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https://github.com/msberends/AMR.git
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(v1.6.0.9002) R-3.0 installation fix
This commit is contained in:
parent
6ff5448192
commit
d277d58475
@ -1,3 +1,4 @@
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^.*\.RData$
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^.*\.Rproj$
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^\.Renviron$
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^\.Rprofile$
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8
.github/workflows/check.yaml
vendored
8
.github/workflows/check.yaml
vendored
@ -66,8 +66,8 @@ jobs:
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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: ubuntu-20.04, r: '3.4', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-20.04, r: '3.3', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-20.04, r: '3.2', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-20.04, r: '3.1', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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# - {os: ubuntu-20.04, r: '3.2', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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# - {os: ubuntu-20.04, r: '3.1', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-20.04, r: '3.0', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-16.04, r: 'devel', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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@ -78,8 +78,8 @@ jobs:
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- {os: ubuntu-16.04, r: '3.5', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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- {os: ubuntu-16.04, r: '3.4', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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- {os: ubuntu-16.04, r: '3.3', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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- {os: ubuntu-16.04, r: '3.2', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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- {os: ubuntu-16.04, r: '3.1', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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# - {os: ubuntu-16.04, r: '3.2', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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# - {os: ubuntu-16.04, r: '3.1', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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- {os: ubuntu-16.04, r: '3.0', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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env:
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@ -1,5 +1,5 @@
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Package: AMR
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Version: 1.6.0.9001
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Version: 1.6.0.9002
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Date: 2021-04-12
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Title: Antimicrobial Resistance Data Analysis
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Authors@R: c(
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3
NEWS.md
3
NEWS.md
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# AMR 1.6.0.9001
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# AMR 1.6.0.9002
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## <small>Last updated: 12 April 2021</small>
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### New
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@ -13,6 +13,7 @@
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* Fix for minor translation errors
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* Printing of microbial codes in a `data.frame` or `tibble` now gives a warning if the data contains old microbial codes (from a previous AMR package version)
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* `first_isolate()` can now take a vector of values for `col_keyantibiotics` and can have an episode length of `Inf`
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* Fixed an installation error on R-3.0
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# AMR 1.6.0
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@ -1095,8 +1095,8 @@ time_track <- function(name = NULL) {
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paste("(until now:", trimws(round(as.numeric(Sys.time()) * 1000) - pkg_env$time_start), "ms)")
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}
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# prevent dependency on package 'backports'
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# these functions were not available in previous versions of R (last checked: R 4.0.3)
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# prevent dependency on package 'backports' ----
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# these functions were not available in previous versions of R (last checked: R 4.0.5)
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# see here for the full list: https://github.com/r-lib/backports
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strrep <- function(x, times) {
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x <- as.character(x)
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@ -1143,3 +1143,10 @@ isNamespaceLoaded <- function(pkg) {
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lengths <- function(x, use.names = TRUE) {
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vapply(x, length, FUN.VALUE = NA_integer_, USE.NAMES = use.names)
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}
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if (as.double(R.Version()$major) + (as.double(R.Version()$minor) / 10) < 3.1) {
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# R-3.0 does not contain these functions, set them here to prevent installation failure
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cospi <- function(...) 1
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sinpi <- function(...) 1
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tanpi <- function(...) 1
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}
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@ -66,6 +66,7 @@ globalVariables(c(".rowid",
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"antibiotics",
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"atc_group1",
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"atc_group2",
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"base_ab",
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"code",
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"cols",
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"count",
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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">1.6.0.9001</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9002</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">1.6.0.9001</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9002</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">1.6.0.9001</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9002</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">1.6.0.9001</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9002</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">1.6.0.9001</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9002</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">1.6.0.9001</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9002</span>
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</span>
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</div>
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@ -236,9 +236,9 @@
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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-1609001" class="section level1">
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<h1 class="page-header" data-toc-text="1.6.0.9001">
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<a href="#amr-1609001" class="anchor"></a>AMR 1.6.0.9001<small> Unreleased </small>
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<div id="amr-1609002" class="section level1">
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<h1 class="page-header" data-toc-text="1.6.0.9002">
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<a href="#amr-1609002" class="anchor"></a>AMR 1.6.0.9002<small> Unreleased </small>
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</h1>
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<div id="last-updated-12-april-2021" class="section level2">
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<h2 class="hasAnchor">
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@ -270,6 +270,7 @@
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<li>
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<code><a href="../reference/first_isolate.html">first_isolate()</a></code> can now take a vector of values for <code>col_keyantibiotics</code> and can have an episode length of <code>Inf</code>
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</li>
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<li>Fixed an installation error on R-3.0</li>
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</ul>
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</div>
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</div>
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@ -313,7 +314,7 @@
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<span class="co">#> Filtering on oxazolidinones: value in column `LNZ` (linezolid) is either "R", "S" or "I"</span></code></pre></div>
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</li>
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<li><p>Support for custom MDRO guidelines, using the new <code><a href="../reference/mdro.html">custom_mdro_guideline()</a></code> function, please see <code><a href="../reference/mdro.html">mdro()</a></code> for additional info</p></li>
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<li><p><code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> generics for classes <code><mic></code> and <code><disk></code></p></li>
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<li><p><code>ggplot()</code> generics for classes <code><mic></code> and <code><disk></code></p></li>
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<li>
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<p>Function <code><a href="../reference/mo_property.html">mo_is_yeast()</a></code>, which determines whether a microorganism is a member of the taxonomic class Saccharomycetes or the taxonomic order Saccharomycetales:</p>
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<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
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@ -370,7 +371,7 @@
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<li>Plotting of MIC and disk diffusion values now support interpretation colouring if you supply the microorganism and antimicrobial agent</li>
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<li>All colours were updated to colour-blind friendly versions for values R, S and I for all plot methods (also applies to tibble printing)</li>
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<li>Interpretation of MIC and disk diffusion values to R/SI will now be translated if the system language is German, Dutch or Spanish (see <code>translate</code>)</li>
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<li>Plotting is now possible with base R using <code><a href="../reference/plot.html">plot()</a></code> and with ggplot2 using <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> on any vector of MIC and disk diffusion values</li>
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<li>Plotting is now possible with base R using <code><a href="../reference/plot.html">plot()</a></code> and with ggplot2 using <code>ggplot()</code> on any vector of MIC and disk diffusion values</li>
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</ul>
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</li>
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<li>Updated SNOMED codes to US Edition of SNOMED CT from 1 September 2020 and added the source to the help page of the <code>microorganisms</code> data set</li>
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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: 2021-04-12T10:33Z
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last_built: 2021-04-12T12:24Z
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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">1.6.0.9001</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9002</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">1.6.0.9001</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9002</span>
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</span>
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</div>
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@ -125,6 +125,7 @@ echo "• Building package •"
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echo "••••••••••••••••••••"
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echo "• Building 'data-raw/AMR_latest.tar.gz'..."
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Rscript -e "x <- devtools::build(path = 'data-raw', vignettes = FALSE, manual = FALSE, binary = FALSE, quiet = TRUE)"
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rm data-raw/AMR_latest.tar.gz
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mv data-raw/AMR_*.tar.gz data-raw/AMR_latest.tar.gz
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echo "• Installing..."
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Rscript -e "devtools::install(quiet = TRUE, dependencies = FALSE)"
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