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(v1.2.0.9025) AMR calculation speed improvement

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dr. M.S. (Matthijs) Berends 2020-07-03 12:14:41 +02:00
parent 46cf423eab
commit 2134fc76e2
11 changed files with 17 additions and 14 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 1.2.0.9024 Version: 1.2.0.9025
Date: 2020-07-03 Date: 2020-07-03
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(

2
NEWS.md
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# AMR 1.2.0.9024 # AMR 1.2.0.9025
## <small>Last updated: 03-Jul-2020</small> ## <small>Last updated: 03-Jul-2020</small>
### New ### New

5
R/rsi_calc.R
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@ -116,7 +116,10 @@ rsi_calc <- function(...,
x_transposed <- as.list(as.data.frame(t(x))) x_transposed <- as.list(as.data.frame(t(x)))
if (only_all_tested == TRUE) { if (only_all_tested == TRUE) {
# no NAs in any column # no NAs in any column
numerator <- sum(sapply(x_transposed, function(y) !any(is.na(y)) & any(y %in% ab_result, na.rm = TRUE))) y <- apply(X = as.data.frame(lapply(x, as.integer), stringsAsFactors = FALSE),
MARGIN = 1,
FUN = base::min)
numerator <- sum(as.integer(y) %in% as.integer(ab_result), na.rm = TRUE)
denominator <- sum(sapply(x_transposed, function(y) !(any(is.na(y))))) denominator <- sum(sapply(x_transposed, function(y) !(any(is.na(y)))))
} else { } else {
# may contain NAs in any column # may contain NAs in any column

2
docs/404.html
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@ -81,7 +81,7 @@
</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">1.2.0.9024</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9025</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">1.2.0.9024</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9025</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">1.2.0.9024</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9025</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">1.2.0.9024</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9025</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">1.2.0.9024</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9025</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">1.2.0.9024</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9025</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-1209024" class="section level1"> <div id="amr-1209025" class="section level1">
<h1 class="page-header" data-toc-text="1.2.0.9024"> <h1 class="page-header" data-toc-text="1.2.0.9025">
<a href="#amr-1209024" class="anchor"></a>AMR 1.2.0.9024<small> Unreleased </small> <a href="#amr-1209025" class="anchor"></a>AMR 1.2.0.9025<small> Unreleased </small>
</h1> </h1>
<div id="last-updated-03-jul-2020" class="section level2"> <div id="last-updated-03-jul-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: 2020-07-03T08:50Z last_built: 2020-07-03T10:14Z
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/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">1.2.0.9024</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9025</span>
</span> </span>
</div> </div>