diff --git a/DESCRIPTION b/DESCRIPTION index 8fa764c7..55655ecc 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR -Version: 2.1.1.9050 -Date: 2024-06-15 +Version: 2.1.1.9051 +Date: 2024-06-16 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) data analysis and to work with microbial and antimicrobial properties by diff --git a/NEWS.md b/NEWS.md index d8d8df8e..273a1598 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 2.1.1.9050 +# AMR 2.1.1.9051 *(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support!)* diff --git a/data-raw/microorganisms.codes.dta b/data-raw/microorganisms.codes.dta index 54371fbd..64b11ef3 100644 Binary files a/data-raw/microorganisms.codes.dta and b/data-raw/microorganisms.codes.dta differ diff --git a/data-raw/microorganisms.codes.feather b/data-raw/microorganisms.codes.feather index e4ffa42e..48c0824a 100644 Binary files a/data-raw/microorganisms.codes.feather and b/data-raw/microorganisms.codes.feather differ diff --git a/data-raw/microorganisms.codes.md5 b/data-raw/microorganisms.codes.md5 index 00119804..c78f4120 100644 --- a/data-raw/microorganisms.codes.md5 +++ b/data-raw/microorganisms.codes.md5 @@ -1 +1 @@ -89e85bfa66228cfba526e375dad7ff37 +f3912da07889fcf0f4d1a8b8f0433ea7 diff --git a/data-raw/microorganisms.codes.rds b/data-raw/microorganisms.codes.rds index 118fad50..80d273fd 100644 Binary files a/data-raw/microorganisms.codes.rds and b/data-raw/microorganisms.codes.rds differ diff --git a/data-raw/microorganisms.codes.sav b/data-raw/microorganisms.codes.sav index 1ffdcd21..8eba08d4 100644 Binary files a/data-raw/microorganisms.codes.sav and b/data-raw/microorganisms.codes.sav differ diff --git a/data-raw/microorganisms.codes.txt b/data-raw/microorganisms.codes.txt index 09a141a3..28d9d0c4 100644 --- a/data-raw/microorganisms.codes.txt +++ b/data-raw/microorganisms.codes.txt @@ -4858,7 +4858,6 @@ "VFL" "B_VIBRI_FLVL" "VFU" "B_VIBRI_FRNS" "VGC" "B_VGCCC" -"VGS" "B_VGCCC_SLMN" "VHI" "B_VIBRI_CHLR" "VHO" "B_GRMNT_HLLS" "VI-" "B_VIBRI" diff --git a/data-raw/microorganisms.codes.xlsx b/data-raw/microorganisms.codes.xlsx index c6dca609..fcbdd5fb 100644 Binary files a/data-raw/microorganisms.codes.xlsx and b/data-raw/microorganisms.codes.xlsx differ diff --git a/data/microorganisms.codes.rda b/data/microorganisms.codes.rda index 606514e6..fc5f6e3a 100644 Binary files a/data/microorganisms.codes.rda and b/data/microorganisms.codes.rda differ diff --git a/index.md b/index.md index 2591f234..3b377d1a 100644 --- a/index.md +++ b/index.md @@ -1,7 +1,7 @@ # The `AMR` Package for R -* Provides an **all-in-one solution** for AMR data analysis in a One Health approach -* Used in over 175 countries, translated into 20 languages +* Provides an **all-in-one solution** for antimicrobial resistance (AMR) data analysis in a One Health approach +* Used in over 175 countries, available in 20 languages * Generates **antibiograms** - traditional, combined, syndromic, and even WISCA * Provides the **full microbiological taxonomy** and extensive info on **all antimicrobial drugs** * Applies all recent **CLSI** and **EUCAST** clinical and veterinary breakpoints for MICs and disk zones @@ -26,7 +26,7 @@ This work was published in the Journal of Statistical Software (Volume 104(3); [ After installing this package, R knows [**~52,000 distinct microbial species**](./reference/microorganisms.html) (updated December 2022) and all [**~600 antibiotic, antimycotic and antiviral drugs**](./reference/antibiotics.html) 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). **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 [University of Groningen](https://www.rug.nl), in collaboration with non-profit organisations [Certe Medical Diagnostics and Advice Foundation](https://www.certe.nl) and [University Medical Center Groningen](https://www.umcg.nl). -##### Used in over 175 countries, translated into 20 languages +##### Used in over 175 countries, available in 20 languages diff --git a/man/microorganisms.codes.Rd b/man/microorganisms.codes.Rd index d6a494ce..d0c22212 100644 --- a/man/microorganisms.codes.Rd +++ b/man/microorganisms.codes.Rd @@ -3,9 +3,9 @@ \docType{data} \name{microorganisms.codes} \alias{microorganisms.codes} -\title{Data Set with 4 972 Common Microorganism Codes} +\title{Data Set with 4 971 Common Microorganism Codes} \format{ -A \link[tibble:tibble]{tibble} with 4 972 observations and 2 variables: +A \link[tibble:tibble]{tibble} with 4 971 observations and 2 variables: \itemize{ \item \code{code}\cr Commonly used code of a microorganism. \emph{This is a unique identifier.} \item \code{mo}\cr ID of the microorganism in the \link{microorganisms} data set