diff --git a/404.html b/404.html index b3fd5646..0c8a96c0 100644 --- a/404.html +++ b/404.html @@ -36,7 +36,7 @@ AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -116,28 +116,28 @@ - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R diff --git a/LICENSE-text.html b/LICENSE-text.html index b51d25c1..e8ebb778 100644 --- a/LICENSE-text.html +++ b/LICENSE-text.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -89,28 +89,28 @@ - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R diff --git a/articles/AMR.html b/articles/AMR.html index 1b1fd517..5ae63b24 100644 --- a/articles/AMR.html +++ b/articles/AMR.html @@ -38,7 +38,7 @@ AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -118,28 +118,28 @@ - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R @@ -204,7 +204,7 @@ website update since they are based on randomly created values and the page was written in R Markdown. However, the methodology remains unchanged. This page was -generated on 26 May 2023. +generated on 27 May 2023. Introduction @@ -260,21 +260,21 @@ make the structure of your data generally look like this: -2023-05-26 +2023-05-27 abcd Escherichia coli S S -2023-05-26 +2023-05-27 abcd Escherichia coli S R -2023-05-26 +2023-05-27 efgh Escherichia coli R diff --git a/articles/EUCAST.html b/articles/EUCAST.html index 6475410d..a5780526 100644 --- a/articles/EUCAST.html +++ b/articles/EUCAST.html @@ -38,7 +38,7 @@ AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -118,28 +118,28 @@ - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R diff --git a/articles/MDR.html b/articles/MDR.html index ddc5d780..08b3ffa1 100644 --- a/articles/MDR.html +++ b/articles/MDR.html @@ -38,7 +38,7 @@ AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -118,28 +118,28 @@ - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R @@ -402,17 +402,17 @@ names or codes, this would have worked exactly the same way: head(my_TB_data) #> rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin -#> 1 R R R S S S -#> 2 S R S S R S -#> 3 S R I R I I -#> 4 R I S I S R -#> 5 S I R I I S -#> 6 R R I S S I +#> 1 R S S R R S +#> 2 R R I I S S +#> 3 S R S S I S +#> 4 R R S R R R +#> 5 I I I S R R +#> 6 S I R R S R #> kanamycin -#> 1 I -#> 2 I +#> 1 S +#> 2 S #> 3 I -#> 4 S +#> 4 R #> 5 S #> 6 R We can now add the interpretation of MDR-TB to our data set. You can @@ -455,40 +455,40 @@ Unique: 5 1 Mono-resistant -3180 -63.60% -3180 -63.60% +3225 +64.50% +3225 +64.50% 2 Negative -1032 -20.64% -4212 -84.24% +963 +19.26% +4188 +83.76% 3 Multi-drug-resistant -462 -9.24% -4674 -93.48% +478 +9.56% +4666 +93.32% 4 Poly-resistant -226 -4.52% -4900 -98.00% +228 +4.56% +4894 +97.88% 5 Extensively drug-resistant -100 -2.00% +106 +2.12% 5000 100.00% diff --git a/articles/PCA.html b/articles/PCA.html index 655dfbb9..a30ee677 100644 --- a/articles/PCA.html +++ b/articles/PCA.html @@ -38,7 +38,7 @@ AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -118,28 +118,28 @@ - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R diff --git a/articles/WHONET.html b/articles/WHONET.html index 1020a931..498d52e9 100644 --- a/articles/WHONET.html +++ b/articles/WHONET.html @@ -38,7 +38,7 @@ AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -118,28 +118,28 @@ - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R diff --git a/articles/datasets.html b/articles/datasets.html index fb8593b2..1ade146b 100644 --- a/articles/datasets.html +++ b/articles/datasets.html @@ -38,7 +38,7 @@ AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -118,28 +118,28 @@ - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R @@ -193,7 +193,7 @@ Data sets for download / own use - 26 May 2023 + 27 May 2023 Source: vignettes/datasets.Rmd datasets.Rmd diff --git a/articles/index.html b/articles/index.html index 909bec9e..15d41a8c 100644 --- a/articles/index.html +++ b/articles/index.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -89,28 +89,28 @@ - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R diff --git a/articles/other_pkg.html b/articles/other_pkg.html index aad5107d..18ef9b92 100644 --- a/articles/other_pkg.html +++ b/articles/other_pkg.html @@ -38,7 +38,7 @@ AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -118,28 +118,28 @@ - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R diff --git a/articles/resistance_predict.html b/articles/resistance_predict.html index 6ee44e72..10ed2fee 100644 --- a/articles/resistance_predict.html +++ b/articles/resistance_predict.html @@ -38,7 +38,7 @@ AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -118,28 +118,28 @@ - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R diff --git a/articles/welcome_to_AMR.html b/articles/welcome_to_AMR.html index 202dd833..69062a3f 100644 --- a/articles/welcome_to_AMR.html +++ b/articles/welcome_to_AMR.html @@ -38,7 +38,7 @@ AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -118,28 +118,28 @@ - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R diff --git a/authors.html b/authors.html index 7fd7f578..fb6d7ca2 100644 --- a/authors.html +++ b/authors.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -89,28 +89,28 @@ - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R diff --git a/extra.css b/extra.css index 695e4d78..819146a5 100644 --- a/extra.css +++ b/extra.css @@ -10,7 +10,7 @@ # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # (2022). AMR: An R Package for Working with Antimicrobial Resistance # # Data. Journal of Statistical Software, 104(3), 1-31. # -# doi:10.18637/jss.v104.i03 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/extra.js b/extra.js index d3ab8d7e..8ec8be52 100644 --- a/extra.js +++ b/extra.js @@ -10,7 +10,7 @@ # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # (2022). AMR: An R Package for Working with Antimicrobial Resistance # # Data. Journal of Statistical Software, 104(3), 1-31. # -# doi:10.18637/jss.v104.i03 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/index.html b/index.html index 071f3e6a..2c67d782 100644 --- a/index.html +++ b/index.html @@ -42,7 +42,7 @@ AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -122,28 +122,28 @@ - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R diff --git a/news/index.html b/news/index.html index e0e6dbee..8a1cea99 100644 --- a/news/index.html +++ b/news/index.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -89,28 +89,28 @@ - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R @@ -159,9 +159,9 @@ -AMR 2.0.0.9022 +AMR 2.0.0.9023 -Changed +Changed Added oxygen tolerance from BacDive to over 25,000 bacteria in the microorganisms data set Added mo_oxygen_tolerance() to retrieve the values Added mo_is_anaerobic() to determine which genera/species are obligate anaerobic bacteria diff --git a/pkgdown.yml b/pkgdown.yml index 6f181499..cd7d5e13 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: 2023-05-26T18:41Z +last_built: 2023-05-27T08:50Z 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 ad21b46b..2e803f85 100644 --- a/reference/AMR-deprecated.html +++ b/reference/AMR-deprecated.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -89,28 +89,28 @@ - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R diff --git a/reference/AMR-options.html b/reference/AMR-options.html index 4b1d1f13..557ccc8c 100644 --- a/reference/AMR-options.html +++ b/reference/AMR-options.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -89,28 +89,28 @@ - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R diff --git a/reference/AMR.html b/reference/AMR.html index 59b91ab0..fd5f416e 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) - 2.0.0.9022 + 2.0.0.9023 @@ -103,28 +103,28 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish, - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R diff --git a/reference/Rplot005.png b/reference/Rplot005.png index 022ca9da..9061d9e2 100644 Binary files a/reference/Rplot005.png and b/reference/Rplot005.png differ diff --git a/reference/Rplot006.png b/reference/Rplot006.png index ffad4293..5c614476 100644 Binary files a/reference/Rplot006.png and b/reference/Rplot006.png differ diff --git a/reference/Rplot007.png b/reference/Rplot007.png index e161a1f6..cb1dd7a9 100644 Binary files a/reference/Rplot007.png and b/reference/Rplot007.png differ diff --git a/reference/Rplot008.png b/reference/Rplot008.png index 1ce8eba1..9fb3a0d0 100644 Binary files a/reference/Rplot008.png and b/reference/Rplot008.png differ diff --git a/reference/Rplot009.png b/reference/Rplot009.png index 850e561b..b4a86c2f 100644 Binary files a/reference/Rplot009.png and b/reference/Rplot009.png differ diff --git a/reference/WHOCC.html b/reference/WHOCC.html index 68edad17..57570045 100644 --- a/reference/WHOCC.html +++ b/reference/WHOCC.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -89,28 +89,28 @@ - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R diff --git a/reference/WHONET.html b/reference/WHONET.html index c01fab5f..8670a0ec 100644 --- a/reference/WHONET.html +++ b/reference/WHONET.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -89,28 +89,28 @@ - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R diff --git a/reference/ab_from_text.html b/reference/ab_from_text.html index bf70739e..02e8eb12 100644 --- a/reference/ab_from_text.html +++ b/reference/ab_from_text.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -89,28 +89,28 @@ - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R diff --git a/reference/ab_property.html b/reference/ab_property.html index 0f139006..f37b5391 100644 --- a/reference/ab_property.html +++ b/reference/ab_property.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -89,28 +89,28 @@ - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R diff --git a/reference/add_custom_antimicrobials.html b/reference/add_custom_antimicrobials.html index cb38d6b7..f4f2d68d 100644 --- a/reference/add_custom_antimicrobials.html +++ b/reference/add_custom_antimicrobials.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -89,28 +89,28 @@ - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R diff --git a/reference/add_custom_microorganisms.html b/reference/add_custom_microorganisms.html index 0221eea2..a3cfb663 100644 --- a/reference/add_custom_microorganisms.html +++ b/reference/add_custom_microorganisms.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -89,28 +89,28 @@ - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R diff --git a/reference/age.html b/reference/age.html index 0777573d..3b936cf8 100644 --- a/reference/age.html +++ b/reference/age.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -89,28 +89,28 @@ - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R @@ -222,16 +222,16 @@ df #> birth_date age age_exact age_at_y2k -#> 1 1931-09-23 91 91.67123 68 -#> 2 1943-05-24 80 80.00548 56 -#> 3 1940-06-21 82 82.92877 59 -#> 4 1961-09-19 61 61.68219 38 -#> 5 1950-09-30 72 72.65205 49 -#> 6 1984-08-13 38 38.78356 15 -#> 7 1942-06-08 80 80.96438 57 -#> 8 1983-08-05 39 39.80548 16 -#> 9 1985-01-31 38 38.31507 14 -#> 10 1992-07-28 30 30.82740 7 +#> 1 1989-07-11 33 33.87671 10 +#> 2 1976-01-27 47 47.32877 23 +#> 3 1952-06-04 70 70.97808 47 +#> 4 1975-04-14 48 48.11781 24 +#> 5 1980-05-09 43 43.04932 19 +#> 6 1959-05-20 64 64.01918 40 +#> 7 1956-11-01 66 66.56712 43 +#> 8 1986-10-27 36 36.58082 13 +#> 9 1989-06-17 33 33.94247 10 +#> 10 1965-07-30 57 57.82466 34 - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R diff --git a/reference/antibiogram.html b/reference/antibiogram.html index cb3876ff..d4eac416 100644 --- a/reference/antibiogram.html +++ b/reference/antibiogram.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -89,28 +89,28 @@ - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R diff --git a/reference/antibiotic_class_selectors.html b/reference/antibiotic_class_selectors.html index f6be8e30..2a91b76d 100644 --- a/reference/antibiotic_class_selectors.html +++ b/reference/antibiotic_class_selectors.html @@ -12,7 +12,7 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -91,28 +91,28 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R @@ -626,11 +626,11 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil #> # A tibble: 5 × 1 #> kefzol #> <sir> -#> 1 R +#> 1 I #> 2 R -#> 3 R -#> 4 S -#> 5 I +#> 3 I +#> 4 I +#> 5 S if (require("dplyr")) { # get AMR for all aminoglycosides e.g., per ward: diff --git a/reference/antibiotics.html b/reference/antibiotics.html index 936a5df7..13129a83 100644 --- a/reference/antibiotics.html +++ b/reference/antibiotics.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -89,28 +89,28 @@ - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R diff --git a/reference/as.ab.html b/reference/as.ab.html index 3e228bf2..3e438f81 100644 --- a/reference/as.ab.html +++ b/reference/as.ab.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -89,28 +89,28 @@ - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R diff --git a/reference/as.av.html b/reference/as.av.html index 24bdbf47..c9489ac6 100644 --- a/reference/as.av.html +++ b/reference/as.av.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -89,28 +89,28 @@ - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R diff --git a/reference/as.disk.html b/reference/as.disk.html index e2541fb6..6e266eba 100644 --- a/reference/as.disk.html +++ b/reference/as.disk.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -89,28 +89,28 @@ - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R diff --git a/reference/as.mic.html b/reference/as.mic.html index 5e37b090..ee8b41c6 100644 --- a/reference/as.mic.html +++ b/reference/as.mic.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -89,28 +89,28 @@ - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R diff --git a/reference/as.mo.html b/reference/as.mo.html index ebfedfe3..f1602799 100644 --- a/reference/as.mo.html +++ b/reference/as.mo.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -89,28 +89,28 @@ - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R diff --git a/reference/as.sir.html b/reference/as.sir.html index d05eefd5..bfa74b81 100644 --- a/reference/as.sir.html +++ b/reference/as.sir.html @@ -12,7 +12,7 @@ All breakpoints used for interpretation are publicly available in the clinical_b AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -91,28 +91,28 @@ All breakpoints used for interpretation are publicly available in the clinical_b - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R @@ -551,16 +551,16 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of #> # A tibble: 50 × 12 #> datetime index ab_input ab_guideline mo_input mo_guideline #> <dttm> <int> <chr> <ab> <chr> <mo> -#> 1 2023-05-26 18:42:01 1 TOB TOB Escherichia… B_[ORD]_ENTRBCTR -#> 2 2023-05-26 18:42:01 1 GEN GEN Escherichia… B_[ORD]_ENTRBCTR -#> 3 2023-05-26 18:42:00 1 CIP CIP Escherichia… B_[ORD]_ENTRBCTR -#> 4 2023-05-26 18:42:00 1 AMP AMP Escherichia… B_[ORD]_ENTRBCTR -#> 5 2023-05-26 18:41:54 1 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR -#> 6 2023-05-26 18:41:54 2 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR -#> 7 2023-05-26 18:41:54 3 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR -#> 8 2023-05-26 18:41:54 4 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR -#> 9 2023-05-26 18:41:54 5 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR -#> 10 2023-05-26 18:41:54 6 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR +#> 1 2023-05-27 08:50:58 1 TOB TOB Escherichia… B_[ORD]_ENTRBCTR +#> 2 2023-05-27 08:50:58 1 GEN GEN Escherichia… B_[ORD]_ENTRBCTR +#> 3 2023-05-27 08:50:57 1 CIP CIP Escherichia… B_[ORD]_ENTRBCTR +#> 4 2023-05-27 08:50:57 1 AMP AMP Escherichia… B_[ORD]_ENTRBCTR +#> 5 2023-05-27 08:50:52 1 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR +#> 6 2023-05-27 08:50:52 2 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR +#> 7 2023-05-27 08:50:52 3 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR +#> 8 2023-05-27 08:50:52 4 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR +#> 9 2023-05-27 08:50:52 5 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR +#> 10 2023-05-27 08:50:52 6 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR #> # ℹ 40 more rows #> # ℹ 6 more variables: guideline <chr>, ref_table <chr>, method <chr>, #> # input <dbl>, outcome <sir>, breakpoint_S_R <chr> diff --git a/reference/atc_online.html b/reference/atc_online.html index f47e8b51..2327b0c0 100644 --- a/reference/atc_online.html +++ b/reference/atc_online.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -89,28 +89,28 @@ - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R diff --git a/reference/av_from_text.html b/reference/av_from_text.html index cfa5466c..64e478d2 100644 --- a/reference/av_from_text.html +++ b/reference/av_from_text.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -89,28 +89,28 @@ - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R diff --git a/reference/av_property.html b/reference/av_property.html index fe2c3c38..e6ffbc2b 100644 --- a/reference/av_property.html +++ b/reference/av_property.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -89,28 +89,28 @@ - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R diff --git a/reference/availability.html b/reference/availability.html index 0846ff26..b6977c52 100644 --- a/reference/availability.html +++ b/reference/availability.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -89,28 +89,28 @@ - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R diff --git a/reference/bug_drug_combinations.html b/reference/bug_drug_combinations.html index 2b26f398..e301b754 100644 --- a/reference/bug_drug_combinations.html +++ b/reference/bug_drug_combinations.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -89,28 +89,28 @@ - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R diff --git a/reference/clinical_breakpoints.html b/reference/clinical_breakpoints.html index 901a506c..e0affbfe 100644 --- a/reference/clinical_breakpoints.html +++ b/reference/clinical_breakpoints.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -89,28 +89,28 @@ - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R diff --git a/reference/count.html b/reference/count.html index e5367377..64214242 100644 --- a/reference/count.html +++ b/reference/count.html @@ -12,7 +12,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible( AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -91,28 +91,28 @@ count_resistant() should be used to count resistant isolates, count_susceptible( - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R diff --git a/reference/custom_eucast_rules.html b/reference/custom_eucast_rules.html index d3778582..470c827a 100644 --- a/reference/custom_eucast_rules.html +++ b/reference/custom_eucast_rules.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -89,28 +89,28 @@ - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R diff --git a/reference/dosage.html b/reference/dosage.html index 46c1c69b..482d1ad9 100644 --- a/reference/dosage.html +++ b/reference/dosage.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -89,28 +89,28 @@ - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R diff --git a/reference/eucast_rules.html b/reference/eucast_rules.html index 86128795..4c7d7def 100644 --- a/reference/eucast_rules.html +++ b/reference/eucast_rules.html @@ -12,7 +12,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -91,28 +91,28 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R diff --git a/reference/example_isolates.html b/reference/example_isolates.html index 06324239..14afa39e 100644 --- a/reference/example_isolates.html +++ b/reference/example_isolates.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -89,28 +89,28 @@ - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R diff --git a/reference/example_isolates_unclean.html b/reference/example_isolates_unclean.html index 5f6623dc..a2624a12 100644 --- a/reference/example_isolates_unclean.html +++ b/reference/example_isolates_unclean.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -89,28 +89,28 @@ - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R diff --git a/reference/first_isolate.html b/reference/first_isolate.html index 7af74428..b0914b9b 100644 --- a/reference/first_isolate.html +++ b/reference/first_isolate.html @@ -12,7 +12,7 @@ AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -91,28 +91,28 @@ - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R diff --git a/reference/g.test.html b/reference/g.test.html index 00f1a855..38d0042c 100644 --- a/reference/g.test.html +++ b/reference/g.test.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -89,28 +89,28 @@ - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R diff --git a/reference/get_episode.html b/reference/get_episode.html index 2c11a20e..98dac5d3 100644 --- a/reference/get_episode.html +++ b/reference/get_episode.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -89,28 +89,28 @@ - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R @@ -263,29 +263,27 @@ df <- example_isolates[sample(seq_len(2000), size = 100), ] get_episode(df$date, episode_days = 60) # indices -#> [1] 3 16 36 32 3 13 40 10 35 39 8 16 32 29 8 38 21 11 15 30 5 20 45 9 12 -#> [26] 8 34 14 31 38 26 10 43 36 11 17 38 39 35 42 17 8 19 43 25 38 6 24 7 2 -#> [51] 17 34 6 10 1 33 9 41 17 7 14 21 11 36 29 25 10 21 36 23 28 18 12 20 41 -#> [76] 28 22 4 21 37 38 37 42 36 35 3 20 44 22 2 10 16 6 7 1 37 28 31 27 33 +#> [1] 34 32 18 15 11 8 45 29 7 7 46 31 27 44 20 38 47 11 42 3 46 4 13 37 4 +#> [26] 9 35 5 46 26 44 40 16 20 21 20 24 27 14 41 20 41 28 27 42 24 22 35 30 22 +#> [51] 16 44 25 35 30 6 12 13 38 8 33 46 29 6 23 6 34 47 11 1 16 40 27 46 5 +#> [76] 10 2 39 48 4 23 46 25 36 19 12 43 17 22 9 47 11 2 45 17 15 42 37 28 8 is_new_episode(df$date, episode_days = 60) # TRUE/FALSE -#> [1] TRUE TRUE TRUE TRUE FALSE TRUE TRUE TRUE TRUE TRUE TRUE FALSE -#> [13] FALSE TRUE FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE -#> [25] TRUE FALSE TRUE TRUE TRUE FALSE TRUE FALSE TRUE FALSE FALSE TRUE -#> [37] FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE TRUE TRUE -#> [49] TRUE TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE TRUE FALSE FALSE -#> [61] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE TRUE -#> [73] FALSE FALSE FALSE FALSE TRUE TRUE FALSE TRUE FALSE FALSE FALSE FALSE -#> [85] FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE -#> [97] FALSE FALSE TRUE FALSE +#> [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE TRUE TRUE +#> [13] TRUE TRUE TRUE TRUE TRUE FALSE TRUE TRUE FALSE TRUE TRUE TRUE +#> [25] FALSE TRUE TRUE TRUE FALSE TRUE FALSE TRUE TRUE FALSE TRUE FALSE +#> [37] TRUE FALSE TRUE TRUE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE +#> [49] TRUE FALSE FALSE FALSE TRUE FALSE FALSE TRUE TRUE FALSE FALSE FALSE +#> [61] TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE +#> [73] FALSE FALSE FALSE TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE TRUE +#> [85] TRUE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE +#> [97] FALSE FALSE FALSE FALSE # filter on results from the third 60-day episode only, using base R df[which(get_episode(df$date, 60) == 3), ] -#> # A tibble: 3 × 46 +#> # A tibble: 1 × 46 #> date patient age gender ward mo PEN OXA FLC AMX #> <date> <chr> <dbl> <chr> <chr> <mo> <sir> <sir> <sir> <sir> -#> 1 2002-07-23 F35553 51 M ICU B_STPHY_AURS R NA S R -#> 2 2002-07-15 C42193 84 M ICU B_STPHY_HMNS R NA R R -#> 3 2002-06-05 24D393 20 F Clinical B_ESCHR_COLI R NA NA NA +#> 1 2002-08-19 A49852 70 M Clinical B_ESCHR_COLI R NA NA NA #> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>, #> # CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>, #> # TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>, @@ -322,16 +320,16 @@ #> # Groups: patient, condition [99] #> patient date condition new_episode #> <chr> <date> <chr> <lgl> -#> 1 023456 2012-11-24 A TRUE -#> 2 035268 2011-05-31 A TRUE -#> 3 060287 2007-03-11 B TRUE -#> 4 065133 2011-12-19 C TRUE -#> 5 067927 2002-02-14 C TRUE -#> 6 078381 2014-07-17 C TRUE -#> 7 082622 2014-02-08 C TRUE -#> 8 092034 2016-08-07 B TRUE -#> 9 097186 2015-10-28 C TRUE -#> 10 0C0688 2014-09-05 C TRUE +#> 1 006827 2009-07-24 B TRUE +#> 2 021648 2004-08-21 A TRUE +#> 3 023456 2011-04-25 C TRUE +#> 4 032343 2003-06-09 C TRUE +#> 5 074321 2015-09-20 C TRUE +#> 6 0D7D34 2011-03-19 B TRUE +#> 7 0E2483 2007-08-10 B TRUE +#> 8 164466 2009-10-07 B TRUE +#> 9 16DC39 2015-11-19 C TRUE +#> 10 189564 2009-12-22 C TRUE #> # ℹ 90 more rows if (require("dplyr")) { @@ -348,16 +346,16 @@ #> # Groups: ward, patient [97] #> ward date patient new_index new_logical #> <chr> <date> <chr> <int> <lgl> -#> 1 Clinical 2012-11-24 023456 1 TRUE -#> 2 ICU 2011-05-31 035268 1 TRUE -#> 3 Clinical 2007-03-11 060287 1 TRUE -#> 4 Clinical 2011-12-19 065133 1 TRUE -#> 5 ICU 2002-02-14 067927 1 TRUE -#> 6 ICU 2014-07-17 078381 1 TRUE -#> 7 ICU 2014-02-08 082622 1 TRUE -#> 8 Clinical 2016-08-07 092034 1 TRUE -#> 9 Clinical 2015-10-28 097186 1 TRUE -#> 10 Clinical 2014-09-05 0C0688 1 TRUE +#> 1 Clinical 2009-07-24 006827 1 TRUE +#> 2 Clinical 2004-08-21 021648 1 TRUE +#> 3 Clinical 2011-04-25 023456 1 TRUE +#> 4 Clinical 2003-06-09 032343 1 TRUE +#> 5 ICU 2015-09-20 074321 1 TRUE +#> 6 ICU 2011-03-19 0D7D34 1 TRUE +#> 7 ICU 2007-08-10 0E2483 1 TRUE +#> 8 Clinical 2009-10-07 164466 1 TRUE +#> 9 ICU 2015-11-19 16DC39 1 TRUE +#> 10 ICU 2009-12-22 189564 1 TRUE #> # ℹ 90 more rows if (require("dplyr")) { @@ -373,9 +371,9 @@ #> # A tibble: 3 × 5 #> ward n_patients n_episodes_365 n_episodes_60 n_episodes_30 #> <chr> <int> <int> <int> <int> -#> 1 Clinical 61 13 41 46 -#> 2 ICU 32 10 21 26 -#> 3 Outpatient 4 3 3 4 +#> 1 Clinical 60 13 37 45 +#> 2 ICU 31 12 22 27 +#> 3 Outpatient 6 3 5 5 # grouping on patients and microorganisms leads to the same # results as first_isolate() when using 'episode-based': @@ -405,18 +403,18 @@ } #> # A tibble: 100 × 4 #> # Groups: patient, mo, ward [98] -#> patient mo ward flag_episode -#> <chr> <mo> <chr> <lgl> -#> 1 F35553 B_STPHY_AURS ICU TRUE -#> 2 F37316 B_STRPT_PNMN ICU TRUE -#> 3 375220 B_ENTRC_FCLS Clinical TRUE -#> 4 082622 B_PSDMN_AERG ICU TRUE -#> 5 C42193 B_STPHY_HMNS ICU TRUE -#> 6 D43733 B_ESCHR_COLI ICU TRUE -#> 7 092034 B_ESCHR_COLI Clinical TRUE -#> 8 F58364 B_STPHY_CONS Clinical TRUE -#> 9 438196 B_STPHY_COHN Clinical TRUE -#> 10 534816 B_STPHY_AURS Clinical TRUE +#> patient mo ward flag_episode +#> <chr> <mo> <chr> <lgl> +#> 1 451000 B_ESCHR_COLI Clinical TRUE +#> 2 741413 B_ESCHR_COLI Clinical TRUE +#> 3 8BBC46 B_ENTRC_FACM Clinical TRUE +#> 4 F09078 B_ESCHR_COLI Clinical TRUE +#> 5 C56827 B_ESCHR_COLI Clinical TRUE +#> 6 D27410 B_BCTRD_FRGL Outpatient TRUE +#> 7 D38469 UNKNOWN ICU TRUE +#> 8 023456 B_PROTS_MRBL Clinical TRUE +#> 9 2FC253 B_ESCHR_COLI ICU TRUE +#> 10 EB1709 B_STRPT_PNMN ICU TRUE #> # ℹ 90 more rows # } diff --git a/reference/ggplot_pca.html b/reference/ggplot_pca.html index 8e9aeaad..c0bd455a 100644 --- a/reference/ggplot_pca.html +++ b/reference/ggplot_pca.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -89,28 +89,28 @@ - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R diff --git a/reference/ggplot_sir.html b/reference/ggplot_sir.html index f5c5777a..3797b430 100644 --- a/reference/ggplot_sir.html +++ b/reference/ggplot_sir.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -89,28 +89,28 @@ - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R diff --git a/reference/guess_ab_col.html b/reference/guess_ab_col.html index b4607eff..622c021e 100644 --- a/reference/guess_ab_col.html +++ b/reference/guess_ab_col.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -89,28 +89,28 @@ - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R diff --git a/reference/index.html b/reference/index.html index 77de5e0e..b3cef810 100644 --- a/reference/index.html +++ b/reference/index.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -89,28 +89,28 @@ - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R diff --git a/reference/intrinsic_resistant.html b/reference/intrinsic_resistant.html index 68c8b675..4f7ecf01 100644 --- a/reference/intrinsic_resistant.html +++ b/reference/intrinsic_resistant.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -89,28 +89,28 @@ - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R diff --git a/reference/italicise_taxonomy.html b/reference/italicise_taxonomy.html index 76214003..cb21c220 100644 --- a/reference/italicise_taxonomy.html +++ b/reference/italicise_taxonomy.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -89,28 +89,28 @@ - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R diff --git a/reference/join.html b/reference/join.html index 7b8e0f1e..05dbc34d 100644 --- a/reference/join.html +++ b/reference/join.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -89,28 +89,28 @@ - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R diff --git a/reference/key_antimicrobials.html b/reference/key_antimicrobials.html index 1d540ca1..5d7f7028 100644 --- a/reference/key_antimicrobials.html +++ b/reference/key_antimicrobials.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -89,28 +89,28 @@ - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R diff --git a/reference/kurtosis.html b/reference/kurtosis.html index 6458a1ff..a4a83e71 100644 --- a/reference/kurtosis.html +++ b/reference/kurtosis.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9022 + 2.0.0.9023 @@ -89,28 +89,28 @@ - + With other pkgs - + AMR & dplyr/tidyverse - + AMR & data.table - + AMR & tidymodels - + AMR & base R @@ -199,9 +199,9 @@ Examples kurtosis(rnorm(10000)) -#> [1] 2.899176 +#> [1] 3.010824 kurtosis(rnorm(10000), excess = TRUE) -#> [1] -0.01410279 +#> [1] 0.1430003
head(my_TB_data) #> rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin -#> 1 R R R S S S -#> 2 S R S S R S -#> 3 S R I R I I -#> 4 R I S I S R -#> 5 S I R I I S -#> 6 R R I S S I +#> 1 R S S R R S +#> 2 R R I I S S +#> 3 S R S S I S +#> 4 R R S R R R +#> 5 I I I S R R +#> 6 S I R R S R #> kanamycin -#> 1 I -#> 2 I +#> 1 S +#> 2 S #> 3 I -#> 4 S +#> 4 R #> 5 S #> 6 R
We can now add the interpretation of MDR-TB to our data set. You can @@ -455,40 +455,40 @@ Unique: 5
vignettes/datasets.Rmd
datasets.Rmd
microorganisms
mo_oxygen_tolerance()
mo_is_anaerobic()
kurtosis(rnorm(10000)) -#> [1] 2.899176 +#> [1] 3.010824 kurtosis(rnorm(10000), excess = TRUE) -#> [1] -0.01410279 +#> [1] 0.1430003