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

Angelique; Dirk; Benjamin F


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<oai_dc:dc xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:oai_dc="http://www.openarchives.org/OAI/2.0/oai_dc/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openarchives.org/OAI/2.0/oai_dc/ http://www.openarchives.org/OAI/2.0/oai_dc.xsd">
  <dc:creator>Angelique</dc:creator>
  <dc:creator>Dirk</dc:creator>
  <dc:creator>Benjamin F</dc:creator>
  <dc:date>2021-07-12</dc:date>
  <dc:description># Digital Contact Tracing

This package provides the simulation, analysis, and figure code for
the manuscript "Digital contact tracing contributes little to COVID-19
outbreak containment" by A. Burdinski, D. Brockmann, and B. F. Maier.

## Prerequisites

The analysis code was used and tested for Python 3.8 on CentOS, Ubuntu, and MacOS.
In order to run code in this collection, first install the requirements:

```bash
pip install -r requirements.txt
```

Models are implemented using [epipack](github.com/benmaier/epipack). To run
large-scale simulations, we use [qsuite](github.com/benmaier/qsuite), a CLI
to facilitate simulations on HPC clusters. `qsuite` will be installed when
dependencies are installed from `requirements.txt`.

## Main model

The main model, including an example configuration,
can be found in directory `main_model/`.
To run the simulation, do

```bash
cd main_model/
qsuite local
```

## Analyses 

Almost all simulations and analyses performed in the paper
can be found in `analysis_collection/tracing_sim/`.

All extracted (summarized) data can be found in
`analysis_collection/data_new.json`.

Code to produce the figures in the main text from distilled analysis
results and analyses for the locally clustered network with
exponential degree distribution can be found in
`figures_main_text_and_new_network_model/`.

Code for plots in the SI can be found in
`analysis_collection/tools.py` except for Fig. S7-S8-- those can
be found in the respective directories 
`analysis_collection/tracing_sim/results_deleting_edges_*`
and `analysis_collection/tracing_sim/results_toy_model/`.

In order to replicate the simulations, change to the directory containing the
respective analysis and run `qsuite local`, e.g. 

```bash
cd analysis_collection/tracing_sim/results_exponential_DF_NMEAS_100_ONLYSAVETIME_False/
qsuite local
```

An illustration to justify the choice of `beta = 10^(-6)` as the long range
redistribution parameter beta can be found by running
`analysis_collection/small_world_parameter.py`.
 </dc:description>
  <dc:identifier>https://zenodo.org/record/5093500</dc:identifier>
  <dc:identifier>10.5281/zenodo.5093500</dc:identifier>
  <dc:identifier>oai:zenodo.org:5093500</dc:identifier>
  <dc:relation>doi:10.5281/zenodo.5093499</dc:relation>
  <dc:relation>url:https://zenodo.org/communities/covid-19</dc:relation>
  <dc:rights>info:eu-repo/semantics/openAccess</dc:rights>
  <dc:rights>https://opensource.org/licenses/MIT</dc:rights>
  <dc:title>Analysis Code: Digital contact tracing contributes little to COVID-19 outbreak containment</dc:title>
  <dc:type>info:eu-repo/semantics/other</dc:type>
  <dc:type>software</dc:type>
</oai_dc:dc>
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