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Analysis Code: Digital contact tracing contributes little to COVID-19 outbreak containment

Angelique; Dirk; Benjamin F


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    <dct:title>Analysis Code: Digital contact tracing contributes little to COVID-19 outbreak containment</dct:title>
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    <dct:description>&lt;p&gt;# Digital Contact Tracing&lt;/p&gt; &lt;p&gt;This package provides the simulation, analysis, and figure code for&lt;br&gt; the manuscript &amp;quot;Digital contact tracing contributes little to COVID-19&lt;br&gt; outbreak containment&amp;quot; by A. Burdinski, D. Brockmann, and B. F. Maier.&lt;/p&gt; &lt;p&gt;## Prerequisites&lt;/p&gt; &lt;p&gt;The analysis code was used and tested for Python 3.8 on CentOS, Ubuntu, and MacOS.&lt;br&gt; In order to run code in this collection, first install the requirements:&lt;/p&gt; &lt;p&gt;```bash&lt;br&gt; pip install -r requirements.txt&lt;br&gt; ```&lt;/p&gt; &lt;p&gt;Models are implemented using [epipack](github.com/benmaier/epipack). To run&lt;br&gt; large-scale simulations, we use [qsuite](github.com/benmaier/qsuite), a CLI&lt;br&gt; to facilitate simulations on HPC clusters. `qsuite` will be installed when&lt;br&gt; dependencies are installed from `requirements.txt`.&lt;/p&gt; &lt;p&gt;## Main model&lt;/p&gt; &lt;p&gt;The main model, including an example configuration,&lt;br&gt; can be found in directory `main_model/`.&lt;br&gt; To run the simulation, do&lt;/p&gt; &lt;p&gt;```bash&lt;br&gt; cd main_model/&lt;br&gt; qsuite local&lt;br&gt; ```&lt;/p&gt; &lt;p&gt;## Analyses&amp;nbsp;&lt;/p&gt; &lt;p&gt;Almost all simulations and analyses performed in the paper&lt;br&gt; can be found in `analysis_collection/tracing_sim/`.&lt;/p&gt; &lt;p&gt;All extracted (summarized) data can be found in&lt;br&gt; `analysis_collection/data_new.json`.&lt;/p&gt; &lt;p&gt;Code to produce the figures in the main text from distilled analysis&lt;br&gt; results and analyses for the locally clustered network with&lt;br&gt; exponential degree distribution can be found in&lt;br&gt; `figures_main_text_and_new_network_model/`.&lt;/p&gt; &lt;p&gt;Code for plots in the SI can be found in&lt;br&gt; `analysis_collection/tools.py` except for Fig. S7-S8-- those can&lt;br&gt; be found in the respective directories&amp;nbsp;&lt;br&gt; `analysis_collection/tracing_sim/results_deleting_edges_*`&lt;br&gt; and `analysis_collection/tracing_sim/results_toy_model/`.&lt;/p&gt; &lt;p&gt;In order to replicate the simulations, change to the directory containing the&lt;br&gt; respective analysis and run `qsuite local`, e.g.&amp;nbsp;&lt;/p&gt; &lt;p&gt;```bash&lt;br&gt; cd analysis_collection/tracing_sim/results_exponential_DF_NMEAS_100_ONLYSAVETIME_False/&lt;br&gt; qsuite local&lt;br&gt; ```&lt;/p&gt; &lt;p&gt;An illustration to justify the choice of `beta = 10^(-6)` as the long range&lt;br&gt; redistribution parameter beta can be found by running&lt;br&gt; `analysis_collection/small_world_parameter.py`.&lt;br&gt; &amp;nbsp;&lt;/p&gt;</dct:description>
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