diff --git a/DESCRIPTION b/DESCRIPTION index af820370..ece811c4 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR -Version: 1.6.0.9018 -Date: 2021-05-04 +Version: 1.6.0.9019 +Date: 2021-05-05 Title: Antimicrobial Resistance Data Analysis Authors@R: c( person(role = c("aut", "cre"), diff --git a/NEWS.md b/NEWS.md index 4c3780d4..dd762700 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,10 +1,10 @@ -# `AMR` 1.6.0.9018 -## Last updated: 4 May 2021 +# `AMR` 1.6.0.9019 +## Last updated: 5 May 2021 ### New * Function `custom_eucast_rules()` that brings support for custom AMR rules in `eucast_rules()` * Function `italicise_taxonomy()` to make taxonomic names within a string italic, with support for markdown and ANSI -* Support for all four methods to determine first isolates as summarised by Hindler *et al* (doi: [10.1086/511864](https://doi.org/10.1086/511864)): isolate-based, patient-based, episode-based and phenotype-based. The last method is now the default. +* Support for all four methods to determine first isolates as summarised by Hindler *et al.* (doi: [10.1086/511864](https://doi.org/10.1086/511864)): isolate-based, patient-based, episode-based and phenotype-based. The last method is now the default. * The `first_isolate()` function gained the argument `method` that has to be "phenotype-based", "episode-based", "patient-based", or "isolate-based". The old behaviour is equal to "episode-based". The new default is "phenotype-based" if antimicrobial test results are available, and "episode-based" otherwise. This new default will yield slightly more isolates for selection (which is a good thing). * Since fungal isolates can also be selected, the functions `key_antibiotics()` and `key_antibiotics_equal()` are now deprecated in favour of the `key_antimicrobials()` and `antimicrobial_equal()` functions. Also, the new `all_antimicrobials()` function works like the old `key_antibiotics()` function, but includes any column with antimicrobial test results. Using `key_antimicrobials()` still only selects six preferred antibiotics for Gram-negatives, six for Gram-positives, and six universal antibiotics. It has a new `antifungal` argument to set antifungal agents (antimycotics). * Using `type == "points"` in the `first_isolate()` function for phenotype-based selection will now consider all antimicrobial drugs in the data set, using the new `all_antimicrobials()` diff --git a/data-raw/AMR_latest.tar.gz b/data-raw/AMR_latest.tar.gz index 1d4b876f..b0ffd41f 100644 Binary files a/data-raw/AMR_latest.tar.gz and b/data-raw/AMR_latest.tar.gz differ diff --git a/docs/404.html b/docs/404.html index 63be1bb7..0807eae5 100644 --- a/docs/404.html +++ b/docs/404.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9018 + 1.6.0.9019 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index ea71ff3d..9572fcb7 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9018 + 1.6.0.9019 diff --git a/docs/articles/index.html b/docs/articles/index.html index 8c3f48fe..ae06b7e0 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9018 + 1.6.0.9019 diff --git a/docs/authors.html b/docs/authors.html index a8f1d456..fee2bd6f 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9018 + 1.6.0.9019 diff --git a/docs/extra.js b/docs/extra.js index 9f781c721..4b877036 100644 --- a/docs/extra.js +++ b/docs/extra.js @@ -54,7 +54,9 @@ $(document).ready(function() { } // remove leading newline in code examples on changelog - $("body .template-news").html($("body .template-news").html().replaceAll('sourceCode R">\n 0) { + $("body .template-news").html($("body .template-news").html().replaceAll('sourceCode R">\n 0) { diff --git a/docs/index.html b/docs/index.html index 81900c84..c14d81cc 100644 --- a/docs/index.html +++ b/docs/index.html @@ -42,7 +42,7 @@ AMR (for R) - 1.6.0.9018 + 1.6.0.9019 diff --git a/docs/news/index.html b/docs/news/index.html index fb159a3c..2fd81cce 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9018 + 1.6.0.9019 @@ -236,12 +236,12 @@ Source: NEWS.md -
-

- Unreleased AMR 1.6.0.9018

-
+
+

+ Unreleased AMR 1.6.0.9019

+

-Last updated: 4 May 2021 +Last updated: 5 May 2021

@@ -250,7 +250,7 @@
  • Function custom_eucast_rules() that brings support for custom AMR rules in eucast_rules()
  • Function italicise_taxonomy() to make taxonomic names within a string italic, with support for markdown and ANSI
    • -
  • Support for all four methods to determine first isolates as summarised by Hindler et al (doi: 10.1086/511864): isolate-based, patient-based, episode-based and phenotype-based. The last method is now the default. +
  • Support for all four methods to determine first isolates as summarised by Hindler et al. (doi: 10.1086/511864): isolate-based, patient-based, episode-based and phenotype-based. The last method is now the default.
    • The first_isolate() function gained the argument method that has to be “phenotype-based”, “episode-based”, “patient-based”, or “isolate-based”. The old behaviour is equal to “episode-based”. The new default is “phenotype-based” if antimicrobial test results are available, and “episode-based” otherwise. This new default will yield slightly more isolates for selection (which is a good thing).
    • Since fungal isolates can also be selected, the functions key_antibiotics() and key_antibiotics_equal() are now deprecated in favour of the key_antimicrobials() and antimicrobial_equal() functions. Also, the new all_antimicrobials() function works like the old key_antibiotics() function, but includes any column with antimicrobial test results. Using key_antimicrobials() still only selects six preferred antibiotics for Gram-negatives, six for Gram-positives, and six universal antibiotics. It has a new antifungal argument to set antifungal agents (antimycotics).
      • diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 12f9ba3b..e235dcfc 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -12,7 +12,7 @@ articles: datasets: datasets.html resistance_predict: resistance_predict.html welcome_to_AMR: welcome_to_AMR.html -last_built: 2021-05-04T13:19Z +last_built: 2021-05-05T13:26Z urls: reference: https://msberends.github.io/AMR//reference article: https://msberends.github.io/AMR//articles diff --git a/docs/reference/index.html b/docs/reference/index.html index 87c26f5f..a8bb8471 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9018 + 1.6.0.9019

    • diff --git a/docs/reference/microorganisms.codes.html b/docs/reference/microorganisms.codes.html index 51131eb5..2693b7e0 100644 --- a/docs/reference/microorganisms.codes.html +++ b/docs/reference/microorganisms.codes.html @@ -82,7 +82,7 @@ AMR (for R) - 1.6.0.9017 + 1.6.0.9019
    diff --git a/docs/survey.html b/docs/survey.html index 91358f34..e7acba4c 100644 --- a/docs/survey.html +++ b/docs/survey.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9018 + 1.6.0.9019
    diff --git a/pkgdown/extra.js b/pkgdown/extra.js index 9f781c721..4b877036 100644 --- a/pkgdown/extra.js +++ b/pkgdown/extra.js @@ -54,7 +54,9 @@ $(document).ready(function() { } // remove leading newline in code examples on changelog - $("body .template-news").html($("body .template-news").html().replaceAll('sourceCode R">\n 0) { + $("body .template-news").html($("body .template-news").html().replaceAll('sourceCode R">\n 0) {