mirror of https://github.com/msberends/AMR.git
(v1.7.1.9001) unit tests
This commit is contained in:
parent
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@ -23,6 +23,8 @@
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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# This GitHub Actions file runs without ANY dependency, so works on all versions of R since R-3.0.
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on:
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push:
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branches:
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@ -96,12 +98,18 @@ jobs:
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run: |
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sudo apt install -y libssl-dev pandoc pandoc-citeproc libxml2-dev libicu-dev libcurl4-openssl-dev libpng-dev
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- name: Query dependencies
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# this will change once a week, so it will cache dependency updates
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run: |
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writeLines(paste(format(Sys.Date(), "week %V %Y"), sprintf("R-%i.%i", getRversion()$major, getRversion()$minor)), ".github/week-R-version")
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shell: Rscript {0}
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- name: Restore cached R packages
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# this step will add the step 'Post Restore cached R packages' on a succesful run
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uses: actions/cache@v2
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with:
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path: ${{ env.R_LIBS_USER }}
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key: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-v4
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key: ${{ matrix.config.os }}-${{ hashFiles('.github/week-R-version') }}-v4
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- name: Unpack AMR and install R dependencies
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if: always()
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@ -48,12 +48,18 @@ jobs:
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- uses: r-lib/actions/setup-pandoc@master
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- name: Query dependencies
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# this will change once a week, so it will cache dependency updates
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run: |
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writeLines(paste(format(Sys.Date(), "week %V %Y"), sprintf("R-%i.%i", getRversion()$major, getRversion()$minor)), ".github/week-R-version")
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shell: Rscript {0}
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- name: Restore cached R packages
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# this step will add the step 'Post Restore cached R packages' on a succesful run
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uses: actions/cache@v2
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with:
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path: ${{ env.R_LIBS_USER }}
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key: macOS-latest-r-release-v5-codecovr
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key: ${{ matrix.config.os }}-${{ hashFiles('.github/week-R-version') }}-v4
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- name: Unpack AMR and install R dependencies
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run: |
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@ -73,6 +79,7 @@ jobs:
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CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
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R_RUN_TINYTEST: true
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run: |
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install.packages("covr", repos = "https://cran.rstudio.com/")
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library(AMR)
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library(tinytest)
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x <- covr::codecov(line_exclusions = list("R/atc_online.R", "R/mo_source.R", "R/translate.R", "R/resistance_predict.R", "R/aa_helper_functions.R", "R/aa_helper_pm_functions.R", "R/zzz.R"))
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@ -1,6 +1,6 @@
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Package: AMR
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Version: 1.7.1.9000
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Date: 2021-06-04
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Version: 1.7.1.9001
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Date: 2021-06-05
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Title: Antimicrobial Resistance Data Analysis
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Authors@R: c(
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person(role = c("aut", "cre"),
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6
NEWS.md
6
NEWS.md
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# `AMR` 1.7.1.9000
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## <small>Last updated: 4 June 2021</small>
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# `AMR` 1.7.1.9001
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## <small>Last updated: 5 June 2021</small>
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### Changed
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* Added more antibiotic class selectors, such as `lincosamides()` and `lipoglycopeptides()`
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@ -8,7 +8,6 @@
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# `AMR` 1.7.1
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### Breaking change
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* Support for CLSI 2020 guideline for interpreting MICs and disk diffusion values (using `as.rsi()`)
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* All antibiotic class selectors (such as `carbapenems()`, `aminoglycosides()`) can now be used for filtering as well, making all their accompanying `filter_*()` functions redundant (such as `filter_carbapenems()`, `filter_aminoglycosides()`). These functions are now deprecated and will be removed in a next release. Examples of how the selectors can be used for filtering:
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```r
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# select columns with results for carbapenems
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```
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### New
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* Support for CLSI 2020 guideline for interpreting MICs and disk diffusion values (using `as.rsi()`)
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* Function `custom_eucast_rules()` that brings support for custom AMR rules in `eucast_rules()`
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* Function `italicise_taxonomy()` to make taxonomic names within a string italic, with support for markdown and ANSI
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* Support for all four methods to determine first isolates as summarised by Hindler *et al.* (doi: [10.1086/511864](https://doi.org/10.1086/511864)): isolate-based, patient-based, episode-based and phenotype-based. The last method is now the default.
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2
R/amr.R
2
R/amr.R
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#' Matthijs S. Berends \cr
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#' m.s.berends \[at\] umcg \[dot\] nl \cr
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#' University of Groningen
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#' Department of Medical Microbiology and Infection Prevention
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#' Department of Medical Microbiology and Infection Prevention \cr
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#' University Medical Center Groningen \cr
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#' Post Office Box 30001 \cr
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#' 9700 RB Groningen \cr
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Binary file not shown.
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# some old R instances have trouble installing tinytest, so we ship it too
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install.packages("data-raw/tinytest_1.2.4.10.tar.gz")
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install.packages("data-raw/AMR_latest.tar.gz", dependencies = FALSE)
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install.packages("covr", repos = "https://cran.rstudio.com/")
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pkg_suggests <- gsub("[^a-zA-Z0-9]+", "", unlist(strsplit(packageDescription("AMR", fields = "Suggests"), ", ?")))
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cat("Packages listed in Suggests:", paste(pkg_suggests, collapse = ", "), "\n")
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9000</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9001</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9000</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9001</span>
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</span>
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</div>
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9000</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9001</span>
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</span>
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</div>
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@ -192,7 +192,7 @@
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<div class="page-header toc-ignore">
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<h1 data-toc-skip>Data sets for download / own use</h1>
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<h4 class="date">04 June 2021</h4>
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<h4 class="date">05 June 2021</h4>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/datasets.Rmd"><code>vignettes/datasets.Rmd</code></a></small>
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<div class="hidden name"><code>datasets.Rmd</code></div>
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9000</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9001</span>
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</span>
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</div>
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9000</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9001</span>
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</span>
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</div>
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9000</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9001</span>
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</span>
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</div>
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9000</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9001</span>
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</span>
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</div>
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<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
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</div>
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<div id="amr-1719000" class="section level1">
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<h1 class="page-header" data-toc-text="1.7.1.9000">
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<a href="#amr-1719000" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9000</h1>
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<div id="last-updated-4-june-2021" class="section level2">
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<div id="amr-1719001" class="section level1">
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<h1 class="page-header" data-toc-text="1.7.1.9001">
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<a href="#amr-1719001" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9001</h1>
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<div id="last-updated-5-june-2021" class="section level2">
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<h2 class="hasAnchor">
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<a href="#last-updated-4-june-2021" class="anchor"></a><small>Last updated: 4 June 2021</small>
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<a href="#last-updated-5-june-2021" class="anchor"></a><small>Last updated: 5 June 2021</small>
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</h2>
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<div id="changed" class="section level3">
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<h3 class="hasAnchor">
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<h3 class="hasAnchor">
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<a href="#breaking-change" class="anchor"></a>Breaking change</h3>
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<ul>
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<li><p>Support for CLSI 2020 guideline for interpreting MICs and disk diffusion values (using <code><a href="../reference/as.rsi.html">as.rsi()</a></code>)</p></li>
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<li>
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<p>All antibiotic class selectors (such as <code><a href="../reference/antibiotic_class_selectors.html">carbapenems()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">aminoglycosides()</a></code>) can now be used for filtering as well, making all their accompanying <code>filter_*()</code> functions redundant (such as <code><a href="../reference/AMR-deprecated.html">filter_carbapenems()</a></code>, <code><a href="../reference/AMR-deprecated.html">filter_aminoglycosides()</a></code>). These functions are now deprecated and will be removed in a next release. Examples of how the selectors can be used for filtering:</p>
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<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
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<h3 class="hasAnchor">
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<a href="#new" class="anchor"></a>New</h3>
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<ul>
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<li>Support for CLSI 2020 guideline for interpreting MICs and disk diffusion values (using <code><a href="../reference/as.rsi.html">as.rsi()</a></code>)</li>
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<li>Function <code><a href="../reference/custom_eucast_rules.html">custom_eucast_rules()</a></code> that brings support for custom AMR rules in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>
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</li>
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<li>Function <code><a href="../reference/italicise_taxonomy.html">italicise_taxonomy()</a></code> to make taxonomic names within a string italic, with support for markdown and ANSI</li>
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datasets: datasets.html
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resistance_predict: resistance_predict.html
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welcome_to_AMR: welcome_to_AMR.html
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last_built: 2021-06-04T19:07Z
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last_built: 2021-06-05T13:10Z
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urls:
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reference: https://msberends.github.io/AMR//reference
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article: https://msberends.github.io/AMR//articles
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9001</span>
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</span>
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</div>
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<p>Matthijs S. Berends <br />
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m.s.berends [at] umcg [dot] nl <br />
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University of Groningen
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Department of Medical Microbiology and Infection Prevention
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Department of Medical Microbiology and Infection Prevention <br />
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University Medical Center Groningen <br />
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Post Office Box 30001 <br />
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9700 RB Groningen <br />
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9000</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9001</span>
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</span>
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</div>
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9000</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9001</span>
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</span>
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</div>
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9000</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9001</span>
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</span>
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</div>
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9000</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9001</span>
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</span>
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</div>
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@ -50,7 +50,7 @@ For suggestions, comments or questions, please contact us at:
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Matthijs S. Berends \cr
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m.s.berends [at] umcg [dot] nl \cr
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University of Groningen
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Department of Medical Microbiology and Infection Prevention
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Department of Medical Microbiology and Infection Prevention \cr
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University Medical Center Groningen \cr
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Post Office Box 30001 \cr
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9700 RB Groningen \cr
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