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(v0.7.1.9022) CI fix for codecov
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parent
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@ -118,7 +118,7 @@ coverage:
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# install missing and outdated packages
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# install missing and outdated packages
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- Rscript -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = FALSE)'
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- Rscript -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = FALSE)'
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# codecov token is set in https://gitlab.com/msberends/AMR/settings/ci_cd
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# codecov token is set in https://gitlab.com/msberends/AMR/settings/ci_cd
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- Rscript -e "cc <- covr::package_coverage()); covr::codecov(coverage = cc, token = '$codecov'); cat('Code coverage:', covr::percent_coverage(cc))"
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- Rscript -e "cc <- covr::package_coverage(line_exclusions = list('R/atc_online.R', 'R/mo_source.R')); covr::codecov(coverage = cc, token = '$codecov'); cat('Code coverage:', covr::percent_coverage(cc))"
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coverage: '/Code coverage: \d+\.\d+/'
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coverage: '/Code coverage: \d+\.\d+/'
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pages:
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pages:
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@ -1,5 +1,5 @@
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Package: AMR
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Package: AMR
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Version: 0.7.1.9021
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Version: 0.7.1.9022
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Date: 2019-08-04
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Date: 2019-08-04
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Title: Antimicrobial Resistance Analysis
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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Authors@R: c(
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2
NEWS.md
2
NEWS.md
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# AMR 0.7.1.9021
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# AMR 0.7.1.9022
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### Breaking
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### Breaking
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* Function `freq()` has moved to a new package, [`clean`](https://github.com/msberends/clean) ([CRAN link](https://cran.r-project.org/package=clean)). Creating frequency tables is actually not the scope of this package (never was) and this function has matured a lot over the last two years. We decided to create a new package for data cleaning and checking and it perfectly fits the `freq()` function. The [`clean`](https://github.com/msberends/clean) package is available on CRAN and will be installed automatically when updating the `AMR` package, that now imports it. In a later stage, the `skewness()` and `kurtosis()` functions will be moved to the `clean` package too.
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* Function `freq()` has moved to a new package, [`clean`](https://github.com/msberends/clean) ([CRAN link](https://cran.r-project.org/package=clean)). Creating frequency tables is actually not the scope of this package (never was) and this function has matured a lot over the last two years. We decided to create a new package for data cleaning and checking and it perfectly fits the `freq()` function. The [`clean`](https://github.com/msberends/clean) package is available on CRAN and will be installed automatically when updating the `AMR` package, that now imports it. In a later stage, the `skewness()` and `kurtosis()` functions will be moved to the `clean` package too.
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@ -78,7 +78,7 @@
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</button>
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</button>
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<span class="navbar-brand">
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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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<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">0.7.1.9021</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9022</span>
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</span>
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</span>
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</div>
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</div>
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@ -78,7 +78,7 @@
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</button>
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</button>
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<span class="navbar-brand">
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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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<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">0.7.1.9021</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9022</span>
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</span>
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</span>
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</div>
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</div>
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@ -78,7 +78,7 @@
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</button>
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</button>
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<span class="navbar-brand">
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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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<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">0.7.1.9021</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9022</span>
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</span>
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</span>
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</div>
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</div>
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@ -42,7 +42,7 @@
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</button>
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</button>
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<span class="navbar-brand">
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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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<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">0.7.1.9021</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9022</span>
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</span>
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</span>
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</div>
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</div>
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</button>
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</button>
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<span class="navbar-brand">
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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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<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">0.7.1.9021</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9022</span>
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</span>
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</span>
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</div>
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</div>
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@ -225,9 +225,9 @@
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</div>
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</div>
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<div id="amr-0-7-1-9021" class="section level1">
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<div id="amr-0-7-1-9022" class="section level1">
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<h1 class="page-header">
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<h1 class="page-header">
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<a href="#amr-0-7-1-9021" class="anchor"></a>AMR 0.7.1.9021<small> Unreleased </small>
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<a href="#amr-0-7-1-9022" class="anchor"></a>AMR 0.7.1.9022<small> Unreleased </small>
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</h1>
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</h1>
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<div id="breaking" class="section level3">
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<div id="breaking" class="section level3">
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<h3 class="hasAnchor">
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<h3 class="hasAnchor">
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@ -1198,7 +1198,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
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<div id="tocnav">
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<div id="tocnav">
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<h2>Contents</h2>
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<h2>Contents</h2>
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<ul class="nav nav-pills nav-stacked">
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<ul class="nav nav-pills nav-stacked">
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<li><a href="#amr-0-7-1-9021">0.7.1.9021</a></li>
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<li><a href="#amr-0-7-1-9022">0.7.1.9022</a></li>
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<li><a href="#amr-0-7-1">0.7.1</a></li>
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<li><a href="#amr-0-7-1">0.7.1</a></li>
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<li><a href="#amr-0-7-0">0.7.0</a></li>
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<li><a href="#amr-0-7-0">0.7.0</a></li>
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<li><a href="#amr-0-6-1">0.6.1</a></li>
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<li><a href="#amr-0-6-1">0.6.1</a></li>
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@ -78,7 +78,7 @@
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</button>
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</button>
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<span class="navbar-brand">
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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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<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">0.7.1.9021</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9022</span>
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</span>
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</span>
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</div>
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</div>
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