head(my_TB_data) #> rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin -#> 1 R S S S I I -#> 2 R I S R S I -#> 3 R I I R S R -#> 4 S I I S R R -#> 5 S R I R S S -#> 6 I R I R R I +#> 1 R S R S R S +#> 2 R I R R I R +#> 3 R I R R R R +#> 4 S I S R I R +#> 5 I S R I R S +#> 6 R S R R S R #> kanamycin -#> 1 I -#> 2 S -#> 3 S +#> 1 R +#> 2 R +#> 3 R #> 4 S #> 5 S #> 6 I
#> Groups (n=4, named as 'order'): diff --git a/articles/WHONET.html b/articles/WHONET.html index 798accda..99d50143 100644 --- a/articles/WHONET.html +++ b/articles/WHONET.html @@ -38,7 +38,7 @@ AMR (for R) - 2.0.0.9039 + 2.0.0.9040 diff --git a/articles/datasets.html b/articles/datasets.html index c3b2792c..14ea70b2 100644 --- a/articles/datasets.html +++ b/articles/datasets.html @@ -38,7 +38,7 @@ AMR (for R) - 2.0.0.9039 + 2.0.0.9040 diff --git a/articles/index.html b/articles/index.html index 135dfbf3..192c9a4e 100644 --- a/articles/index.html +++ b/articles/index.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9039 + 2.0.0.9040 diff --git a/articles/other_pkg.html b/articles/other_pkg.html index 5c5fd612..308d60b2 100644 --- a/articles/other_pkg.html +++ b/articles/other_pkg.html @@ -38,7 +38,7 @@ AMR (for R) - 2.0.0.9039 + 2.0.0.9040 diff --git a/articles/resistance_predict.html b/articles/resistance_predict.html index 08728e41..cbe97d6e 100644 --- a/articles/resistance_predict.html +++ b/articles/resistance_predict.html @@ -38,7 +38,7 @@ AMR (for R) - 2.0.0.9039 + 2.0.0.9040 diff --git a/articles/welcome_to_AMR.html b/articles/welcome_to_AMR.html index 1b726e5e..5dce36fb 100644 --- a/articles/welcome_to_AMR.html +++ b/articles/welcome_to_AMR.html @@ -38,7 +38,7 @@ AMR (for R) - 2.0.0.9039 + 2.0.0.9040 diff --git a/authors.html b/authors.html index a23dc204..a55092e4 100644 --- a/authors.html +++ b/authors.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9039 + 2.0.0.9040 diff --git a/index.html b/index.html index bf254c69..352a4c4e 100644 --- a/index.html +++ b/index.html @@ -42,7 +42,7 @@ AMR (for R) - 2.0.0.9039 + 2.0.0.9040 diff --git a/news/index.html b/news/index.html index f7be9224..9a158118 100644 --- a/news/index.html +++ b/news/index.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9039 + 2.0.0.9040 @@ -159,9 +159,9 @@ -AMR 2.0.0.9039 +AMR 2.0.0.9040 -New +New Clinical breakpoints and intrinsic resistance of EUCAST 2023 and CLSI 2023 have been added for as.sir(). EUCAST 2023 (v13.0) is now the new default guideline for all MIC and disks diffusion interpretations The EUCAST dosage guideline of v13.0 has been added to the dosage data set ECOFF: the clinical_breakpoints data set now contains epidemiological cut-off (ECOFF) values. These ECOFFs can be used for MIC/disk interpretation using as.sir(..., breakpoint_type = "ECOFF"), which is an important new addition for veterinary microbiology. @@ -176,7 +176,7 @@ Added microbial codes for Gram-negative/positive anaerobic bacteria -Changed +Changed Updated algorithm of as.mo() by giving more weight to fungi mo_rank() now returns NA for ‘unknown’ microorganisms (B_ANAER, B_ANAER-NEG, B_ANAER-POS, B_GRAMN, B_GRAMP, F_FUNGUS, F_YEAST, and UNKNOWN) diff --git a/pkgdown.yml b/pkgdown.yml index f86eee73..642e0743 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: 2023-07-12T14:24Z +last_built: 2023-07-12T14:31Z 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 170a31a3..6ccfce63 100644 --- a/reference/AMR-deprecated.html +++ b/reference/AMR-deprecated.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9039 + 2.0.0.9040 diff --git a/reference/AMR-options.html b/reference/AMR-options.html index e64ef6de..ecec8dd8 100644 --- a/reference/AMR-options.html +++ b/reference/AMR-options.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9039 + 2.0.0.9040 diff --git a/reference/AMR.html b/reference/AMR.html index ff838ee7..004cbe87 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) - 2.0.0.9039 + 2.0.0.9040 diff --git a/reference/WHOCC.html b/reference/WHOCC.html index 1c0f63bb..a5473296 100644 --- a/reference/WHOCC.html +++ b/reference/WHOCC.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9039 + 2.0.0.9040 diff --git a/reference/WHONET.html b/reference/WHONET.html index 4ac2525b..d147a145 100644 --- a/reference/WHONET.html +++ b/reference/WHONET.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9039 + 2.0.0.9040 diff --git a/reference/ab_from_text.html b/reference/ab_from_text.html index e2823cf6..4307f762 100644 --- a/reference/ab_from_text.html +++ b/reference/ab_from_text.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9039 + 2.0.0.9040 diff --git a/reference/ab_property.html b/reference/ab_property.html index 93f2c0cc..d45dcb7d 100644 --- a/reference/ab_property.html +++ b/reference/ab_property.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9039 + 2.0.0.9040 diff --git a/reference/add_custom_antimicrobials.html b/reference/add_custom_antimicrobials.html index b1daf22d..1ee85c47 100644 --- a/reference/add_custom_antimicrobials.html +++ b/reference/add_custom_antimicrobials.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9039 + 2.0.0.9040 diff --git a/reference/add_custom_microorganisms.html b/reference/add_custom_microorganisms.html index 105538d5..4106cb4e 100644 --- a/reference/add_custom_microorganisms.html +++ b/reference/add_custom_microorganisms.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9039 + 2.0.0.9040 diff --git a/reference/age.html b/reference/age.html index c238406a..365b7a5b 100644 --- a/reference/age.html +++ b/reference/age.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9039 + 2.0.0.9040 @@ -222,16 +222,16 @@ df #> birth_date age age_exact age_at_y2k -#> 1 1946-01-13 77 77.49315 53 -#> 2 1954-06-11 69 69.08493 45 -#> 3 1966-03-23 57 57.30411 33 -#> 4 1943-02-24 80 80.37808 56 -#> 5 1991-04-09 32 32.25753 8 -#> 6 1933-09-03 89 89.85479 66 -#> 7 1931-12-10 91 91.58630 68 -#> 8 1954-07-04 69 69.02192 45 -#> 9 1983-03-03 40 40.35890 16 -#> 10 1949-12-31 73 73.52877 50 +#> 1 1949-01-10 74 74.50137 50 +#> 2 1948-12-16 74 74.56986 51 +#> 3 1936-08-14 86 86.90959 63 +#> 4 1973-03-04 50 50.35616 26 +#> 5 1934-02-04 89 89.43288 65 +#> 6 1996-08-20 26 26.89315 3 +#> 7 1932-07-16 90 90.98904 67 +#> 8 1983-07-06 40 40.01644 16 +#> 9 1938-07-03 85 85.02466 61 +#> 10 1972-03-06 51 51.35068 27
as.sir()
dosage
clinical_breakpoints
as.sir(..., breakpoint_type = "ECOFF")
as.mo()
mo_rank()
NA
B_ANAER
B_ANAER-NEG
B_ANAER-POS
B_GRAMN
B_GRAMP
F_FUNGUS
F_YEAST
UNKNOWN
kurtosis(rnorm(10000)) -#> [1] 2.955967 +#> [1] 3.076585 kurtosis(rnorm(10000), excess = TRUE) -#> [1] -0.03244247 +#> [1] 0.002587789