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

Angelique; Dirk; Benjamin F


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  <identifier identifierType="DOI">10.5281/zenodo.5093500</identifier>
  <creators>
    <creator>
      <creatorName>Angelique</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-9305-1493</nameIdentifier>
      <affiliation>Burdinski</affiliation>
    </creator>
    <creator>
      <creatorName>Dirk</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-5708-2922</nameIdentifier>
      <affiliation>Brockmann</affiliation>
    </creator>
    <creator>
      <creatorName>Benjamin F</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-7414-8823</nameIdentifier>
      <affiliation>Maier</affiliation>
    </creator>
  </creators>
  <titles>
    <title>Analysis Code: Digital contact tracing contributes little to COVID-19 outbreak containment</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2021</publicationYear>
  <dates>
    <date dateType="Issued">2021-07-12</date>
  </dates>
  <resourceType resourceTypeGeneral="Software"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/5093500</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.5093499</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsPartOf">https://zenodo.org/communities/covid-19</relatedIdentifier>
  </relatedIdentifiers>
  <rightsList>
    <rights rightsURI="https://opensource.org/licenses/MIT">MIT License</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&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;</description>
  </descriptions>
</resource>
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