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doc fix
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@ -1,5 +1,5 @@
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Package: AMR
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Version: 0.6.1.9035
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Version: 0.6.1.9036
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Date: 2019-05-23
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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@ -23,6 +23,10 @@ globalVariables(c(".",
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"..property",
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"ab",
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"abbreviations",
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"mdr",
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"mono_count",
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"second",
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"xdr",
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"antibiotic",
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"Antibiotic",
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"antibiotics",
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@ -23,7 +23,7 @@
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#'
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#' These function can be used to determine first isolates (see \code{\link{first_isolate}}). Using key antibiotics to determine first isolates is more reliable than without key antibiotics. These selected isolates will then be called first \emph{weighted} isolates.
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#' @param x table with antibiotics coloms, like \code{AMX} or \code{amox}
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#' @param x,y characters to compare
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#' @param y,z characters to compare
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#' @inheritParams first_isolate
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#' @param universal_1,universal_2,universal_3,universal_4,universal_5,universal_6 column names of \strong{broad-spectrum} antibiotics, case-insensitive. At default, the columns containing these antibiotics will be guessed with \code{\link{guess_ab_col}}.
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#' @param GramPos_1,GramPos_2,GramPos_3,GramPos_4,GramPos_5,GramPos_6 column names of antibiotics for \strong{Gram positives}, case-insensitive. At default, the columns containing these antibiotics will be guessed with \code{\link{guess_ab_col}}.
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@ -218,13 +218,15 @@ key_antibiotics <- function(x,
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#' @importFrom dplyr progress_estimated %>%
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#' @rdname key_antibiotics
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#' @export
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key_antibiotics_equal <- function(x,
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y,
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key_antibiotics_equal <- function(y,
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z,
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type = c("keyantibiotics", "points"),
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ignore_I = TRUE,
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points_threshold = 2,
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info = FALSE) {
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# x is active row, y is lag
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# y is active row, z is lag
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x <- y
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y <- z
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type <- type[1]
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@ -78,7 +78,7 @@
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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="Released version">0.6.1.9035</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9036</span>
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</span>
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</div>
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@ -78,7 +78,7 @@
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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="Released version">0.6.1.9035</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9036</span>
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</span>
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</div>
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@ -78,7 +78,7 @@
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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="Released version">0.6.1.9035</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9036</span>
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</span>
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</div>
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@ -42,7 +42,7 @@
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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="Released version">0.6.1.9035</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9036</span>
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</span>
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</div>
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@ -78,7 +78,7 @@
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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="Released version">0.6.1.9035</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9036</span>
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</span>
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</div>
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@ -78,7 +78,7 @@
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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="Released version">0.6.1.9035</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9036</span>
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</span>
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</div>
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@ -80,7 +80,7 @@
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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="Released version">0.6.1.9035</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9036</span>
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</span>
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</div>
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@ -262,7 +262,7 @@
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<span class='kw'>GramNeg_5</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"CAZ"</span>), <span class='kw'>GramNeg_6</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>,
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<span class='st'>"MEM"</span>), <span class='kw'>warnings</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
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<span class='fu'>key_antibiotics_equal</span>(<span class='no'>x</span>, <span class='no'>y</span>, <span class='kw'>type</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"keyantibiotics"</span>, <span class='st'>"points"</span>),
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<span class='fu'>key_antibiotics_equal</span>(<span class='no'>y</span>, <span class='no'>z</span>, <span class='kw'>type</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"keyantibiotics"</span>, <span class='st'>"points"</span>),
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<span class='kw'>ignore_I</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>points_threshold</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>info</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
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<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
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@ -296,6 +296,10 @@
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<th>...</th>
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<td><p>other parameters passed on to function</p></td>
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</tr>
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<tr>
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<th>y, z</th>
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<td><p>characters to compare</p></td>
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</tr>
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<tr>
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<th>type</th>
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<td><p>type to determine weighed isolates; can be <code>"keyantibiotics"</code> or <code>"points"</code>, see Details</p></td>
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@ -312,10 +316,6 @@
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<th>info</th>
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<td><p>print progress</p></td>
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</tr>
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<tr>
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<th>x, y</th>
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<td><p>characters to compare</p></td>
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</tr>
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</table>
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<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
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@ -19,7 +19,7 @@ key_antibiotics(x, col_mo = NULL, universal_1 = guess_ab_col(x, "AMX"),
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GramNeg_5 = guess_ab_col(x, "CAZ"), GramNeg_6 = guess_ab_col(x,
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"MEM"), warnings = TRUE, ...)
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key_antibiotics_equal(x, y, type = c("keyantibiotics", "points"),
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key_antibiotics_equal(y, z, type = c("keyantibiotics", "points"),
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ignore_I = TRUE, points_threshold = 2, info = FALSE)
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}
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\arguments{
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@ -37,6 +37,8 @@ key_antibiotics_equal(x, y, type = c("keyantibiotics", "points"),
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\item{...}{other parameters passed on to function}
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\item{y, z}{characters to compare}
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\item{type}{type to determine weighed isolates; can be \code{"keyantibiotics"} or \code{"points"}, see Details}
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\item{ignore_I}{logical to determine whether antibiotic interpretations with \code{"I"} will be ignored when \code{type = "keyantibiotics"}, see Details}
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@ -44,8 +46,6 @@ key_antibiotics_equal(x, y, type = c("keyantibiotics", "points"),
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\item{points_threshold}{points until the comparison of key antibiotics will lead to inclusion of an isolate when \code{type = "points"}, see Details}
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\item{info}{print progress}
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\item{x, y}{characters to compare}
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}
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\description{
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These function can be used to determine first isolates (see \code{\link{first_isolate}}). Using key antibiotics to determine first isolates is more reliable than without key antibiotics. These selected isolates will then be called first \emph{weighted} isolates.
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