From 033ca49817933e4f55fd4df55fedac31f9dd6e21 Mon Sep 17 00:00:00 2001 From: "Matthijs S. Berends" Date: Thu, 25 Jun 2020 19:20:50 +0200 Subject: [PATCH] (v1.2.0.9015) ab_from_text() --- DESCRIPTION | 2 +- NAMESPACE | 1 + NEWS.md | 4 ++-- R/ab_from_text.R | 1 + _pkgdown.yml | 1 + docs/404.html | 2 +- docs/LICENSE-text.html | 2 +- docs/articles/index.html | 2 +- docs/authors.html | 2 +- docs/index.html | 2 +- docs/news/index.html | 11 +++++------ docs/pkgdown.yml | 2 +- docs/reference/index.html | 8 +++++++- 13 files changed, 24 insertions(+), 16 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index c44e49c6..034fab43 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.2.0.9014 +Version: 1.2.0.9015 Date: 2020-06-25 Title: Antimicrobial Resistance Analysis Authors@R: c( diff --git a/NAMESPACE b/NAMESPACE index 2f1ebb79..d189314f 100755 --- a/NAMESPACE +++ b/NAMESPACE @@ -66,6 +66,7 @@ export(ab_atc_group2) export(ab_cid) export(ab_class) export(ab_ddd) +export(ab_from_text) export(ab_group) export(ab_info) export(ab_loinc) diff --git a/NEWS.md b/NEWS.md index ebe195af..778e1a17 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 1.2.0.9014 +# AMR 1.2.0.9015 ## Last updated: 25-Jun-2020 ### New @@ -40,7 +40,7 @@ * Fixed a bug in `bug_drug_combinations()` for when only one antibiotic was in the input data * Changed the summary for class ``, to highlight the %SI vs. %R * Improved error handling, giving more useful info when functions return an error -* Algorithm improvements to `as.ab()` +* Algorithm improvements to `as.ab()`, many more misspellings are now translatable * Added Monuril as trade name for fosfomycin # AMR 1.2.0 diff --git a/R/ab_from_text.R b/R/ab_from_text.R index 2edef087..c5e39598 100644 --- a/R/ab_from_text.R +++ b/R/ab_from_text.R @@ -30,6 +30,7 @@ #' `df %>% mutate(abx = ab_from_text(clinical_text, collapse = "|"))` #' #' This function is also internally used by [as.ab()], although it then only returns the first hit. +#' @export #' @examples #' # mind the bad spelling of amoxicillin in this line, #' # straight from a true health care record: diff --git a/_pkgdown.yml b/_pkgdown.yml index 4d144008..b14fec84 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -94,6 +94,7 @@ reference: contents: - starts_with("as.") - "`eucast_rules`" + - "`ab_from_text`" - "`guess_ab_col`" - "`mo_source`" - title: "Enhancing your data" diff --git a/docs/404.html b/docs/404.html index d99ed4d5..20e4bb6f 100644 --- a/docs/404.html +++ b/docs/404.html @@ -81,7 +81,7 @@ AMR (for R) - 1.2.0.9014 + 1.2.0.9015 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index a3c366c0..7f22924c 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -81,7 +81,7 @@ AMR (for R) - 1.2.0.9014 + 1.2.0.9015 diff --git a/docs/articles/index.html b/docs/articles/index.html index d8d1ea9f..9872d93b 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.2.0.9014 + 1.2.0.9015 diff --git a/docs/authors.html b/docs/authors.html index add975f4..d050bcd0 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -81,7 +81,7 @@ AMR (for R) - 1.2.0.9014 + 1.2.0.9015 diff --git a/docs/index.html b/docs/index.html index 62dd4c9e..81b9a28b 100644 --- a/docs/index.html +++ b/docs/index.html @@ -43,7 +43,7 @@ AMR (for R) - 1.2.0.9014 + 1.2.0.9015 diff --git a/docs/news/index.html b/docs/news/index.html index fe6d6366..b214d5a4 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.2.0.9014 + 1.2.0.9015 @@ -229,9 +229,9 @@ Source: NEWS.md -
-

-AMR 1.2.0.9014 Unreleased +
+

+AMR 1.2.0.9015 Unreleased

@@ -285,8 +285,7 @@
  • Fixed a bug in bug_drug_combinations() for when only one antibiotic was in the input data
  • Changed the summary for class <mo>, to highlight the %SI vs. %R
  • Improved error handling, giving more useful info when functions return an error
    • -
  • Algorithm improvements to as.ab() -
    • +
  • Algorithm improvements to as.ab(), many more misspellings are now translatable
  • Added Monuril as trade name for fosfomycin

    • diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index bce17854..83bd9533 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -10,7 +10,7 @@ articles: WHONET: WHONET.html benchmarks: benchmarks.html resistance_predict: resistance_predict.html -last_built: 2020-06-25T15:34Z +last_built: 2020-06-25T17:20Z urls: reference: https://msberends.gitlab.io/AMR/reference article: https://msberends.gitlab.io/AMR/articles diff --git a/docs/reference/index.html b/docs/reference/index.html index 6f6480ea..3337d7f8 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.2.0.9014 + 1.2.0.9015
    @@ -286,6 +286,12 @@

    Apply EUCAST rules

    + +

    ab_from_text()

    + +

    Retrieve antimicrobial drugs from text

    + +

    guess_ab_col()