png and b/reference/Rplot008.png differ diff --git a/reference/Rplot009.png b/reference/Rplot009.png index 2095e86f..23ccfdd5 100644 Binary files a/reference/Rplot009.png and b/reference/Rplot009.png differ diff --git a/reference/WHOCC.html b/reference/WHOCC.html index 83a8a688..70eb8f95 100644 --- a/reference/WHOCC.html +++ b/reference/WHOCC.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9008 + 2.0.0.9009 diff --git a/reference/WHONET.html b/reference/WHONET.html index 453c92bf..3ed6da8a 100644 --- a/reference/WHONET.html +++ b/reference/WHONET.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9008 + 2.0.0.9009 diff --git a/reference/ab_from_text.html b/reference/ab_from_text.html index 501f5f4c..e3a6b3ad 100644 --- a/reference/ab_from_text.html +++ b/reference/ab_from_text.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9008 + 2.0.0.9009 diff --git a/reference/ab_property.html b/reference/ab_property.html index 27951d8a..3f542140 100644 --- a/reference/ab_property.html +++ b/reference/ab_property.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9008 + 2.0.0.9009 diff --git a/reference/add_custom_antimicrobials.html b/reference/add_custom_antimicrobials.html index 3ef2ad59..e338eb19 100644 --- a/reference/add_custom_antimicrobials.html +++ b/reference/add_custom_antimicrobials.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9008 + 2.0.0.9009 diff --git a/reference/add_custom_microorganisms.html b/reference/add_custom_microorganisms.html index 6d76e4c6..a45ac088 100644 --- a/reference/add_custom_microorganisms.html +++ b/reference/add_custom_microorganisms.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9008 + 2.0.0.9009 diff --git a/reference/age.html b/reference/age.html index 643db3bb..aaffab62 100644 --- a/reference/age.html +++ b/reference/age.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9008 + 2.0.0.9009 @@ -205,16 +205,16 @@ df #> birth_date age age_exact age_at_y2k -#> 1 1948-03-22 75 75.06575 51 -#> 2 1971-11-19 51 51.40274 28 -#> 3 1988-03-07 35 35.10685 11 -#> 4 1999-11-11 23 23.42466 0 -#> 5 1946-07-04 76 76.78082 53 -#> 6 1974-10-29 48 48.46027 25 -#> 7 1969-12-08 53 53.35068 30 -#> 8 1969-04-23 53 53.97808 30 -#> 9 1954-03-03 69 69.11781 45 -#> 10 1966-11-10 56 56.42740 33 +#> 1 1948-06-20 74 74.82466 51 +#> 2 1965-01-08 58 58.27123 34 +#> 3 1970-04-04 53 53.03562 29 +#> 4 1995-07-29 27 27.71781 4 +#> 5 1998-11-21 24 24.40274 1 +#> 6 1990-11-23 32 32.39726 9 +#> 7 1934-09-09 88 88.60274 65 +#> 8 1982-09-28 40 40.55068 17 +#> 9 1963-06-12 59 59.84658 36 +#> 10 1953-05-04 69 69.95342 46
vignettes/datasets.Rmd
datasets.Rmd
sir_interpretation_history()
clinical_breakpoints
kurtosis(rnorm(10000)) -#> [1] 3.017473 +#> [1] 2.95229 kurtosis(rnorm(10000), excess = TRUE) -#> [1] -0.005038699 +#> [1] 0.08987438