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<h1>Read data from 4D database</h1>
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<div class="hidden name"><code>read.4D.Rd</code></div>
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</div>
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<div class="ref-description">
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<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>
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<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>,
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<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>,
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<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>,
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<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>,
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<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>
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<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
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<table class="ref-arguments">
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<colgroup><col class="name" /><col class="desc" /></colgroup>
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<tr>
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<th>file</th>
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<td><p>the name of the file which the data are to be read from.
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Each row of the table appears as one line of the file. If it does
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not contain an <em>absolute</em> path, the file name is
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<em>relative</em> to the current working directory,
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<code><a href='https://www.rdocumentation.org/packages/base/topics/getwd'>getwd</a>()</code>. Tilde-expansion is performed where supported.
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This can be a compressed file (see <code><a href='https://www.rdocumentation.org/packages/base/topics/connections'>file</a></code>).</p>
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<p>Alternatively, <code>file</code> can be a readable text-mode
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<a href='https://www.rdocumentation.org/packages/base/topics/connections'>connection</a> (which will be opened for reading if
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necessary, and if so <code><a href='https://www.rdocumentation.org/packages/base/topics/connections'>close</a></code>d (and hence destroyed) at
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the end of the function call). (If <code><a href='https://www.rdocumentation.org/packages/base/topics/showConnections'>stdin</a>()</code> is used,
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the prompts for lines may be somewhat confusing. Terminate input
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with a blank line or an EOF signal, <code>Ctrl-D</code> on Unix and
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<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
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cleared before return.)</p>
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<p><code>file</code> can also be a complete URL. (For the supported URL
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schemes, see the ‘URLs’ section of the help for
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<code><a href='https://www.rdocumentation.org/packages/base/topics/connections'>url</a></code>.)</p></td>
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</tr>
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<tr>
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<th>info</th>
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<td><p>a logical to indicate whether info about the import should be printed, defaults to <code>TRUE</code> in interactive sessions</p></td>
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</tr>
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<tr>
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<th>header</th>
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<td><p>a logical value indicating whether the file contains the
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names of the variables as its first line. If missing, the value is
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determined from the file format: <code>header</code> is set to <code>TRUE</code>
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if and only if the first row contains one fewer field than the
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number of columns.</p></td>
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</tr>
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<tr>
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<th>row.names</th>
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<td><p>a vector of row names. This can be a vector giving
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the actual row names, or a single number giving the column of the
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table which contains the row names, or character string giving the
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name of the table column containing the row names.</p>
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<p>If there is a header and the first row contains one fewer field than
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the number of columns, the first column in the input is used for the
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row names. Otherwise if <code>row.names</code> is missing, the rows are
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numbered.</p>
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<p>Using <code>row.names = NULL</code> forces row numbering. Missing or
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<code>NULL</code> <code>row.names</code> generate row names that are considered
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to be ‘automatic’ (and not preserved by <code><a href='https://www.rdocumentation.org/packages/base/topics/matrix'>as.matrix</a></code>).</p></td>
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</tr>
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<tr>
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<th>sep</th>
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<td><p>the field separator character. Values on each line of the
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file are separated by this character. If <code>sep = ""</code> (the
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default for <code>read.table</code>) the separator is ‘white space’,
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that is one or more spaces, tabs, newlines or carriage returns.</p></td>
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</tr>
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<tr>
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<th>quote</th>
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<td><p>the set of quoting characters. To disable quoting
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altogether, use <code>quote = ""</code>. See <code><a href='https://www.rdocumentation.org/packages/base/topics/scan'>scan</a></code> for the
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behaviour on quotes embedded in quotes. Quoting is only considered
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for columns read as character, which is all of them unless
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<code>colClasses</code> is specified.</p></td>
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</tr>
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<tr>
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<th>dec</th>
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<td><p>the character used in the file for decimal points.</p></td>
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</tr>
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<tr>
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<th>na.strings</th>
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<td><p>a character vector of strings which are to be
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interpreted as <code><a href='https://www.rdocumentation.org/packages/base/topics/NA'>NA</a></code> values. Blank fields are also
|
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considered to be missing values in logical, integer, numeric and
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complex fields. Note that the test happens <em>after</em>
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white space is stripped from the input, so <code>na.strings</code>
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values may need their own white space stripped in advance.</p></td>
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</tr>
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<tr>
|
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<th>skip</th>
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<td><p>integer: the number of lines of the data file to skip before
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beginning to read data.</p></td>
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</tr>
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<tr>
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<th>check.names</th>
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<td><p>logical. If <code>TRUE</code> then the names of the
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variables in the data frame are checked to ensure that they are
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syntactically valid variable names. If necessary they are adjusted
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(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
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that there are no duplicates.</p></td>
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</tr>
|
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<tr>
|
|
<th>strip.white</th>
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<td><p>logical. Used only when <code>sep</code> has
|
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been specified, and allows the stripping of leading and trailing
|
|
white space from unquoted <code>character</code> fields (<code>numeric</code> fields
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are always stripped). See <code><a href='https://www.rdocumentation.org/packages/base/topics/scan'>scan</a></code> for further details
|
|
(including the exact meaning of ‘white space’),
|
|
remembering that the columns may include the row names.</p></td>
|
|
</tr>
|
|
<tr>
|
|
<th>fill</th>
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<td><p>logical. If <code>TRUE</code> then in case the rows have unequal
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|
length, blank fields are implicitly added. See ‘Details’.</p></td>
|
|
</tr>
|
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<tr>
|
|
<th>blank.lines.skip</th>
|
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<td><p>logical: if <code>TRUE</code> blank lines in the
|
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input are ignored.</p></td>
|
|
</tr>
|
|
<tr>
|
|
<th>stringsAsFactors</th>
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<td><p>logical: should character vectors be converted
|
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to factors? Note that this is overridden by <code>as.is</code> and
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<code>colClasses</code>, both of which allow finer control.</p></td>
|
|
</tr>
|
|
<tr>
|
|
<th>fileEncoding</th>
|
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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 ‘Encoding’ section of the help for
|
|
<code><a href='https://www.rdocumentation.org/packages/base/topics/connections'>file</a></code>, the ‘R Data Import/Export Manual’ and
|
|
‘Note’.</p></td>
|
|
</tr>
|
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<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
|
|
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 ‘Value’
|
|
and ‘Note’.</p></td>
|
|
</tr>
|
|
</table>
|
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<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
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<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>
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|
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<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>
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<p><img src='figures/logo.png' height=40px style=margin-bottom:5px /> <br />
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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 omprehensive tutorial</a> about how to conduct AMR analysis and find <a href='https://msberends.gitlab.io/AMR/reference'>the complete documentation of all functions</a>, which reads a lot easier than in R.</p>
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