diff --git a/DESCRIPTION b/DESCRIPTION index aaa2949f..a108c602 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR -Version: 2.1.1.9046 -Date: 2024-06-12 +Version: 2.1.1.9047 +Date: 2024-06-13 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 5ad38a72..59627cb0 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 2.1.1.9046 +# AMR 2.1.1.9047 *(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 64d660a4..58ebc3e9 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 27831491..87f81463 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 3460220d..349a6a90 100644 --- a/data-raw/microorganisms.codes.md5 +++ b/data-raw/microorganisms.codes.md5 @@ -1 +1 @@ -684dc6117966c478ecc7f5c87e0964d0 +0a874ae6f76e12fabd57b997cb13ebc1 diff --git a/data-raw/microorganisms.codes.parquet b/data-raw/microorganisms.codes.parquet index bb73d142..e69de29b 100644 Binary files a/data-raw/microorganisms.codes.parquet and b/data-raw/microorganisms.codes.parquet differ diff --git a/data-raw/microorganisms.codes.rds b/data-raw/microorganisms.codes.rds index 72375c91..5df62618 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 b94e8ce9..b64e7006 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 655029d0..efb173af 100644 --- a/data-raw/microorganisms.codes.txt +++ b/data-raw/microorganisms.codes.txt @@ -3200,6 +3200,7 @@ "MRPA" "B_PSDMN_AERG" "MRSA" "B_STPHY_AURS" "MRSE" "B_STPHY_EPDR" +"MRSP" "B_STPHY_PSDN" "MSA" "B_MYCPLS_SLVR" "MSB" "B_MRGNL_MRGN_SIBN" "MSC" "B_MYCBC_SCRF" diff --git a/data-raw/microorganisms.codes.xlsx b/data-raw/microorganisms.codes.xlsx index ff49edf4..7953483e 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 30537375..d65fed4b 100644 Binary files a/data/microorganisms.codes.rda and b/data/microorganisms.codes.rda differ diff --git a/index.md b/index.md index c8d46935..2591f234 100644 --- a/index.md +++ b/index.md @@ -5,10 +5,9 @@ * 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 -* Corrects for duplicate isolates using 4 methods, **calculates** and **predicts** AMR per antibiotic class +* Corrects for duplicate isolates, **calculates** and **predicts** AMR per antibiotic class * Integrates with **WHONET**, ATC, **EARS-Net**, PubChem, **LOINC**, **SNOMED CT**, and **NCBI** * 100% free of costs and dependencies, highly suitable for places with **limited resources** -* **Easy to use** and **easy to learn**, with a **community** of contributors from around the globe

https://msberends.github.io/AMR

@@ -245,8 +244,8 @@ It will be downloaded and installed automatically. For RStudio, click on the men #### Latest development version -[![check-recent](https://github.com/msberends/AMR/workflows/check-old/badge.svg?branch=main)](https://codecov.io/gh/msberends/AMR?branch=main) -[![check-recent](https://github.com/msberends/AMR/workflows/check-recent/badge.svg?branch=main)](https://codecov.io/gh/msberends/AMR?branch=main) +[![check-old](https://github.com/msberends/AMR/actions/workflows/check-old.yaml/badge.svg?branch=main)](https://github.com/msberends/AMR/actions/workflows/check-old.yaml?query=branch%3Amain) +[![check-recent](https://github.com/msberends/AMR/actions/workflows/check-recent.yaml/badge.svg?branch=main)](https://github.com/msberends/AMR/actions/workflows/check-recent.yaml?query=branch%3Amain) [![CodeFactor](https://www.codefactor.io/repository/github/msberends/amr/badge)](https://www.codefactor.io/repository/github/msberends/amr) [![Codecov](https://codecov.io/gh/msberends/AMR/branch/main/graph/badge.svg)](https://codecov.io/gh/msberends/AMR?branch=main) diff --git a/inst/tinytest/test-sir.R b/inst/tinytest/test-sir.R index ce681e01..89d3c502 100644 --- a/inst/tinytest/test-sir.R +++ b/inst/tinytest/test-sir.R @@ -133,13 +133,13 @@ expect_identical(out1, as.sir(c("S", "S", "R", "R"))) if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) { out2 <- data.frame(mo = "Escherichia coli", ab = "ertapenem", - some_mics = as.mic(c(0.256, 0.5, 1, 2))) |> - mutate(across(where(is.mic), function(x) as.sir(x, mo = "mo", ab = "ab", guideline = "EUCAST 2023"))) |> + some_mics = as.mic(c(0.256, 0.5, 1, 2))) %>% + mutate(across(where(is.mic), function(x) as.sir(x, mo = "mo", ab = "ab", guideline = "EUCAST 2023"))) %>% pull(some_mics) out3 <- data.frame(mo = "Escherichia coli", ab = "ertapenem", - some_mics = as.mic(c(0.256, 0.5, 1, 2))) |> - mutate_if(is.mic, as.sir, mo = "mo", ab = "ab", guideline = "EUCAST 2023") |> + some_mics = as.mic(c(0.256, 0.5, 1, 2))) %>% + mutate_if(is.mic, as.sir, mo = "mo", ab = "ab", guideline = "EUCAST 2023") %>% pull(some_mics) expect_identical(out1, out2) diff --git a/man/microorganisms.codes.Rd b/man/microorganisms.codes.Rd index 4fda2ed0..b3619e87 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 4 957 Common Microorganism Codes} +\title{Data Set with 4 958 Common Microorganism Codes} \format{ -A \link[tibble:tibble]{tibble} with 4 957 observations and 2 variables: +A \link[tibble:tibble]{tibble} with 4 958 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