mirror of
https://github.com/msberends/AMR.git
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(v1.1.0.9003) CI fix
This commit is contained in:
parent
77d8f97e0c
commit
9fce546901
@ -64,10 +64,9 @@ R-release-test-only:
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- Rscript -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE, install_lintr = TRUE)'
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- Rscript -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE, install_lintr = TRUE)'
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- Rscript -e 'devtools::test(stop_on_failure = FALSE)'
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- Rscript -e 'devtools::test(stop_on_failure = FALSE)'
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cache:
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cache:
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key: release_4_0
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key: release
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paths:
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paths:
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- installed_deps/
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- installed_deps/
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policy: pull # no uploading after run
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R-release:
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R-release:
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stage: check
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stage: check
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@ -91,7 +90,7 @@ R-release:
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- '*.Rcheck/*'
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- '*.Rcheck/*'
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expire_in: '1 month'
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expire_in: '1 month'
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cache:
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cache:
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key: release_4_0
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key: release
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paths:
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paths:
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- installed_deps/
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- installed_deps/
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@ -118,7 +117,7 @@ R-devel:
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- '*.Rcheck/*'
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- '*.Rcheck/*'
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expire_in: '1 month'
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expire_in: '1 month'
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cache:
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cache:
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key: devel_4_1
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key: devel
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paths:
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paths:
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- installed_deps/
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- installed_deps/
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@ -126,17 +125,17 @@ lintr:
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stage: lint
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stage: lint
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allow_failure: true
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allow_failure: true
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when: always
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when: always
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cache:
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key: release_4_0
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paths:
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- installed_deps/
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policy: pull # no uploading after run
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only:
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only:
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- premaster
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- premaster
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- master
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- master
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script:
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script:
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# check all syntax with lintr
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# check all syntax with lintr
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- Rscript -e 'lintr::lint_package()'
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- Rscript -e 'lintr::lint_package()'
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cache:
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key: release
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paths:
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- installed_deps/
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policy: pull # no uploading after run
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pages:
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pages:
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stage: website
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stage: website
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@ -154,11 +153,6 @@ codecovr:
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stage: coverage
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stage: coverage
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allow_failure: true
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allow_failure: true
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when: always
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when: always
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cache:
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key: release_4_0
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paths:
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- installed_deps/
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policy: pull # no uploading after run
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only:
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only:
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- premaster
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- premaster
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- master
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- master
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@ -168,3 +162,8 @@ codecovr:
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# Sys.setenv(NOT_CRAN = 'true'), because otherwise skip_on_cran() will be applied on Covr too, resulting in extremely low coverage percentages
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# Sys.setenv(NOT_CRAN = 'true'), because otherwise skip_on_cran() will be applied on Covr too, resulting in extremely low coverage percentages
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- Rscript -e "Sys.setenv(NOT_CRAN = 'true'); cc <- covr::package_coverage(line_exclusions = list('R/atc_online.R', 'R/mo_history.R', 'R/mo_source.R', 'R/resistance_predict.R')); covr::codecov(coverage = cc, token = '$codecov'); cat('Code coverage:', covr::percent_coverage(cc))"
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- Rscript -e "Sys.setenv(NOT_CRAN = 'true'); cc <- covr::package_coverage(line_exclusions = list('R/atc_online.R', 'R/mo_history.R', 'R/mo_source.R', 'R/resistance_predict.R')); covr::codecov(coverage = cc, token = '$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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cache:
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key: release
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paths:
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- installed_deps/
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policy: pull # no uploading after run
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@ -1,6 +1,6 @@
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Package: AMR
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Package: AMR
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Version: 1.1.0.9002
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Version: 1.1.0.9003
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Date: 2020-04-30
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Date: 2020-05-01
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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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person(role = c("aut", "cre"),
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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 1.1.0.9002
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# AMR 1.1.0.9003
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## <small>Last updated: 30-Apr-2020</small>
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## <small>Last updated: 01-May-2020</small>
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### Changed
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### Changed
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* Small fix for some text input that could not be coerced as valid MIC values
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* Small fix for some text input that could not be coerced as valid MIC values
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@ -81,7 +81,7 @@
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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="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
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<a class="navbar-link" href="https://msberends.gitlab.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">1.1.0.9002</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9003</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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@ -81,7 +81,7 @@
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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">1.1.0.9002</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9003</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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@ -81,7 +81,7 @@
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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">1.1.0.9002</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9003</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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@ -81,7 +81,7 @@
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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">1.1.0.9002</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9003</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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@ -43,7 +43,7 @@
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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">1.1.0.9002</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9003</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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@ -81,7 +81,7 @@
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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">1.1.0.9002</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9003</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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@ -229,13 +229,13 @@
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<small>Source: <a href='https://gitlab.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
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<small>Source: <a href='https://gitlab.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
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</div>
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</div>
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<div id="amr-1-1-0-9002" class="section level1">
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<div id="amr-1-1-0-9003" class="section level1">
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<h1 class="page-header" data-toc-text="1.1.0.9002">
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<h1 class="page-header" data-toc-text="1.1.0.9003">
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<a href="#amr-1-1-0-9002" class="anchor"></a>AMR 1.1.0.9002<small> Unreleased </small>
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<a href="#amr-1-1-0-9003" class="anchor"></a>AMR 1.1.0.9003<small> Unreleased </small>
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</h1>
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</h1>
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<div id="last-updated-30-apr-2020" class="section level2">
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<div id="last-updated-01-may-2020" class="section level2">
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<h2 class="hasAnchor">
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<h2 class="hasAnchor">
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<a href="#last-updated-30-apr-2020" class="anchor"></a><small>Last updated: 30-Apr-2020</small>
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<a href="#last-updated-01-may-2020" class="anchor"></a><small>Last updated: 01-May-2020</small>
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</h2>
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</h2>
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<div id="changed" class="section level3">
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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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@ -10,7 +10,7 @@ articles:
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WHONET: WHONET.html
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WHONET: WHONET.html
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benchmarks: benchmarks.html
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benchmarks: benchmarks.html
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resistance_predict: resistance_predict.html
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resistance_predict: resistance_predict.html
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last_built: 2020-04-30T16:46Z
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last_built: 2020-05-01T07:13Z
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urls:
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urls:
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reference: https://msberends.gitlab.io/AMR/reference
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reference: https://msberends.gitlab.io/AMR/reference
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article: https://msberends.gitlab.io/AMR/articles
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article: https://msberends.gitlab.io/AMR/articles
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@ -81,7 +81,7 @@
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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">1.1.0.9002</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9003</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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@ -288,10 +288,4 @@ test_that("as.mo works", {
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expect_warning(x[[1]] <- "invalid code")
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expect_warning(x[[1]] <- "invalid code")
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expect_warning(c(x[1], "test"))
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expect_warning(c(x[1], "test"))
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# joining on mo class
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expect_identical(class(bind_rows(example_isolates,
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example_isolates,
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example_isolates)$mo),
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"mo")
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})
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})
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