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which subjects can be transferred. The edgelist is computed from a database that
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    <div class="page-header">
    <h1>Compute the edgelist of a network from a database of movements records.</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>edgelist_from_base.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>This function computes the edgelist of a network of facilities across
which subjects can be transferred. The edgelist is computed from a database that
contains the records of the subjects' stays in the facilities.</p>
    </div>

    <div id="ref-usage">
    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">edgelist_from_base</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>  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>  condition <span class="op">=</span> <span class="st">"dates"</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>  verbose <span class="op">=</span> <span class="cn">FALSE</span></span>
<span><span class="op">)</span></span></code></pre></div>
    </div>

    <div id="arguments">
    <h2>Arguments</h2>
    <dl><dt>base</dt>
<dd><p>(data.table) A database of records of stays of subjects in
facilities. The table should have at least the following columns:</p><ul><li><p><b>subjectID</b> (character) unique subject identifier</p></li>
<li><p><b>facilityID</b> (character) unique facility identifier</p></li>
<li><p><b>admDate</b> (POSIXct) date of admission in the facility</p></li>
<li><p><b>disDate</b> (POSIXct) date of discharge of the facility</p></li>
</ul></dd>


<dt>window_threshold</dt>
<dd><p>(integer) A number of days. If two stays of a subject
at two facilities occurred within this window, this constitutes a
connection between the two facilities (given that potential other
conditions are met).</p></dd>


<dt>count_option</dt>
<dd><p>(character) How to count connections. Options are
"successive", "probability" or "all". See details.</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.
For use with count_option="probability".
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>condition</dt>
<dd><p>(character) Condition(s) used to decide what constitutes a
connection. Can be "dates", "flags", or "both". See details.</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>verbose</dt>
<dd><p>TRUE to print computation steps</p></dd>

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

<p>A list of two data.tables, which are the edgelists. One in long
    format (el_long), and one aggregated by pair of nodes (el_aggr).</p>
    </div>
    <div id="details">
    <h2>Details</h2>
    <p>The edgelist contains the information on the connections between
    nodes of the network, that is the movements of subjects between
    facilities. The edgelist can be in two different formats: long or
    aggregated. In long format, each row corresponds to a single movement
    between two facilities, therefore only two columns are needed, one
    containing the origin facilities of a movement, the other containing the
    target facilities. In aggregated format, the edgelist is aggregated by
    unique pairs of origin-target facilities.</p>
    </div>
    <div id="see-also">
    <h2>See also</h2>
    <div class="dont-index"><p><code><a href="matrix_from_edgelist.html">matrix_from_edgelist</a></code>, <code><a href="matrix_from_base.html">matrix_from_base</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">edgelist_from_base</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> $el_aggr</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>     origin target N</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  1:    f01    f02 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  2:    f01    f03 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  3:    f01    f04 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  4:    f01    f06 5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  5:    f01    f07 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  6:    f01    f08 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  7:    f02    f01 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  8:    f02    f03 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  9:    f02    f04 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10:    f02    f05 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 11:    f02    f06 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 12:    f02    f07 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 13:    f02    f08 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 14:    f02    f09 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 15:    f02    f10 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 16:    f03    f01 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 17:    f03    f02 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 18:    f03    f04 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 19:    f03    f05 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 20:    f03    f06 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 21:    f03    f07 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 22:    f03    f08 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 23:    f03    f09 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 24:    f03    f10 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 25:    f04    f01 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 26:    f04    f02 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 27:    f04    f03 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 28:    f04    f05 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 29:    f04    f06 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 30:    f04    f07 5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 31:    f04    f08 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 32:    f04    f09 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 33:    f05    f01 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 34:    f05    f02 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 35:    f05    f04 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 36:    f05    f06 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 37:    f05    f07 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 38:    f05    f08 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 39:    f05    f09 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 40:    f05    f10 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 41:    f06    f01 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 42:    f06    f02 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 43:    f06    f03 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 44:    f06    f04 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 45:    f06    f05 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 46:    f06    f07 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 47:    f06    f08 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 48:    f06    f09 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 49:    f06    f10 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 50:    f07    f01 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 51:    f07    f02 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 52:    f07    f03 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 53:    f07    f04 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 54:    f07    f06 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 55:    f07    f08 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 56:    f07    f10 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 57:    f08    f01 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 58:    f08    f02 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 59:    f08    f03 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 60:    f08    f04 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 61:    f08    f05 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 62:    f08    f07 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 63:    f08    f10 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 64:    f09    f02 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 65:    f09    f03 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 66:    f09    f04 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 67:    f09    f06 5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 68:    f09    f08 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 69:    f09    f10 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 70:    f10    f01 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 71:    f10    f02 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 72:    f10    f03 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 73:    f10    f04 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 74:    f10    f05 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 75:    f10    f06 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 76:    f10    f07 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 77:    f10    f08 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>     origin target N</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $el_long</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>       sID origin target</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>   1: s053    f01    f02</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>   2: s025    f01    f03</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>   3: s040    f01    f04</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>   4: s043    f01    f04</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>   5: s057    f01    f04</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  ---                   </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 142: s060    f10    f06</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 143: s095    f10    f06</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 144: s014    f10    f07</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 145: s024    f10    f07</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 146: s070    f10    f08</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
</code></pre></div>
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