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    <h1>Create HospiNet object from subject database</h1>
    <small class="dont-index">Source: <a href="https://github.com/PascalCrepey/HospitalNetwork/blob/HEAD/R/NetworkBuilding.R" class="external-link"><code>R/NetworkBuilding.R</code></a></small>
    <div class="hidden name"><code>hospinet_from_subject_database.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>This function creates a HospiNet object from the database containing subjects stays.</p>
    </div>

    <div id="ref-usage">
    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">hospinet_from_subject_database</span><span class="op">(</span></span>
<span>  <span class="va">base</span>,</span>
<span>  window_threshold <span class="op">=</span> <span class="fl">365</span>,</span>
<span>  count_option <span class="op">=</span> <span class="st">"successive"</span>,</span>
<span>  condition <span class="op">=</span> <span class="st">"dates"</span>,</span>
<span>  prob_params <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.0036</span>, <span class="fl">1</span><span class="op">/</span><span class="fl">365</span>, <span class="fl">0.128</span><span class="op">)</span>,</span>
<span>  noloops <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span>  nmoves_threshold <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span>  flag_vars <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span>  flag_values <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span>  create_MetricsTable <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span>  verbose <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span>  shinySession <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span>  <span class="va">...</span></span>
<span><span class="op">)</span></span></code></pre></div>
    </div>

    <div id="arguments">
    <h2>Arguments</h2>
    <dl><dt>base</dt>
<dd><p>(hospinet.base) A database of records of stays of subjects in
facilities. This can be obtained using the function <code><a href="checkBase.html">checkBase</a></code>.</p></dd>


<dt>window_threshold</dt>
<dd><p>(numeric)
A threshold for the number of days between discharge and admission to be counted as a transfer. Set to 0 for same day transfer, default is 365 days.</p></dd>


<dt>count_option</dt>
<dd><p>(character) TODO. Default is "successive".</p></dd>


<dt>condition</dt>
<dd><p>(character) TODO. Default is "dates".</p></dd>


<dt>prob_params</dt>
<dd><p>(vector of numeric) Three numerical values to calculate
the probability that a movement causes an introduction from hospital A
to hospital B. See Donker T, Wallinga J, Grundmann H. (2010) &lt;doi:10.1371/journal.pcbi.1000715&gt; for more details.
prob_params[1] is the rate of acquisition in hospital A (related to LOS
in hospital A). Default: 0.0036
prob_params[2] is the rate of loss of colonisation (related to time
between admissions). Default: 1/365
prob_params[4] is the rate of transmission to other patients in hospital
B (related to LOS in hospital B). Default: 0.128</p></dd>


<dt>noloops</dt>
<dd><p>(boolean).
Should transfers within the same nodes (loops) be kept or set to 0. Defaults to TRUE, removing loops (setting matrix diagonal to 0).</p></dd>


<dt>nmoves_threshold</dt>
<dd><p>(numeric)
A threshold for the minimum number of subject transfer between two facilities. Set to NULL to deactivate, default to NULL.</p></dd>


<dt>flag_vars</dt>
<dd><p>(list) Additional variables that can help flag a transfer,
besides the dates of admission and discharge. Must be a named list of two
character vectors which are the names of the columns that can flag a
transfer: the column that can flag a potential origin, and the column
that can flag a potential target. The list must be named with "origin"
and "transfer". Eg: list("origin" = "var1", "target" = "var2"). See
details.</p></dd>


<dt>flag_values</dt>
<dd><p>(list) A named list of two character vectors which contain
the values of the variables in flag_var that are matched to flag a
potential transfer. The list must be named with "origin" and
"transfer". The character vectors might be of length greater than
one. Eg: list("origin" = c("value1", "value2"), "target" = c("value2",
"value2")). The values in 'origin' and 'target' are the values that flag
a potential origin of a transfer, or a potential target,
respectively. See details.</p></dd>


<dt>create_MetricsTable</dt>
<dd><p>(boolean)
Should the metrics table be created along with the network. Setting to FALSE will speed up the results. Default is TRUE.</p></dd>


<dt>verbose</dt>
<dd><p>TRUE to print computation steps</p></dd>


<dt>shinySession</dt>
<dd><p>(NULL) internal variable to deal with the progress bar</p></dd>


<dt>...</dt>
<dd><p>Additional parameters to be sent to checkBase in case the database has not been checked yet.</p></dd>

</dl></div>
    <div id="value">
    <h2>Value</h2>
    

<p>The function returns a HospiNet object.</p>
    </div>
    <div id="details">
    <h2>Details</h2>
    <p>This function will build a HospiNet object from a line-listed
subject database. The HospiNet object has all of the functions stored as
active bindings which can be accessed in the usual way. For more info, see
<code><a href="HospiNet.html">HospiNet</a></code>.
Note that the subject database will need to be run through <code><a href="checkBase.html">checkBase</a></code>
before going into this function.</p>
    </div>
    <div id="see-also">
    <h2>See also</h2>
    <div class="dont-index"><p><code><a href="HospiNet.html">HospiNet</a></code></p></div>
    </div>

    <div id="ref-examples">
    <h2>Examples</h2>
    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">mydb</span> <span class="op">&lt;-</span> <span class="fu"><a href="create_fake_subjectDB.html">create_fake_subjectDB</a></span><span class="op">(</span>n_subjects <span class="op">=</span> <span class="fl">100</span>, n_facilities <span class="op">=</span> <span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">myBase</span> <span class="op">&lt;-</span> <span class="fu"><a href="checkBase.html">checkBase</a></span><span class="op">(</span><span class="va">mydb</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Checking for missing values...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Checking for duplicated records...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Removed 0 duplicates</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Done.</span>
<span class="r-in"><span><span class="fu">hospinet_from_subject_database</span><span class="op">(</span><span class="va">myBase</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 facilities and 147 movements.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Movement window is 365 days. </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Constructing full matrix</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>     f01 f02 f03 f04 f05 f06 f07 f08 f09 f10</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> f01   0   2   2   1   2   2   0   1   3   2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> f02   3   0   2   0   0   0   4   0   4   1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> f03   1   1   0   0   3   2   4   1   1   3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> f04   0   1   1   0   1   4   0   0   4   2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> f05   4   3   0   1   0   2   3   0   0   2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> f06   5   1   3   1   2   0   1   5   2   1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> f07   1   0   2   0   2   1   0   3   0   2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> f08   2   2   0   2   2   0   0   0   0   2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> f09   3   3   5   2   1   1   0   0   0   1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> f10   1   0   2   3   1   2   1   2   4   0</span>
</code></pre></div>
    </div>
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