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(v1.6.0.9058) unit tests
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parent
808024c5f4
commit
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39
.github/workflows/codecovr.yaml
vendored
39
.github/workflows/codecovr.yaml
vendored
@ -43,39 +43,40 @@ jobs:
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steps:
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- uses: actions/checkout@v2
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- uses: r-lib/actions/setup-r@master
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- uses: r-lib/actions/setup-r@v1
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with:
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r-version: release
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- uses: r-lib/actions/setup-pandoc@master
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- name: Query dependencies
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run: |
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install.packages('remotes')
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saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
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writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
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shell: Rscript {0}
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- name: Cache R packages
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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@v1
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with:
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path: ${{ env.R_LIBS_USER }}
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key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
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restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
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key: macOS-latest-r-release-v4
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- name: Install dependencies
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- name: Unpack AMR and install R dependencies
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run: |
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install.packages(c("remotes", "tinytest"))
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remotes::install_deps(dependencies = TRUE)
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remotes::install_cran("covr")
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remotes::install_local("data-raw/AMR_latest.tar.gz")
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tar -xf data-raw/AMR_latest.tar.gz
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Rscript -e "source('data-raw/_install_deps.R')"
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Rscript -e "install.packages('covr')"
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shell: bash
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- name: Show session info
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run: |
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options(width = 100)
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utils::sessionInfo()
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as.data.frame(utils::installed.packages())[, "Version", drop = FALSE]
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shell: Rscript {0}
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- name: Test coverage
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run: |
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library(AMR)
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library(tinytest)
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source_files <- list.files("R", pattern = ".R$", full.names = TRUE)
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test_files <- list.files("inst/tinytest", full.names = TRUE)
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source_files <- list.files("AMR/R", pattern = ".R$", full.names = TRUE)
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test_files <- list.files("AMR/inst/tinytest", full.names = TRUE)
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cov <- covr::file_coverage(source_files = source_files, test_files = test_files, parent_env = asNamespace("AMR"), 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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attr(cov, which = "package") <- list(path = ".") # until https://github.com/r-lib/covr/issues/478 is solved
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attr(cov, which = "package") <- list(path = "AMR") # until https://github.com/r-lib/covr/issues/478 is solved
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covr::codecov(cov, quiet = FALSE)
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shell: Rscript {0}
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@ -1,6 +1,6 @@
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Package: AMR
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Version: 1.6.0.9056
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Date: 2021-05-21
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Version: 1.6.0.9058
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Date: 2021-05-22
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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` 1.6.0.9056
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## <small>Last updated: 21 May 2021</small>
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# `AMR` 1.6.0.9058
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## <small>Last updated: 22 May 2021</small>
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### Breaking change
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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.
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Binary file not shown.
@ -25,17 +25,15 @@
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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.patched.tar.gz")
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install.packages("data-raw/AMR_latest.tar.gz", dependencies = FALSE)
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descr <- readLines("AMR/DESCRIPTION")
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pkg_suggests <- gsub(".*Suggests: (.*)*?[A-Z].*", "\\1", paste0(descr, "*", collapse = ""), perl = FALSE)
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pkg_suggests <- unlist(strsplit(pkg_suggests, "[,* ]"))
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pkg_suggests <- pkg_suggests[pkg_suggests != ""]
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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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to_install <- pkg_suggests[!pkg_suggests %in% rownames(utils::installed.packages())]
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to_update <- as.data.frame(utils::old.packages(repos = "https://cran.rstudio.com/"), stringsAsFactors = FALSE)
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to_update <- to_update[which(to_update$Package %in% pkg_suggests), "Package", drop = TRUE]
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if (length(to_install) == 0) {
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message("Nothing to install")
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}
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for (i in seq_len(length(to_install))) {
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cat("Installing package", to_install[i], "\n")
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tryCatch(install.packages(to_install[i], repos = "https://cran.rstudio.com/", dependencies = TRUE, quiet = TRUE),
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@ -44,6 +42,11 @@ for (i in seq_len(length(to_install))) {
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error = function(e) message(e$message))
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}
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to_update <- as.data.frame(utils::old.packages(repos = "https://cran.rstudio.com/"), stringsAsFactors = FALSE)
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to_update <- to_update[which(to_update$Package %in% pkg_suggests), "Package", drop = TRUE]
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if (length(to_update) == 0) {
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message("Nothing to update")
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}
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for (i in seq_len(length(to_update))) {
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cat("Updating package", to_update[i], "\n")
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tryCatch(update.packages(to_update[i], repos = "https://cran.rstudio.com/", ask = FALSE),
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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">1.6.0.9056</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9058</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">1.6.0.9056</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9058</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">1.6.0.9056</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9058</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">21 May 2021</h4>
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<h4 class="date">22 May 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">1.6.0.9056</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9058</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">1.6.0.9056</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9058</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">1.6.0.9056</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9058</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">1.6.0.9056</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9058</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-1609056" class="section level1">
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<h1 class="page-header" data-toc-text="1.6.0.9056">
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<a href="#amr-1609056" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9056</h1>
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<div id="last-updated-21-may-2021" class="section level2">
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<div id="amr-1609058" class="section level1">
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<h1 class="page-header" data-toc-text="1.6.0.9058">
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<a href="#amr-1609058" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9058</h1>
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<div id="last-updated-22-may-2021" class="section level2">
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<h2 class="hasAnchor">
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<a href="#last-updated-21-may-2021" class="anchor"></a><small>Last updated: 21 May 2021</small>
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<a href="#last-updated-22-may-2021" class="anchor"></a><small>Last updated: 22 May 2021</small>
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</h2>
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<div id="breaking-change" 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: 2021-05-21T18:27Z
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last_built: 2021-05-22T06:56Z
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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">1.6.0.9056</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9058</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">1.6.0.9056</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9058</span>
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</span>
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</div>
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