From 9cf054903b10343a4fa5104d1478f4eb80437074 Mon Sep 17 00:00:00 2001 From: Matthijs Berends Date: Wed, 12 Jul 2023 11:42:29 +0100 Subject: [PATCH] version bump --- DESCRIPTION | 2 +- NEWS.md | 2 +- man/AMR.Rd | 2 +- man/microorganisms.groups.Rd | 4 ++-- 4 files changed, 5 insertions(+), 5 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 3a953fda..c50e1e73 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 2.0.0.9035 +Version: 2.0.0.9037 Date: 2023-07-11 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) diff --git a/NEWS.md b/NEWS.md index aa994c98..b99896f7 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 2.0.0.9035 +# AMR 2.0.0.9037 ## New * Clinical breakpoints and intrinsic resistance of EUCAST 2023 and CLSI 2023 have been added for `as.sir()`. EUCAST 2023 (v13.0) is now the new default guideline for all MIC and disks diffusion interpretations diff --git a/man/AMR.Rd b/man/AMR.Rd index 0f4b2845..48d89359 100644 --- a/man/AMR.Rd +++ b/man/AMR.Rd @@ -32,7 +32,7 @@ The \code{AMR} package is a \href{https://msberends.github.io/AMR/#copyright}{fr This work was published in the Journal of Statistical Software (Volume 104(3); \doi{jss.v104.i03}) and formed the basis of two PhD theses (\doi{10.33612/diss.177417131} and \doi{10.33612/diss.192486375}). -After installing this package, R knows \href{https://msberends.github.io/AMR/reference/microorganisms.html}{\strong{~52 000 microorganisms}} (updated December 2022) and all \href{https://msberends.github.io/AMR/reference/antibiotics.html}{\strong{~600 antibiotic, antimycotic and antiviral drugs}} by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). \strong{It was designed to work in any setting, including those with very limited resources}. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the \href{https://www.rug.nl}{University of Groningen}, in collaboration with non-profit organisations \href{https://www.certe.nl}{Certe Medical Diagnostics and Advice Foundation} and \href{https://www.umcg.nl}{University Medical Center Groningen}. +After installing this package, R knows \href{https://msberends.github.io/AMR/reference/microorganisms.html}{\strong{~52 000 microorganisms}} (updated december 2022) and all \href{https://msberends.github.io/AMR/reference/antibiotics.html}{\strong{~600 antibiotic, antimycotic and antiviral drugs}} by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). \strong{It was designed to work in any setting, including those with very limited resources}. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the \href{https://www.rug.nl}{University of Groningen}, in collaboration with non-profit organisations \href{https://www.certe.nl}{Certe Medical Diagnostics and Advice Foundation} and \href{https://www.umcg.nl}{University Medical Center Groningen}. The \code{AMR} package is available in English, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish, Turkish, and Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages. } diff --git a/man/microorganisms.groups.Rd b/man/microorganisms.groups.Rd index 7d26ec91..2eea863e 100644 --- a/man/microorganisms.groups.Rd +++ b/man/microorganisms.groups.Rd @@ -3,9 +3,9 @@ \docType{data} \name{microorganisms.groups} \alias{microorganisms.groups} -\title{Data Set with 444 Microorganisms In Species Groups} +\title{Data Set with 448 Microorganisms In Species Groups} \format{ -A \link[tibble:tibble]{tibble} with 444 observations and 4 variables: +A \link[tibble:tibble]{tibble} with 448 observations and 4 variables: \itemize{ \item \code{mo_group}\cr ID of the species group / microbiological complex \item \code{mo}\cr ID of the microorganism belonging in the species group / microbiological complex