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https://github.com/msberends/AMR.git
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(v1.7.1.9004) more extensive unit tests
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parent
556bf0014d
commit
c44d9392ca
32
.github/workflows/check.yaml
vendored
32
.github/workflows/check.yaml
vendored
@ -57,25 +57,33 @@ jobs:
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- {os: windows-latest, r: 'devel', allowfail: true}
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- {os: ubuntu-20.04, r: 'devel', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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# these are the current release of R
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- {os: macOS-latest, r: 'release', allowfail: false}
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- {os: windows-latest, r: 'release', allowfail: false}
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- {os: ubuntu-20.04, r: 'release', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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# these are the previous release of R
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- {os: macOS-latest, r: 'oldrel', allowfail: false}
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- {os: windows-latest, r: 'oldrel', allowfail: false}
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- {os: ubuntu-20.04, r: 'oldrel', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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# test against all released versions of R >= 3.0, we support them all!
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# test all systems against all released versions of R >= 3.0, we support them all!
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- {os: macOS-latest, r: '4.1', allowfail: false}
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- {os: windows-latest, r: '4.1', allowfail: false}
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- {os: ubuntu-20.04, r: '4.1', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: macOS-latest, r: '4.0', allowfail: false}
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- {os: windows-latest, r: '4.0', allowfail: false}
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- {os: ubuntu-20.04, r: '4.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: macOS-latest, r: '3.6', allowfail: false}
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- {os: windows-latest, r: '3.6', allowfail: false}
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- {os: ubuntu-20.04, r: '3.6', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: macOS-latest, r: '3.5', allowfail: false}
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- {os: windows-latest, r: '3.5', allowfail: false}
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- {os: ubuntu-20.04, r: '3.5', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: macOS-latest, r: '3.4', allowfail: false}
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- {os: windows-latest, r: '3.4', allowfail: false}
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- {os: ubuntu-20.04, r: '3.4', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: macOS-latest, r: '3.3', allowfail: false}
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- {os: windows-latest, r: '3.3', allowfail: false}
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- {os: ubuntu-20.04, r: '3.3', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: macOS-latest, r: '3.2', allowfail: false}
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- {os: windows-latest, r: '3.2', allowfail: false}
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- {os: ubuntu-20.04, r: '3.2', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: macOS-latest, r: '3.1', allowfail: false}
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- {os: windows-latest, r: '3.1', allowfail: false}
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- {os: ubuntu-20.04, r: '3.1', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: macOS-latest, r: '3.0', allowfail: false}
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- {os: windows-latest, r: '3.0', allowfail: false}
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- {os: ubuntu-20.04, r: '3.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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env:
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@ -163,5 +171,5 @@ jobs:
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if: always()
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uses: actions/upload-artifact@v2
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with:
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name: artifacts-${{ matrix.config.os }}-r${{ matrix.config.r }}
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name: artifacts-r-${{ matrix.config.r }}-${{ matrix.config.os }}
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path: AMR.Rcheck
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@ -1,6 +1,6 @@
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Package: AMR
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Version: 1.7.1.9003
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Date: 2021-06-14
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Version: 1.7.1.9004
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Date: 2021-06-15
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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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4
NEWS.md
4
NEWS.md
@ -1,5 +1,5 @@
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# `AMR` 1.7.1.9003
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## <small>Last updated: 14 June 2021</small>
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# `AMR` 1.7.1.9004
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## <small>Last updated: 15 June 2021</small>
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### Changed
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* Added more antibiotic class selectors: `aminopenicillins()`, `lincosamides()`, `lipoglycopeptides()`, `polymyxins()`, `quinolones()`, `streptogramins()` and `ureidopenicillins()`
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6
R/mo.R
6
R/mo.R
@ -2048,15 +2048,11 @@ parse_and_convert <- function(x) {
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x <- as.data.frame(x, stringsAsFactors = FALSE)[[1]]
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}
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}
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x_class <- class(x)
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x <- as.character(x)
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x[is.null(x)] <- NA
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parsed <- iconv(x, to = "UTF-8")
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parsed <- iconv(as.character(x), to = "UTF-8")
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parsed[is.na(parsed) & !is.na(x)] <- iconv(x[is.na(parsed) & !is.na(x)], from = "Latin1", to = "ASCII//TRANSLIT")
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parsed <- gsub('"', "", parsed, fixed = TRUE)
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parsed <- gsub(" +", " ", parsed, perl = TRUE)
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parsed <- trimws(parsed)
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class(parsed) <- x_class
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parsed
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}, error = function(e) stop(e$message, call. = FALSE)) # this will also be thrown when running `as.mo(no_existing_object)`
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parsed
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Binary file not shown.
@ -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">1.7.1.9003</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9004</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">1.7.1.9003</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9004</span>
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</span>
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</div>
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@ -39,7 +39,7 @@
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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">1.7.1.9003</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9004</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">14 June 2021</h4>
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<h4 class="date">15 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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@ -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">1.7.1.9003</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9004</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">1.7.1.9003</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9004</span>
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</span>
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</div>
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@ -42,7 +42,7 @@
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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">1.7.1.9003</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9004</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">1.7.1.9003</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9004</span>
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</span>
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</div>
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@ -236,12 +236,12 @@
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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-1719003" class="section level1">
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<h1 class="page-header" data-toc-text="1.7.1.9003">
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<a href="#amr-1719003" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9003</h1>
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<div id="last-updated-14-june-2021" class="section level2">
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<div id="amr-1719004" class="section level1">
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<h1 class="page-header" data-toc-text="1.7.1.9004">
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<a href="#amr-1719004" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9004</h1>
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<div id="last-updated-15-june-2021" class="section level2">
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<h2 class="hasAnchor">
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<a href="#last-updated-14-june-2021" class="anchor"></a><small>Last updated: 14 June 2021</small>
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<a href="#last-updated-15-june-2021" class="anchor"></a><small>Last updated: 15 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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@ -12,7 +12,7 @@ articles:
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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: 2021-06-14T20:36Z
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last_built: 2021-06-15T08:50Z
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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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@ -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">1.7.1.9003</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9004</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">1.7.1.9003</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9004</span>
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</span>
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</div>
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