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dr. M.S. (Matthijs) Berends
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<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@ -45,15 +49,15 @@
<link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script>
<meta property="og:title" content="Read data from 4D database — read.4D" />
<meta property="og:description" content="This function is only useful for the MMB department of the UMCG. Use this function to import data by just defining the file parameter. It will automatically transform birth dates and calculate patients age, translate the column names to English, transform the MO codes with as.mo and transform all antimicrobial columns with as.rsi." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
<meta name="twitter:card" content="summary" />
<!-- mathjax -->
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<![endif]-->
</head>
<body>
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</button>
<span class="navbar-brand">
<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">0.7.1.9055</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0</span>
</span>
</div>
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</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
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</li>
</ul>
<form class="navbar-form navbar-right" role="search">
<form class="navbar-form navbar-right hidden-xs hidden-sm" role="search">
<div class="form-group">
<input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off">
</div>
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</div><!--/.navbar -->
</header>
<div class="row">
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</div>
<div class="ref-description">
<p>This function is only useful for the MMB department of the UMCG. Use this function to <strong>import data by just defining the <code>file</code> parameter</strong>. It will automatically transform birth dates and calculate patients age, translate the column names to English, transform the MO codes with <code><a href='as.mo.html'>as.mo</a></code> and transform all antimicrobial columns with <code><a href='as.rsi.html'>as.rsi</a></code>.</p>
</div>
<pre class="usage"><span class='fu'>read.4D</span>(<span class='no'>file</span>, <span class='kw'>info</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/interactive'>interactive</a></span>(), <span class='kw'>header</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>row.names</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>sep</span> <span class='kw'>=</span> <span class='st'>"\t"</span>, <span class='kw'>quote</span> <span class='kw'>=</span> <span class='st'>"\"'"</span>, <span class='kw'>dec</span> <span class='kw'>=</span> <span class='st'>","</span>, <span class='kw'>na.strings</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"NA"</span>, <span class='st'>""</span>,
<pre class="usage"><span class='fu'>read.4D</span>(<span class='no'>file</span>, <span class='kw'>info</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span>(), <span class='kw'>header</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>row.names</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>sep</span> <span class='kw'>=</span> <span class='st'>"\t"</span>, <span class='kw'>quote</span> <span class='kw'>=</span> <span class='st'>"\"'"</span>, <span class='kw'>dec</span> <span class='kw'>=</span> <span class='st'>","</span>, <span class='kw'>na.strings</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"NA"</span>, <span class='st'>""</span>,
<span class='st'>"."</span>), <span class='kw'>skip</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>check.names</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>strip.white</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>fill</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>blank.lines.skip</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>stringsAsFactors</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>fileEncoding</span> <span class='kw'>=</span> <span class='st'>"UTF-8"</span>, <span class='kw'>encoding</span> <span class='kw'>=</span> <span class='st'>"UTF-8"</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@ -249,19 +252,19 @@
Each row of the table appears as one line of the file. If it does
not contain an <em>absolute</em> path, the file name is
<em>relative</em> to the current working directory,
<code><a href='https://www.rdocumentation.org/packages/base/topics/getwd'>getwd</a>()</code>. Tilde-expansion is performed where supported.
This can be a compressed file (see <code><a href='https://www.rdocumentation.org/packages/base/topics/connections'>file</a></code>).</p>
<code><a href='https://rdrr.io/r/base/getwd.html'>getwd</a>()</code>. Tilde-expansion is performed where supported.
This can be a compressed file (see <code><a href='https://rdrr.io/r/base/connections.html'>file</a></code>).</p>
<p>Alternatively, <code>file</code> can be a readable text-mode
<a href='https://www.rdocumentation.org/packages/base/topics/connections'>connection</a> (which will be opened for reading if
necessary, and if so <code><a href='https://www.rdocumentation.org/packages/base/topics/connections'>close</a></code>d (and hence destroyed) at
the end of the function call). (If <code><a href='https://www.rdocumentation.org/packages/base/topics/showConnections'>stdin</a>()</code> is used,
<a href='https://rdrr.io/r/base/connections.html'>connection</a> (which will be opened for reading if
necessary, and if so <code><a href='https://rdrr.io/r/base/connections.html'>close</a></code>d (and hence destroyed) at
the end of the function call). (If <code><a href='https://rdrr.io/r/base/showConnections.html'>stdin</a>()</code> is used,
the prompts for lines may be somewhat confusing. Terminate input
with a blank line or an EOF signal, <code>Ctrl-D</code> on Unix and
<code>Ctrl-Z</code> on Windows. Any pushback on <code><a href='https://www.rdocumentation.org/packages/base/topics/showConnections'>stdin()</a></code> will be
<code>Ctrl-Z</code> on Windows. Any pushback on <code><a href='https://rdrr.io/r/base/showConnections.html'>stdin()</a></code> will be
cleared before return.)</p>
<p><code>file</code> can also be a complete URL. (For the supported URL
schemes, see the &#8216;URLs&#8217; section of the help for
<code><a href='https://www.rdocumentation.org/packages/base/topics/connections'>url</a></code>.)</p></td>
<code><a href='https://rdrr.io/r/base/connections.html'>url</a></code>.)</p></td>
</tr>
<tr>
<th>info</th>
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numbered.</p>
<p>Using <code>row.names = NULL</code> forces row numbering. Missing or
<code>NULL</code> <code>row.names</code> generate row names that are considered
to be &#8216;automatic&#8217; (and not preserved by <code><a href='https://www.rdocumentation.org/packages/base/topics/matrix'>as.matrix</a></code>).</p></td>
to be &#8216;automatic&#8217; (and not preserved by <code><a href='https://rdrr.io/r/base/matrix.html'>as.matrix</a></code>).</p></td>
</tr>
<tr>
<th>sep</th>
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<tr>
<th>quote</th>
<td><p>the set of quoting characters. To disable quoting
altogether, use <code>quote = ""</code>. See <code><a href='https://www.rdocumentation.org/packages/base/topics/scan'>scan</a></code> for the
altogether, use <code>quote = ""</code>. See <code><a href='https://rdrr.io/r/base/scan.html'>scan</a></code> for the
behaviour on quotes embedded in quotes. Quoting is only considered
for columns read as character, which is all of them unless
<code>colClasses</code> is specified.</p></td>
@ -311,7 +314,7 @@
<tr>
<th>na.strings</th>
<td><p>a character vector of strings which are to be
interpreted as <code><a href='https://www.rdocumentation.org/packages/base/topics/NA'>NA</a></code> values. Blank fields are also
interpreted as <code><a href='https://rdrr.io/r/base/NA.html'>NA</a></code> values. Blank fields are also
considered to be missing values in logical, integer, numeric and
complex fields. Note that the test happens <em>after</em>
white space is stripped from the input, so <code>na.strings</code>
@ -327,7 +330,7 @@
<td><p>logical. If <code>TRUE</code> then the names of the
variables in the data frame are checked to ensure that they are
syntactically valid variable names. If necessary they are adjusted
(by <code><a href='https://www.rdocumentation.org/packages/base/topics/make.names'>make.names</a></code>) so that they are, and also to ensure
(by <code><a href='https://rdrr.io/r/base/make.names.html'>make.names</a></code>) so that they are, and also to ensure
that there are no duplicates.</p></td>
</tr>
<tr>
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<td><p>logical. Used only when <code>sep</code> has
been specified, and allows the stripping of leading and trailing
white space from unquoted <code>character</code> fields (<code>numeric</code> fields
are always stripped). See <code><a href='https://www.rdocumentation.org/packages/base/topics/scan'>scan</a></code> for further details
are always stripped). See <code><a href='https://rdrr.io/r/base/scan.html'>scan</a></code> for further details
(including the exact meaning of &#8216;white space&#8217;),
remembering that the columns may include the row names.</p></td>
</tr>
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<td><p>character string: if non-empty declares the
encoding used on a file (not a connection) so the character data can
be re-encoded. See the &#8216;Encoding&#8217; section of the help for
<code><a href='https://www.rdocumentation.org/packages/base/topics/connections'>file</a></code>, the &#8216;R Data Import/Export Manual&#8217; and
<code><a href='https://rdrr.io/r/base/connections.html'>file</a></code>, the &#8216;R Data Import/Export Manual&#8217; and
&#8216;Note&#8217;.</p></td>
</tr>
<tr>
<th>encoding</th>
<td><p>encoding to be assumed for input strings. It is
used to mark character strings as known to be in
Latin-1 or UTF-8 (see <code><a href='https://www.rdocumentation.org/packages/base/topics/Encoding'>Encoding</a></code>): it is not used to
Latin-1 or UTF-8 (see <code><a href='https://rdrr.io/r/base/Encoding.html'>Encoding</a></code>): it is not used to
re-encode the input, but allows <span style="R">R</span> to handle encoded strings in
their native encoding (if one of those two). See &#8216;Value&#8217;
and &#8216;Note&#8217;.</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>Column names will be transformed, but the original column names are set as a "label" attribute and can be seen in e.g. RStudio Viewer.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
</ul>
</ul>
</div>
</div>
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div>
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
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