(v2.1.1.9047) unit test and index

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 2.1.1.9046
+Version: 2.1.1.9047
-Date: 2024-06-12
+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

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!)*
 

data-raw/microorganisms.codes.md5

@@ -1 +1 @@
-684dc6117966c478ecc7f5c87e0964d0
+0a874ae6f76e12fabd57b997cb13ebc1

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"

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
 
 <div style="display: flex; font-size: 0.8em;">
 <p style="text-align:left; width: 50%;"><small><a href="https://msberends.github.io/AMR/">https://msberends.github.io/AMR</a></small></p>
@@ -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-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/workflows/check-recent/badge.svg?branch=main)](https://codecov.io/gh/msberends/AMR?branch=main)
+[![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)
 

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))) |> 
+                     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"))) |> 
+    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))) |> 
+                     some_mics = as.mic(c(0.256, 0.5, 1, 2))) %>% 
-    mutate_if(is.mic, as.sir, mo = "mo", ab = "ab", guideline = "EUCAST 2023") |> 
+    mutate_if(is.mic, as.sir, mo = "mo", ab = "ab", guideline = "EUCAST 2023") %>% 
     pull(some_mics)
   
   expect_identical(out1, out2)

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