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(v1.2.0.9034) code cleaning

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dr. M.S. (Matthijs) Berends 2020-07-13 09:17:24 +02:00
parent c0cf7ab02b
commit 6ab468362d
36 changed files with 266 additions and 265 deletions
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4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 1.2.0.9033 Version: 1.2.0.9034
Date: 2020-07-12 Date: 2020-07-13
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(
person(role = c("aut", "cre"), person(role = c("aut", "cre"),

4
NEWS.md
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# AMR 1.2.0.9033 # AMR 1.2.0.9034
## <small>Last updated: 12-Jul-2020</small> ## <small>Last updated: 13-Jul-2020</small>
### New ### New
* Function `ab_from_text()` to retrieve antimicrobial drug names, doses and forms of administration from clinical texts in e.g. health care records, which also corrects for misspelling since it uses `as.ab()` internally * Function `ab_from_text()` to retrieve antimicrobial drug names, doses and forms of administration from clinical texts in e.g. health care records, which also corrects for misspelling since it uses `as.ab()` internally

4
R/mdro.R
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@ -470,7 +470,7 @@ mdro <- function(x,
} }
x_transposed <- as.list(as.data.frame(t(x[, cols, drop = FALSE]))) x_transposed <- as.list(as.data.frame(t(x[, cols, drop = FALSE])))
row_filter <- sapply(x_transposed, function(y) search_function(y %in% search_result, na.rm = TRUE)) row_filter <- sapply(x_transposed, function(y) search_function(y %in% search_result, na.rm = TRUE))
row_filter <- x[row_filter, "row_number", drop = TRUE] row_filter <- x[which(row_filter), "row_number", drop = TRUE]
rows <- rows[rows %in% row_filter] rows <- rows[rows %in% row_filter]
x[rows, "MDRO"] <<- to x[rows, "MDRO"] <<- to
x[rows, "reason"] <<- paste0(any_all, " of the required antibiotics ", ifelse(any_all == "any", "is", "are"), " R") x[rows, "reason"] <<- paste0(any_all, " of the required antibiotics ", ifelse(any_all == "any", "is", "are"), " R")
@ -508,7 +508,7 @@ mdro <- function(x,
# for PDR; all agents are R (or I if combine_SI = FALSE) # for PDR; all agents are R (or I if combine_SI = FALSE)
x_transposed <- as.list(as.data.frame(t(x[rows, lst_vector, drop = FALSE]))) x_transposed <- as.list(as.data.frame(t(x[rows, lst_vector, drop = FALSE])))
row_filter <- sapply(x_transposed, function(y) all(y %in% search_result, na.rm = TRUE)) row_filter <- sapply(x_transposed, function(y) all(y %in% search_result, na.rm = TRUE))
x[row_filter, "classes_affected"] <<- 999 x[which(row_filter), "classes_affected"] <<- 999
} }
if (info == TRUE) { if (info == TRUE) {

1
codecov.yml
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@ -21,6 +21,7 @@
codecov: codecov:
require_ci_to_pass: no # allow fail require_ci_to_pass: no # allow fail
branch: master
comment: no comment: no

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.github.io/AMR/index.html">AMR (for R)</a> <a class="navbar-link" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9033</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9034</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">1.2.0.9033</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9034</span>
</span> </span>
</div> </div>

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docs/articles/index.html
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</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">1.2.0.9033</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9034</span>
</span> </span>
</div> </div>

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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">1.2.0.9033</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9034</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">1.2.0.9033</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9034</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">1.2.0.9033</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9034</span>
</span> </span>
</div> </div>
@ -229,13 +229,13 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small> <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div> </div>
<div id="amr-1209033" class="section level1"> <div id="amr-1209034" class="section level1">
<h1 class="page-header" data-toc-text="1.2.0.9033"> <h1 class="page-header" data-toc-text="1.2.0.9034">
<a href="#amr-1209033" class="anchor"></a>AMR 1.2.0.9033<small> Unreleased </small> <a href="#amr-1209034" class="anchor"></a>AMR 1.2.0.9034<small> Unreleased </small>
</h1> </h1>
<div id="last-updated-12-jul-2020" class="section level2"> <div id="last-updated-13-jul-2020" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">
<a href="#last-updated-12-jul-2020" class="anchor"></a><small>Last updated: 12-Jul-2020</small> <a href="#last-updated-13-jul-2020" class="anchor"></a><small>Last updated: 13-Jul-2020</small>
</h2> </h2>
<div id="new" class="section level3"> <div id="new" class="section level3">
<h3 class="hasAnchor"> <h3 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: 2020-07-12T09:42Z last_built: 2020-07-13T07:17Z
urls: urls:
reference: https://msberends.github.io/AMR/reference reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles article: https://msberends.github.io/AMR/articles

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docs/reference/index.html
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</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">1.2.0.9033</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9034</span>
</span> </span>
</div> </div>