From fe09e9252b14409c1b6b46bf812ff6ca83767457 Mon Sep 17 00:00:00 2001 From: Matthijs Berends Date: Tue, 27 Dec 2022 16:03:03 +0100 Subject: [PATCH] custom mo update --- DESCRIPTION | 2 +- NEWS.md | 6 ++++-- _pkgdown.yml | 1 + 3 files changed, 6 insertions(+), 3 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 7fd5548b..ab5fd5cb 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.8.2.9070 +Version: 1.8.2.9071 Date: 2022-12-27 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) diff --git a/NEWS.md b/NEWS.md index 6a354457..ac2b9210 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 1.8.2.9070 +# AMR 1.8.2.9071 *(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)* @@ -12,7 +12,7 @@ This is a new major release of the AMR package, with great new additions but als * 20 new antibiotics added and updated all DDDs and ATC codes * Extended support for antiviral agents (`antivirals` data set), with many new functions * Now available in 16 languages -* Many new interesting functions, such as `rsi_confidence_interval()` and `mean_amr_distance()` +* Many new interesting functions, such as `rsi_confidence_interval()` and `mean_amr_distance()`, and `add_custom_microorganisms()` to add custom microorganisms to this package * Many small bug fixes ## New @@ -35,6 +35,8 @@ The `microorganisms` no longer relies on the Catalogue of Life, but on the List We previously relied on our own experience to categorise species into pathogenic groups, but we were very happy to encounter the very recent work of Bartlett *et al.* (2022, DOI [10.1099/mic.0.001269](https://doi.org/10.1099/mic.0.001269)) who extensively studied medical-scientific literature to categorise all bacterial species into groups. See `mo_matching_score()` on how their work was incorporated into the `prevalence` column of the `microorganisms` data set. Using their results, the `as.mo()` and all `mo_*()` functions are now much better capable of converting user input to valid taxonomic records. +The new function `add_custom_microorganisms()` allows users to add custom microorganisms to the `AMR` package. + We also made the following changes regarding the included taxonomy or microorganisms functions: * Updated full microbiological taxonomy according to the latest daily LPSN data set (December 2022) and latest yearly GBIF taxonomy backbone (November 2022) diff --git a/_pkgdown.yml b/_pkgdown.yml index b48afc00..02a0c02d 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -130,6 +130,7 @@ reference: contents: - "`as.mo`" - "`mo_property`" + - "`add_custom_microorganisms`" - "`mo_source`" - title: "Preparing data: antibiotics"