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@ -1288,21 +1288,21 @@
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<h1 id="frequently-asked-questions">Frequently Asked Questions<a class="headerlink" href="#frequently-asked-questions" title="Permanent link">¶</a></h1>
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<h2 id="cannot-connect-to-your-mysql-server">Cannot connect to your MySQL server<a class="headerlink" href="#cannot-connect-to-your-mysql-server" title="Permanent link">¶</a></h2>
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<details class="failure" open="open"><summary>Problem</summary><div class="highlight"><pre><span></span><code>**Error in .local<span class="o">(</span>drv, <span class="se">\.</span>..<span class="o">)</span> :** **Failed to connect to database: Error:
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<details class="failure" open="open"><summary>Problem</summary><div class="highlight"><pre><span></span><code>**Error <span class="k">in</span> .local<span class="o">(</span>drv, <span class="se">\.</span>..<span class="o">)</span> :** **Failed to connect to database: Error:
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Can<span class="se">\'</span>t initialize character <span class="nb">set</span> unknown <span class="o">(</span>path: compiled<span class="se">\_</span>in<span class="o">)</span>** :
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Calls: dbConnect -> dbConnect -> .local -> .Call
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Execution halted
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<span class="o">[</span>Tue Mar <span class="m">10</span> <span class="m">19</span>:40:15 <span class="m">2020</span><span class="o">]</span>
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Error in rule download_dataset:
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Error <span class="k">in</span> rule download_dataset:
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jobid: <span class="m">531</span>
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output: data/raw/p60/locations_raw.csv
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RuleException:
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CalledProcessError in line <span class="m">20</span> of /home/ubuntu/rapids/rules/preprocessing.snakefile:
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CalledProcessError <span class="k">in</span> line <span class="m">20</span> of /home/ubuntu/rapids/rules/preprocessing.snakefile:
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Command <span class="s1">'set -euo pipefail; Rscript --vanilla /home/ubuntu/rapids/.snakemake/scripts/tmp_2jnvqs7.download_dataset.R'</span> returned non-zero <span class="nb">exit</span> status <span class="m">1</span>.
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File <span class="s2">"/home/ubuntu/rapids/rules/preprocessing.snakefile"</span>, line <span class="m">20</span>, in __rule_download_dataset
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File <span class="s2">"/home/ubuntu/anaconda3/envs/moshi-env/lib/python3.7/concurrent/futures/thread.py"</span>, line <span class="m">57</span>, in run
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File <span class="s2">"/home/ubuntu/rapids/rules/preprocessing.snakefile"</span>, line <span class="m">20</span>, <span class="k">in</span> __rule_download_dataset
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File <span class="s2">"/home/ubuntu/anaconda3/envs/moshi-env/lib/python3.7/concurrent/futures/thread.py"</span>, line <span class="m">57</span>, <span class="k">in</span> run
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Shutting down, this might take some time.
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Exiting because a job execution failed. Look above <span class="k">for</span> error message
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</code></pre></div>
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@ -1323,7 +1323,7 @@ Exiting because a job execution failed. Look above <span class="k">for</span> er
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</details>
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<hr />
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<h2 id="error-table-xxx-doesnt-exist-while-running-the-download_phone_data-or-download_fitbit_data-rule">Error <code>Table XXX doesn't exist</code> while running the <code>download_phone_data</code> or <code>download_fitbit_data</code> rule.<a class="headerlink" href="#error-table-xxx-doesnt-exist-while-running-the-download_phone_data-or-download_fitbit_data-rule" title="Permanent link">¶</a></h2>
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<details class="failure" open="open"><summary>Problem</summary><div class="highlight"><pre><span></span><code>Error in .local<span class="o">(</span>conn, statement, ...<span class="o">)</span> :
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<details class="failure" open="open"><summary>Problem</summary><div class="highlight"><pre><span></span><code>Error <span class="k">in</span> .local<span class="o">(</span>conn, statement, ...<span class="o">)</span> :
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could not run statement: Table <span class="s1">'db_name.table_name'</span> doesn<span class="err">'</span>t exist
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Calls: colnames ... .local -> dbSendQuery -> dbSendQuery -> .local -> .Call
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Execution halted
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@ -1446,7 +1446,7 @@ ERROR: configuration failed <span class="k">for</span> package <span class="s1">
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<details class="failure" open="open"><summary>Problem</summary><p>You get the following error:
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<div class="highlight"><pre><span></span><code>CondaMultiError: CondaVerificationError: The package <span class="k">for</span> tk located at /home/ubuntu/miniconda2/pkgs/tk-8.6.9-hed695b0_1003
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appears to be corrupted. The path <span class="s1">'include/mysqlStubs.h'</span>
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specified in the package manifest cannot be found.
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specified <span class="k">in</span> the package manifest cannot be found.
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ClobberError: This transaction has incompatible packages due to a shared path.
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packages: conda-forge/linux-64::llvm-openmp-10.0.0-hc9558a2_0, anaconda/linux-64::intel-openmp-2019.4-243
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path: <span class="s1">'lib/libiomp5.so'</span>
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@ -1456,8 +1456,8 @@ ClobberError: This transaction has incompatible packages due to a shared path.
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</details>
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<h2 id="embedded-nul-in-string">Embedded nul in string<a class="headerlink" href="#embedded-nul-in-string" title="Permanent link">¶</a></h2>
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<details class="failure" open="open"><summary>Problem</summary><p>You get the following error when downloading sensor data:
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<div class="highlight"><pre><span></span><code>Error in result_fetch<span class="o">(</span>res@ptr, <span class="nv">n</span> <span class="o">=</span> n<span class="o">)</span> :
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embedded nul in string:
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<div class="highlight"><pre><span></span><code>Error <span class="k">in</span> result_fetch<span class="o">(</span>res@ptr, <span class="nv">n</span> <span class="o">=</span> n<span class="o">)</span> :
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embedded nul <span class="k">in</span> string:
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</code></pre></div></p>
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</details>
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<details class="done" open="open"><summary>Solution</summary><p>This problem is due to the way <code>RMariaDB</code> handles a mismatch between data types in R and MySQL (see <a href="https://github.com/r-dbi/RMariaDB/issues/121">this issue</a>). Since it seems this problem won’t be handled by <code>RMariaDB</code>, you have two options:</p>
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@ -1475,7 +1475,7 @@ ClobberError: This transaction has incompatible packages due to a shared path.
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</details>
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<h2 id="there-is-no-package-called-rmariadb">There is no package called <code>RMariaDB</code><a class="headerlink" href="#there-is-no-package-called-rmariadb" title="Permanent link">¶</a></h2>
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<details class="failure" open="open"><summary>Problem</summary><p>You get the following error when executing RAPIDS:
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<div class="highlight"><pre><span></span><code>Error in library<span class="o">(</span>RMariaDB<span class="o">)</span> : there is no package called <span class="s1">'RMariaDB'</span>
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<div class="highlight"><pre><span></span><code>Error <span class="k">in</span> library<span class="o">(</span>RMariaDB<span class="o">)</span> : there is no package called <span class="s1">'RMariaDB'</span>
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Execution halted
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</code></pre></div></p>
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</details>
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@ -1357,6 +1357,10 @@ For a detailed description of how this is calculated, see <a href="../../citatio
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<td><code>[CLUSTER_ON]</code></td>
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<td>Set this flag to <code>PARTICIPANT_DATASET</code> to create clusters based on the entire participant’s dataset or to <code>TIME_SEGMENT</code> to create clusters based on all the instances of the corresponding time segment (e.g. all mornings).</td>
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</tr>
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<tr>
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<td><code>[CLUSTERING_ALGORITHM]</code></td>
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<td>The original Doryab et al implementation uses <code>DBSCAN</code>, <code>OPTICS</code> is also available with similar (but not identical) clustering results and lower memory consumption.</td>
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</tr>
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</tbody>
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</table>
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<p>Features description for <code>[PHONE_LOCATIONS][PROVIDERS][DORYAB]</code>:</p>
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@ -1477,6 +1481,8 @@ For a detailed description of how this is calculated, see <a href="../../citatio
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Significant locations are determined using DBSCAN clustering on locations that a patient visit over the course of the period of data collection.</p>
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<p><strong>The Circadian Calculation</strong>
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For a detailed description of how this is calculated, see <a href="../../citation#doryab-locations">Canzian et al</a>.</p>
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<p><strong>Fine Tuning Clustering Parameters</strong>
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Based on an experiment where we collected fused location data for 7 days with a mean accuracy of 86 & SD of 350.874635, we determined that <code>EPS/MAX_EPS</code>=100 produced closer clustering results to reality. Higher values (>100) missed out some significant places like a short grocery visit while lower values (<100) picked up traffic lights and stop signs while driving as significant locations. We recommend you set <code>EPS</code> based on the accuracy of your location data (the more accurate your data is, the lower you should be able to set EPS).</p>
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</div>
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@ -1,171 +1,171 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<urlset xmlns="http://www.sitemaps.org/schemas/sitemap/0.9"><url>
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<loc>None</loc>
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<lastmod>2021-01-07</lastmod>
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<lastmod>2021-01-14</lastmod>
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<changefreq>daily</changefreq>
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</url><url>
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<loc>None</loc>
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<lastmod>2021-01-07</lastmod>
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<lastmod>2021-01-14</lastmod>
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<changefreq>daily</changefreq>
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</url><url>
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<loc>None</loc>
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<lastmod>2021-01-07</lastmod>
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<lastmod>2021-01-14</lastmod>
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<changefreq>daily</changefreq>
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</url><url>
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<loc>None</loc>
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<lastmod>2021-01-07</lastmod>
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<lastmod>2021-01-14</lastmod>
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<changefreq>daily</changefreq>
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</url><url>
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<loc>None</loc>
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<lastmod>2021-01-07</lastmod>
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<lastmod>2021-01-14</lastmod>
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<changefreq>daily</changefreq>
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</url><url>
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<loc>None</loc>
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<lastmod>2021-01-07</lastmod>
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<lastmod>2021-01-14</lastmod>
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<changefreq>daily</changefreq>
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</url><url>
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<loc>None</loc>
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<lastmod>2021-01-07</lastmod>
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<lastmod>2021-01-14</lastmod>
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<changefreq>daily</changefreq>
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</url><url>
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<loc>None</loc>
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<lastmod>2021-01-07</lastmod>
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<lastmod>2021-01-14</lastmod>
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<changefreq>daily</changefreq>
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</url><url>
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<loc>None</loc>
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<lastmod>2021-01-07</lastmod>
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<lastmod>2021-01-14</lastmod>
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<changefreq>daily</changefreq>
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</url><url>
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<loc>None</loc>
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<lastmod>2021-01-07</lastmod>
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<lastmod>2021-01-14</lastmod>
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<changefreq>daily</changefreq>
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</url><url>
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<loc>None</loc>
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<lastmod>2021-01-07</lastmod>
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<lastmod>2021-01-14</lastmod>
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<changefreq>daily</changefreq>
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</url><url>
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<loc>None</loc>
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<lastmod>2021-01-07</lastmod>
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<lastmod>2021-01-14</lastmod>
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<changefreq>daily</changefreq>
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</url><url>
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<loc>None</loc>
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<lastmod>2021-01-07</lastmod>
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<lastmod>2021-01-14</lastmod>
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<changefreq>daily</changefreq>
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</url><url>
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<loc>None</loc>
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<lastmod>2021-01-07</lastmod>
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<lastmod>2021-01-14</lastmod>
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<changefreq>daily</changefreq>
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</url><url>
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<loc>None</loc>
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<lastmod>2021-01-07</lastmod>
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<lastmod>2021-01-14</lastmod>
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<changefreq>daily</changefreq>
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</url><url>
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<loc>None</loc>
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<lastmod>2021-01-07</lastmod>
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<lastmod>2021-01-14</lastmod>
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<changefreq>daily</changefreq>
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</url><url>
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<loc>None</loc>
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<lastmod>2021-01-07</lastmod>
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<lastmod>2021-01-14</lastmod>
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<changefreq>daily</changefreq>
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</url><url>
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<loc>None</loc>
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<lastmod>2021-01-07</lastmod>
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<lastmod>2021-01-14</lastmod>
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<changefreq>daily</changefreq>
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</url><url>
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<loc>None</loc>
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<lastmod>2021-01-07</lastmod>
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<lastmod>2021-01-14</lastmod>
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<changefreq>daily</changefreq>
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</url><url>
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<loc>None</loc>
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<lastmod>2021-01-07</lastmod>
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<lastmod>2021-01-14</lastmod>
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<changefreq>daily</changefreq>
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</url><url>
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<loc>None</loc>
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<lastmod>2021-01-07</lastmod>
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<lastmod>2021-01-14</lastmod>
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<changefreq>daily</changefreq>
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</url><url>
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<loc>None</loc>
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<lastmod>2021-01-07</lastmod>
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<lastmod>2021-01-14</lastmod>
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<changefreq>daily</changefreq>
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</url><url>
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<loc>None</loc>
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<lastmod>2021-01-07</lastmod>
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<lastmod>2021-01-14</lastmod>
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<changefreq>daily</changefreq>
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</url><url>
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<loc>None</loc>
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<lastmod>2021-01-07</lastmod>
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<lastmod>2021-01-14</lastmod>
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<changefreq>daily</changefreq>
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</url><url>
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<loc>None</loc>
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<lastmod>2021-01-07</lastmod>
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<lastmod>2021-01-14</lastmod>
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<changefreq>daily</changefreq>
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</url><url>
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<loc>None</loc>
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<lastmod>2021-01-07</lastmod>
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<lastmod>2021-01-14</lastmod>
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<changefreq>daily</changefreq>
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</url><url>
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<loc>None</loc>
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<lastmod>2021-01-07</lastmod>
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<lastmod>2021-01-14</lastmod>
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<changefreq>daily</changefreq>
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</url><url>
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<loc>None</loc>
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<lastmod>2021-01-07</lastmod>
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<lastmod>2021-01-14</lastmod>
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<changefreq>daily</changefreq>
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</url><url>
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<loc>None</loc>
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<lastmod>2021-01-07</lastmod>
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<lastmod>2021-01-14</lastmod>
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<changefreq>daily</changefreq>
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</url><url>
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<loc>None</loc>
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<lastmod>2021-01-07</lastmod>
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<lastmod>2021-01-14</lastmod>
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<changefreq>daily</changefreq>
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</url><url>
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<loc>None</loc>
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<lastmod>2021-01-07</lastmod>
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<lastmod>2021-01-14</lastmod>
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<changefreq>daily</changefreq>
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</url><url>
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<loc>None</loc>
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<lastmod>2021-01-07</lastmod>
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<lastmod>2021-01-14</lastmod>
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<changefreq>daily</changefreq>
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</url><url>
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<loc>None</loc>
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<lastmod>2021-01-07</lastmod>
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<lastmod>2021-01-14</lastmod>
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<changefreq>daily</changefreq>
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</url><url>
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<loc>None</loc>
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<lastmod>2021-01-07</lastmod>
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<lastmod>2021-01-14</lastmod>
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<changefreq>daily</changefreq>
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</url><url>
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<loc>None</loc>
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<lastmod>2021-01-07</lastmod>
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<lastmod>2021-01-14</lastmod>
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<changefreq>daily</changefreq>
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</url><url>
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<loc>None</loc>
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<lastmod>2021-01-07</lastmod>
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<lastmod>2021-01-14</lastmod>
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<changefreq>daily</changefreq>
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</url><url>
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<loc>None</loc>
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<lastmod>2021-01-07</lastmod>
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<lastmod>2021-01-14</lastmod>
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<changefreq>daily</changefreq>
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</url><url>
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<loc>None</loc>
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<lastmod>2021-01-07</lastmod>
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<lastmod>2021-01-14</lastmod>
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<changefreq>daily</changefreq>
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</url><url>
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<loc>None</loc>
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<lastmod>2021-01-07</lastmod>
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<lastmod>2021-01-14</lastmod>
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<changefreq>daily</changefreq>
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</url><url>
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<loc>None</loc>
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<lastmod>2021-01-07</lastmod>
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<lastmod>2021-01-14</lastmod>
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<changefreq>daily</changefreq>
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</url><url>
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<loc>None</loc>
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<lastmod>2021-01-07</lastmod>
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<lastmod>2021-01-14</lastmod>
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<changefreq>daily</changefreq>
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</url><url>
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<loc>None</loc>
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<lastmod>2021-01-07</lastmod>
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<lastmod>2021-01-14</lastmod>
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<changefreq>daily</changefreq>
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</url>
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</urlset>
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