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

Angelique; Dirk; Benjamin F


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{
  "publisher": "Zenodo", 
  "DOI": "10.5281/zenodo.5093500", 
  "author": [
    {
      "family": "Angelique"
    }, 
    {
      "family": "Dirk"
    }, 
    {
      "family": "Benjamin F"
    }
  ], 
  "issued": {
    "date-parts": [
      [
        2021, 
        7, 
        12
      ]
    ]
  }, 
  "abstract": "<p># Digital Contact Tracing</p>\n\n<p>This package provides the simulation, analysis, and figure code for<br>\nthe manuscript &quot;Digital contact tracing contributes little to COVID-19<br>\noutbreak containment&quot; by A. Burdinski, D. Brockmann, and B. F. Maier.</p>\n\n<p>## Prerequisites</p>\n\n<p>The analysis code was used and tested for Python 3.8 on CentOS, Ubuntu, and MacOS.<br>\nIn order to run code in this collection, first install the requirements:</p>\n\n<p>```bash<br>\npip install -r requirements.txt<br>\n```</p>\n\n<p>Models are implemented using [epipack](github.com/benmaier/epipack). To run<br>\nlarge-scale simulations, we use [qsuite](github.com/benmaier/qsuite), a CLI<br>\nto facilitate simulations on HPC clusters. `qsuite` will be installed when<br>\ndependencies are installed from `requirements.txt`.</p>\n\n<p>## Main model</p>\n\n<p>The main model, including an example configuration,<br>\ncan be found in directory `main_model/`.<br>\nTo run the simulation, do</p>\n\n<p>```bash<br>\ncd main_model/<br>\nqsuite local<br>\n```</p>\n\n<p>## Analyses&nbsp;</p>\n\n<p>Almost all simulations and analyses performed in the paper<br>\ncan be found in `analysis_collection/tracing_sim/`.</p>\n\n<p>All extracted (summarized) data can be found in<br>\n`analysis_collection/data_new.json`.</p>\n\n<p>Code to produce the figures in the main text from distilled analysis<br>\nresults and analyses for the locally clustered network with<br>\nexponential degree distribution can be found in<br>\n`figures_main_text_and_new_network_model/`.</p>\n\n<p>Code for plots in the SI can be found in<br>\n`analysis_collection/tools.py` except for Fig. S7-S8-- those can<br>\nbe found in the respective directories&nbsp;<br>\n`analysis_collection/tracing_sim/results_deleting_edges_*`<br>\nand `analysis_collection/tracing_sim/results_toy_model/`.</p>\n\n<p>In order to replicate the simulations, change to the directory containing the<br>\nrespective analysis and run `qsuite local`, e.g.&nbsp;</p>\n\n<p>```bash<br>\ncd analysis_collection/tracing_sim/results_exponential_DF_NMEAS_100_ONLYSAVETIME_False/<br>\nqsuite local<br>\n```</p>\n\n<p>An illustration to justify the choice of `beta = 10^(-6)` as the long range<br>\nredistribution parameter beta can be found by running<br>\n`analysis_collection/small_world_parameter.py`.<br>\n&nbsp;</p>", 
  "title": "Analysis Code: Digital contact tracing contributes little to COVID-19 outbreak containment", 
  "type": "article", 
  "id": "5093500"
}
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