mirror of
https://github.com/msberends/AMR.git
synced 2024-12-25 19:26:13 +01:00
(v1.2.0.9025) AMR calculation speed improvement
This commit is contained in:
parent
46cf423eab
commit
2134fc76e2
@ -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
2
NEWS.md
@ -1,4 +1,4 @@
|
|||||||
# 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
|
||||||
|
@ -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
|
||||||
|
@ -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>
|
||||||
|
|
||||||
|
@ -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>
|
||||||
|
|
||||||
|
@ -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>
|
||||||
|
|
||||||
|
@ -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>
|
||||||
|
|
||||||
|
@ -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>
|
||||||
|
|
||||||
|
@ -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">
|
||||||
|
@ -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
|
||||||
|
@ -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>
|
||||||
|
|
||||||
|
Loading…
Reference in New Issue
Block a user