diff --git a/404.html b/404.html index a79b4721..dd008d13 100644 --- a/404.html +++ b/404.html @@ -16,8 +16,8 @@ - - + + diff --git a/LICENSE-text.html b/LICENSE-text.html index 705bfe52..5b5ce819 100644 --- a/LICENSE-text.html +++ b/LICENSE-text.html @@ -1,5 +1,5 @@ -License • AMR (for R) +License • AMR (for R) Skip to contents diff --git a/articles/AMR.html b/articles/AMR.html index 8e2a14c9..0107679b 100644 --- a/articles/AMR.html +++ b/articles/AMR.html @@ -16,8 +16,8 @@ - - + + @@ -87,7 +87,7 @@ 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 18 October 2024.

+generated on 21 November 2024.

Introduction

@@ -143,21 +143,21 @@ make the structure of your data generally look like this:

-2024-10-18 +2024-11-21 abcd Escherichia coli S S -2024-10-18 +2024-11-21 abcd Escherichia coli S R -2024-10-18 +2024-11-21 efgh Escherichia coli R diff --git a/articles/AMR_for_Python.html b/articles/AMR_for_Python.html index af4c0017..dc79c53e 100644 --- a/articles/AMR_for_Python.html +++ b/articles/AMR_for_Python.html @@ -16,8 +16,8 @@ - - + + diff --git a/articles/EUCAST.html b/articles/EUCAST.html index ede710b8..ada87e45 100644 --- a/articles/EUCAST.html +++ b/articles/EUCAST.html @@ -16,8 +16,8 @@ - - + + diff --git a/articles/MDR.html b/articles/MDR.html index b6a504f7..c6f9cc58 100644 --- a/articles/MDR.html +++ b/articles/MDR.html @@ -16,8 +16,8 @@ - - + + diff --git a/articles/PCA.html b/articles/PCA.html index 9dd33775..0d32158e 100644 --- a/articles/PCA.html +++ b/articles/PCA.html @@ -16,8 +16,8 @@ - - + + diff --git a/articles/WHONET.html b/articles/WHONET.html index e99073f6..2165add2 100644 --- a/articles/WHONET.html +++ b/articles/WHONET.html @@ -16,8 +16,8 @@ - - + + diff --git a/articles/datasets.html b/articles/datasets.html index 945b6457..889072df 100644 --- a/articles/datasets.html +++ b/articles/datasets.html @@ -16,8 +16,8 @@ - - + + @@ -76,7 +76,7 @@

This base R code will work in any version of R since April 2013 (R-3.0). Moreover, this code works identically with the data.table package, only by starting with:

-example_isolates <- data.table::as.data.table(example_isolates)
+example_isolates <- data.table::as.data.table(example_isolates)

Generating antibiograms @@ -679,7 +679,7 @@

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 99718b78..f12611af 100644 --- a/news/index.html +++ b/news/index.html @@ -1,5 +1,5 @@ -Changelog • AMR (for R) +Changelog • AMR (for R) Skip to contents diff --git a/pkgdown.yml b/pkgdown.yml index 1fa65204..38c05539 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -11,7 +11,7 @@ articles: resistance_predict: resistance_predict.html welcome_to_AMR: welcome_to_AMR.html WHONET: WHONET.html -last_built: 2024-10-18T09:04Z +last_built: 2024-11-21T09:13Z urls: reference: https://msberends.github.io/AMR/reference article: https://msberends.github.io/AMR/articles diff --git a/reference/AMR-options.html b/reference/AMR-options.html index 61f7e558..35886622 100644 --- a/reference/AMR-options.html +++ b/reference/AMR-options.html @@ -1,5 +1,5 @@ -Options for the AMR package — AMR-options • AMR (for R) +Options for the AMR package — AMR-options • AMR (for R) Skip to contents diff --git a/reference/AMR.html b/reference/AMR.html index e5667396..f80ddf60 100644 --- a/reference/AMR.html +++ b/reference/AMR.html @@ -1,5 +1,5 @@ -The AMR Package — AMR • AMR (for R)The AMR Package — AMR • AMR (for R)WHOCC: WHO Collaborating Centre for Drug Statistics Methodology — WHOCC • AMR (for R) +WHOCC: WHO Collaborating Centre for Drug Statistics Methodology — WHOCC • AMR (for R) Skip to contents diff --git a/reference/WHONET.html b/reference/WHONET.html index 77560033..5953b684 100644 --- a/reference/WHONET.html +++ b/reference/WHONET.html @@ -1,5 +1,5 @@ -Data Set with 500 Isolates - WHONET Example — WHONET • AMR (for R) +Data Set with 500 Isolates - WHONET Example — WHONET • AMR (for R) Skip to contents diff --git a/reference/ab_from_text.html b/reference/ab_from_text.html index eef5bfe2..d6d0d6e3 100644 --- a/reference/ab_from_text.html +++ b/reference/ab_from_text.html @@ -1,5 +1,5 @@ -Retrieve Antimicrobial Drug Names and Doses from Clinical Text — ab_from_text • AMR (for R) +Retrieve Antimicrobial Drug Names and Doses from Clinical Text — ab_from_text • AMR (for R) Skip to contents diff --git a/reference/ab_property.html b/reference/ab_property.html index e9073b1c..e484be6a 100644 --- a/reference/ab_property.html +++ b/reference/ab_property.html @@ -1,5 +1,5 @@ -Get Properties of an Antibiotic — ab_property • AMR (for R) +Get Properties of an Antibiotic — ab_property • AMR (for R) Skip to contents diff --git a/reference/add_custom_antimicrobials.html b/reference/add_custom_antimicrobials.html index 667994e1..c154af08 100644 --- a/reference/add_custom_antimicrobials.html +++ b/reference/add_custom_antimicrobials.html @@ -1,5 +1,5 @@ -Add Custom Antimicrobials — add_custom_antimicrobials • AMR (for R) +Add Custom Antimicrobials — add_custom_antimicrobials • AMR (for R) Skip to contents diff --git a/reference/add_custom_microorganisms.html b/reference/add_custom_microorganisms.html index 2c6f7b0e..083acfd2 100644 --- a/reference/add_custom_microorganisms.html +++ b/reference/add_custom_microorganisms.html @@ -1,5 +1,5 @@ -Add Custom Microorganisms — add_custom_microorganisms • AMR (for R) +Add Custom Microorganisms — add_custom_microorganisms • AMR (for R) Skip to contents diff --git a/reference/age.html b/reference/age.html index cc41a30b..cdc293ba 100644 --- a/reference/age.html +++ b/reference/age.html @@ -1,5 +1,5 @@ -Age in Years of Individuals — age • AMR (for R) +Age in Years of Individuals — age • AMR (for R) Skip to contents @@ -110,16 +110,16 @@ df #> birth_date age age_exact age_at_y2k -#> 1 1965-12-05 58 58.86885 34 -#> 2 1980-03-01 44 44.63115 19 -#> 3 1949-11-01 74 74.96175 50 -#> 4 1947-02-14 77 77.67486 52 -#> 5 1940-02-19 84 84.66120 59 -#> 6 1988-01-10 36 36.77049 11 -#> 7 1997-08-27 27 27.14208 2 -#> 8 1978-01-26 46 46.72678 21 -#> 9 1972-06-17 52 52.33607 27 -#> 10 1986-08-10 38 38.18852 13 +#> 1 1965-12-05 58 58.96175 34 +#> 2 1980-03-01 44 44.72404 19 +#> 3 1949-11-01 75 75.05464 50 +#> 4 1947-02-14 77 77.76776 52 +#> 5 1940-02-19 84 84.75410 59 +#> 6 1988-01-10 36 36.86339 11 +#> 7 1997-08-27 27 27.23497 2 +#> 8 1978-01-26 46 46.81967 21 +#> 9 1972-06-17 52 52.42896 27 +#> 10 1986-08-10 38 38.28142 13