head(my_TB_data) #> rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin -#> 1 R I R R R I -#> 2 R S R S S S -#> 3 I S I I S I -#> 4 R S S R R I -#> 5 S R R S S I -#> 6 R I R R I S +#> 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 #> kanamycin -#> 1 S -#> 2 R +#> 1 I +#> 2 I #> 3 S -#> 4 R -#> 5 S -#> 6 I
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 -3205 -64.10% -3205 -64.10% +3243 +64.86% +3243 +64.86% 2 Negative -987 -19.74% -4192 -83.84% +937 +18.74% +4180 +83.60% 3 Multi-drug-resistant -475 -9.50% -4667 -93.34% +463 +9.26% +4643 +92.86% 4 Poly-resistant -217 -4.34% -4884 -97.68% +257 +5.14% +4900 +98.00% 5 Extensively drug-resistant -116 -2.32% +100 +2.00% 5000 100.00% diff --git a/articles/PCA.html b/articles/PCA.html index 6669d655..cdb6efb8 100644 --- a/articles/PCA.html +++ b/articles/PCA.html @@ -38,7 +38,7 @@ AMR (for R) - 2.0.0.9007 + 2.0.0.9008 @@ -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 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
#> Groups (n=4, named as 'order'): diff --git a/articles/SPSS.html b/articles/SPSS.html index b626fb6d..1b49ff5e 100644 --- a/articles/SPSS.html +++ b/articles/SPSS.html @@ -38,7 +38,7 @@ AMR (for R) - 2.0.0.9007 + 2.0.0.9008 diff --git a/articles/WHONET.html b/articles/WHONET.html index 0464ada5..864dfe84 100644 --- a/articles/WHONET.html +++ b/articles/WHONET.html @@ -38,7 +38,7 @@ AMR (for R) - 2.0.0.9007 + 2.0.0.9008 diff --git a/articles/datasets.html b/articles/datasets.html index 7d093caa..0e60b784 100644 --- a/articles/datasets.html +++ b/articles/datasets.html @@ -38,7 +38,7 @@ AMR (for R) - 2.0.0.9007 + 2.0.0.9008 diff --git a/articles/index.html b/articles/index.html index c084befa..c74066d8 100644 --- a/articles/index.html +++ b/articles/index.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9007 + 2.0.0.9008 diff --git a/articles/resistance_predict.html b/articles/resistance_predict.html index 005d54da..90cd6374 100644 --- a/articles/resistance_predict.html +++ b/articles/resistance_predict.html @@ -38,7 +38,7 @@ AMR (for R) - 2.0.0.9007 + 2.0.0.9008 diff --git a/articles/welcome_to_AMR.html b/articles/welcome_to_AMR.html index d4d6ccae..5fee48ac 100644 --- a/articles/welcome_to_AMR.html +++ b/articles/welcome_to_AMR.html @@ -38,7 +38,7 @@ AMR (for R) - 2.0.0.9007 + 2.0.0.9008 diff --git a/authors.html b/authors.html index 94614354..23d97110 100644 --- a/authors.html +++ b/authors.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9007 + 2.0.0.9008 diff --git a/index.html b/index.html index 041acd92..9aafedeb 100644 --- a/index.html +++ b/index.html @@ -42,7 +42,7 @@ AMR (for R) - 2.0.0.9007 + 2.0.0.9008 diff --git a/news/index.html b/news/index.html index 963518d7..c207376a 100644 --- a/news/index.html +++ b/news/index.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9007 + 2.0.0.9008 @@ -142,9 +142,9 @@ -AMR 2.0.0.9007 +AMR 2.0.0.9008 -Changed +Changed formatting fix for sir_interpretation_history() Fixed some WHONET codes for microorganisms and consequently a couple of entries in clinical_breakpoints diff --git a/pkgdown.yml b/pkgdown.yml index ba975ee0..c4641a84 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: 2023-04-15T07:37Z +last_built: 2023-04-15T08:38Z 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 6a29a5ed..88e27c95 100644 --- a/reference/AMR-deprecated.html +++ b/reference/AMR-deprecated.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9007 + 2.0.0.9008 diff --git a/reference/AMR-options.html b/reference/AMR-options.html index 769fe838..4cf99743 100644 --- a/reference/AMR-options.html +++ b/reference/AMR-options.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9007 + 2.0.0.9008 diff --git a/reference/AMR.html b/reference/AMR.html index 84937ec7..9e545ad8 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) - 2.0.0.9007 + 2.0.0.9008 diff --git a/reference/Rplot005.png b/reference/Rplot005.png index 60e91628..cbf0ff4e 100644 Binary files a/reference/Rplot005.png and b/reference/Rplot005.png differ diff --git a/reference/Rplot006.png b/reference/Rplot006.png index 56754b30..6c26182d 100644 Binary files a/reference/Rplot006.png and b/reference/Rplot006.png differ diff --git a/reference/Rplot007.png b/reference/Rplot007.png index ffb60c5b..d73c0681 100644 Binary files a/reference/Rplot007.png and b/reference/Rplot007.png differ diff --git a/reference/Rplot008.png b/reference/Rplot008.png index 41022be9..fecbc15e 100644 Binary files a/reference/Rplot008.png and b/reference/Rplot008.png differ diff --git a/reference/Rplot009.png b/reference/Rplot009.png index 450725b0..2095e86f 100644 Binary files a/reference/Rplot009.png and b/reference/Rplot009.png differ diff --git a/reference/WHOCC.html b/reference/WHOCC.html index 94abee68..83a8a688 100644 --- a/reference/WHOCC.html +++ b/reference/WHOCC.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9007 + 2.0.0.9008 diff --git a/reference/WHONET.html b/reference/WHONET.html index c12b1479..453c92bf 100644 --- a/reference/WHONET.html +++ b/reference/WHONET.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9007 + 2.0.0.9008 diff --git a/reference/ab_from_text.html b/reference/ab_from_text.html index 6127193e..501f5f4c 100644 --- a/reference/ab_from_text.html +++ b/reference/ab_from_text.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9007 + 2.0.0.9008 diff --git a/reference/ab_property.html b/reference/ab_property.html index 5663008a..27951d8a 100644 --- a/reference/ab_property.html +++ b/reference/ab_property.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9007 + 2.0.0.9008 diff --git a/reference/add_custom_antimicrobials.html b/reference/add_custom_antimicrobials.html index 01ce5198..3ef2ad59 100644 --- a/reference/add_custom_antimicrobials.html +++ b/reference/add_custom_antimicrobials.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9007 + 2.0.0.9008 diff --git a/reference/add_custom_microorganisms.html b/reference/add_custom_microorganisms.html index 2ee54309..6d76e4c6 100644 --- a/reference/add_custom_microorganisms.html +++ b/reference/add_custom_microorganisms.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9007 + 2.0.0.9008 diff --git a/reference/age.html b/reference/age.html index 100aa407..643db3bb 100644 --- a/reference/age.html +++ b/reference/age.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9007 + 2.0.0.9008 @@ -205,16 +205,16 @@ df #> birth_date age age_exact age_at_y2k -#> 1 1937-05-14 85 85.92055 62 -#> 2 1953-03-15 70 70.08493 46 -#> 3 1953-09-11 69 69.59178 46 -#> 4 1950-12-19 72 72.32055 49 -#> 5 1974-01-01 49 49.28493 26 -#> 6 1960-09-22 62 62.56164 39 -#> 7 1940-03-25 83 83.05753 59 -#> 8 1957-07-27 65 65.71781 42 -#> 9 1986-12-19 36 36.32055 13 -#> 10 1998-05-29 24 24.87945 1 +#> 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
sir_interpretation_history()
clinical_breakpoints
kurtosis(rnorm(10000)) -#> [1] 2.960476 +#> [1] 3.017473 kurtosis(rnorm(10000), excess = TRUE) -#> [1] -0.01258413 +#> [1] -0.005038699