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(v1.2.0.9013) unit test fix

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dr. M.S. (Matthijs) Berends 2020-06-22 13:18:40 +02:00
parent 779a4e8348
commit 8a66e475d7
14 changed files with 25 additions and 21 deletions
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2
DESCRIPTION
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Package: AMR Package: AMR
Version: 1.2.0.9012 Version: 1.2.0.9013
Date: 2020-06-22 Date: 2020-06-22
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(

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NEWS.md
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# AMR 1.2.0.9012 # AMR 1.2.0.9013
## <small>Last updated: 22-Jun-2020</small> ## <small>Last updated: 22-Jun-2020</small>
### New ### New

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R/rsi.R
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#' @seealso [as.mic()] #' @seealso [as.mic()]
#' @inheritSection AMR Read more on our website! #' @inheritSection AMR Read more on our website!
#' @examples #' @examples
#' summary(example_isolates) # see all R/SI results at a glance
#'
#' # For INTERPRETING disk diffusion and MIC values ----------------------- #' # For INTERPRETING disk diffusion and MIC values -----------------------
#' #'
#' # a whole data set, even with combined MIC values and disk zones #' # a whole data set, even with combined MIC values and disk zones

2
docs/404.html
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a> <a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9012</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9013</span>
</span> </span>
</div> </div>

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docs/LICENSE-text.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9012</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9013</span>
</span> </span>
</div> </div>

2
docs/articles/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9012</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9013</span>
</span> </span>
</div> </div>

2
docs/authors.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9012</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9013</span>
</span> </span>
</div> </div>

2
docs/index.html
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@ -43,7 +43,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9012</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9013</span>
</span> </span>
</div> </div>

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docs/news/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9012</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9013</span>
</span> </span>
</div> </div>
@ -229,9 +229,9 @@
<small>Source: <a href='https://gitlab.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small> <small>Source: <a href='https://gitlab.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div> </div>
<div id="amr-1209012" class="section level1"> <div id="amr-1209013" class="section level1">
<h1 class="page-header" data-toc-text="1.2.0.9012"> <h1 class="page-header" data-toc-text="1.2.0.9013">
<a href="#amr-1209012" class="anchor"></a>AMR 1.2.0.9012<small> Unreleased </small> <a href="#amr-1209013" class="anchor"></a>AMR 1.2.0.9013<small> Unreleased </small>
</h1> </h1>
<div id="last-updated-22-jun-2020" class="section level2"> <div id="last-updated-22-jun-2020" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">

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docs/pkgdown.yml
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@ -10,7 +10,7 @@ articles:
WHONET: WHONET.html WHONET: WHONET.html
benchmarks: benchmarks.html benchmarks: benchmarks.html
resistance_predict: resistance_predict.html resistance_predict: resistance_predict.html
last_built: 2020-06-22T10:13Z last_built: 2020-06-22T11:18Z
urls: urls:
reference: https://msberends.gitlab.io/AMR/reference reference: https://msberends.gitlab.io/AMR/reference
article: https://msberends.gitlab.io/AMR/articles article: https://msberends.gitlab.io/AMR/articles

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docs/reference/as.rsi.html
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@ -82,7 +82,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9013</span>
</span> </span>
</div> </div>
@ -342,7 +342,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<div class='dont-index'><p><code><a href='as.mic.html'>as.mic()</a></code></p></div> <div class='dont-index'><p><code><a href='as.mic.html'>as.mic()</a></code></p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># For INTERPRETING disk diffusion and MIC values -----------------------</span> <pre class="examples"><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>example_isolates</span>) <span class='co'># see all R/SI results at a glance</span>
<span class='co'># For INTERPRETING disk diffusion and MIC values -----------------------</span>
<span class='co'># a whole data set, even with combined MIC values and disk zones</span> <span class='co'># a whole data set, even with combined MIC values and disk zones</span>
<span class='no'>df</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>microorganism</span> <span class='kw'>=</span> <span class='st'>"E. coli"</span>, <span class='no'>df</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>microorganism</span> <span class='kw'>=</span> <span class='st'>"E. coli"</span>,

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docs/reference/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9012</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9013</span>
</span> </span>
</div> </div>

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man/as.rsi.Rd
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@ -99,6 +99,8 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://
} }
\examples{ \examples{
summary(example_isolates) # see all R/SI results at a glance
# For INTERPRETING disk diffusion and MIC values ----------------------- # For INTERPRETING disk diffusion and MIC values -----------------------
# a whole data set, even with combined MIC values and disk zones # a whole data set, even with combined MIC values and disk zones

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tests/testthat/test-rsi.R
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@ -27,7 +27,6 @@ test_that("rsi works", {
expect_true(as.rsi("S") < as.rsi("I")) expect_true(as.rsi("S") < as.rsi("I"))
expect_true(as.rsi("I") < as.rsi("R")) expect_true(as.rsi("I") < as.rsi("R"))
expect_true(as.rsi("R") > as.rsi("S"))
expect_true(is.rsi(as.rsi("S"))) expect_true(is.rsi(as.rsi("S")))
# print plots, should not raise errors # print plots, should not raise errors
@ -40,11 +39,10 @@ test_that("rsi works", {
expect_equal(suppressWarnings(as.logical(as.rsi("INVALID VALUE"))), NA) expect_equal(suppressWarnings(as.logical(as.rsi("INVALID VALUE"))), NA)
expect_equal(summary(as.rsi(c("S", "R"))), c("Class" = "rsi", expect_equal(summary(as.rsi(c("S", "R"))), c("Class" = "rsi",
"<NA>" = "0", "%R" = "50% (n=1)",
"Sum S" = "1", "%SI" = "50% (n=1)",
"Sum IR" = "1", "- %S" = "50% (n=1)",
"-Sum R" = "1", "- %I" = "0% (n=0)"))
"-Sum I" = "0"))
expect_identical(as.logical(lapply(example_isolates, is.rsi.eligible)), expect_identical(as.logical(lapply(example_isolates, is.rsi.eligible)),
rep(FALSE, length(example_isolates))) rep(FALSE, length(example_isolates)))