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(v2.1.1.9046) unit test fix
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Package: AMR
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Package: AMR
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Version: 2.1.1.9045
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Version: 2.1.1.9046
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Date: 2024-06-12
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Date: 2024-06-12
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Title: Antimicrobial Resistance Data Analysis
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Title: Antimicrobial Resistance Data Analysis
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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2
NEWS.md
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NEWS.md
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# AMR 2.1.1.9045
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# AMR 2.1.1.9046
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*(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!)*
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*(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!)*
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8
index.md
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index.md
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# The `AMR` Package for R <a href="https://msberends.github.io/AMR/"><img src="./logo.svg" align="right" height="139" /></a>
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# The `AMR` Package for R <a href="https://msberends.github.io/AMR/"><img src="./logo.svg" align="right" height="139" /></a>
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* Provides an **all-in-one solution** for AMR data analysis in a One Health approach
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* Provides an **all-in-one solution** for AMR data analysis in a One Health approach
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* Used in over 175 countries, translated into 20 languages
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* Generates **antibiograms** - traditional, combined, syndromic, and even WISCA
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* Generates **antibiograms** - traditional, combined, syndromic, and even WISCA
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* Provides the **full microbiological taxonomy** and extensive info on **all antimicrobial drugs**
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* Provides the **full microbiological taxonomy** and extensive info on **all antimicrobial drugs**
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* Applies all recent **CLSI and EUCAST clinical and veterinary breakpoints** for MICs and disk zones
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* Applies all recent **CLSI** and **EUCAST** clinical and veterinary breakpoints for MICs and disk zones
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* Corrects for duplicate isolates, **calculates and predicts AMR** per antibiotic class
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* Corrects for duplicate isolates using 4 methods, **calculates** and **predicts** AMR per antibiotic class
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* Integrates with **WHONET**, ATC, **EARS-Net**, PubChem, **LOINC**, **SNOMED CT**, and **NCBI**
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* Integrates with **WHONET**, ATC, **EARS-Net**, PubChem, **LOINC**, **SNOMED CT**, and **NCBI**
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* Works on Windows, macOS and Linux with **all versions of R** since R-3.0 and is completely **dependency-free**, highly suitable for places with **limited resources**
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* 100% free of costs and dependencies, highly suitable for places with **limited resources**
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* **Easy to use** and **easy to learn**, with a **community** of contributors from around the globe
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<div style="display: flex; font-size: 0.8em;">
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<div style="display: flex; font-size: 0.8em;">
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<p style="text-align:left; width: 50%;"><small><a href="https://msberends.github.io/AMR/">https://msberends.github.io/AMR</a></small></p>
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<p style="text-align:left; width: 50%;"><small><a href="https://msberends.github.io/AMR/">https://msberends.github.io/AMR</a></small></p>
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@ -95,10 +95,8 @@ if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
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example_isolates %>% select(AMX) %>% count_df(combine_SI = FALSE) %>% pull(value),
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example_isolates %>% select(AMX) %>% count_df(combine_SI = FALSE) %>% pull(value),
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c(
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c(
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suppressWarnings(example_isolates$AMX %>% count_S()),
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suppressWarnings(example_isolates$AMX %>% count_S()),
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0,
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example_isolates$AMX %>% count_I(),
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example_isolates$AMX %>% count_I(),
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example_isolates$AMX %>% count_R(),
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example_isolates$AMX %>% count_R()
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0
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)
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)
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)
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)
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