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(v1.2.0.9034) code cleaning
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Package: AMR
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Version: 1.2.0.9033
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Date: 2020-07-12
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Version: 1.2.0.9034
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Date: 2020-07-13
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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person(role = c("aut", "cre"),
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4
NEWS.md
4
NEWS.md
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# AMR 1.2.0.9033
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## <small>Last updated: 12-Jul-2020</small>
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# AMR 1.2.0.9034
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## <small>Last updated: 13-Jul-2020</small>
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### New
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* 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
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4
R/mdro.R
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R/mdro.R
@ -470,7 +470,7 @@ mdro <- function(x,
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}
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x_transposed <- as.list(as.data.frame(t(x[, cols, drop = FALSE])))
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row_filter <- sapply(x_transposed, function(y) search_function(y %in% search_result, na.rm = TRUE))
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row_filter <- x[row_filter, "row_number", drop = TRUE]
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row_filter <- x[which(row_filter), "row_number", drop = TRUE]
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rows <- rows[rows %in% row_filter]
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x[rows, "MDRO"] <<- to
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x[rows, "reason"] <<- paste0(any_all, " of the required antibiotics ", ifelse(any_all == "any", "is", "are"), " R")
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@ -508,7 +508,7 @@ mdro <- function(x,
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# for PDR; all agents are R (or I if combine_SI = FALSE)
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x_transposed <- as.list(as.data.frame(t(x[rows, lst_vector, drop = FALSE])))
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row_filter <- sapply(x_transposed, function(y) all(y %in% search_result, na.rm = TRUE))
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x[row_filter, "classes_affected"] <<- 999
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x[which(row_filter), "classes_affected"] <<- 999
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}
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if (info == TRUE) {
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@ -21,6 +21,7 @@
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codecov:
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require_ci_to_pass: no # allow fail
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branch: master
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comment: no
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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="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">1.2.0.9033</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9034</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">1.2.0.9033</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9034</span>
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</span>
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</div>
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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">1.2.0.9033</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9034</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">1.2.0.9033</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9034</span>
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</span>
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</div>
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@ -43,7 +43,7 @@
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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">1.2.0.9033</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9034</span>
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</span>
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</div>
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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">1.2.0.9033</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9034</span>
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</span>
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</div>
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@ -229,13 +229,13 @@
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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-1209033" class="section level1">
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<h1 class="page-header" data-toc-text="1.2.0.9033">
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<a href="#amr-1209033" class="anchor"></a>AMR 1.2.0.9033<small> Unreleased </small>
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<div id="amr-1209034" class="section level1">
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<h1 class="page-header" data-toc-text="1.2.0.9034">
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<a href="#amr-1209034" class="anchor"></a>AMR 1.2.0.9034<small> Unreleased </small>
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</h1>
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<div id="last-updated-12-jul-2020" class="section level2">
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<div id="last-updated-13-jul-2020" class="section level2">
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<h2 class="hasAnchor">
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<a href="#last-updated-12-jul-2020" class="anchor"></a><small>Last updated: 12-Jul-2020</small>
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<a href="#last-updated-13-jul-2020" class="anchor"></a><small>Last updated: 13-Jul-2020</small>
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</h2>
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<div id="new" class="section level3">
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<h3 class="hasAnchor">
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@ -10,7 +10,7 @@ articles:
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WHONET: WHONET.html
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benchmarks: benchmarks.html
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resistance_predict: resistance_predict.html
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last_built: 2020-07-12T09:42Z
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last_built: 2020-07-13T07:17Z
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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">1.2.0.9033</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9034</span>
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</span>
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</div>
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