contactsurveys

contactsurveys is an R package to download contact survey data, which can be used to derive social mixing matrices (see, for example, the socialmixr package). This code was initially in the socialmixr package, but the code for downloading surveys has been moved into this package.

Installation

The development version can be installed using remotes

remotes::install_github("epiforecasts/contactsurveys")

Example usage

library(contactsurveys)

contactsurveys provides access to all surveys in the Social contact data community on Zenodo.

Listing surveys

The available surveys can be listed (if an internet connection is available) with list_surveys()

social_contact_surveys <- list_surveys(verbose = FALSE)
dim(social_contact_surveys)

## [1] 47  4

head(social_contact_surveys)

## Key: <date_added>
##    date_added                             title            creator
##        <char>                            <char>             <char>
## 1: 2017-11-07       POLYMOD social contact data       Joël Mossong
## 2: 2017-12-07      Social contact data for Peru Carlos G. Grijalva
## 3: 2017-12-22  Social contact data for Zimbabwe   Alessia Melegaro
## 4: 2018-01-23    Social contact data for France   Guillaume Béraud
## 5: 2018-02-05 Social contact data for Hong Kong       Kathy  Leung
## 6: 2018-06-14   Social contact data for Vietnam        Horby Peter
##                                       url
##                                    <char>
## 1: https://doi.org/10.5281/zenodo.3874557
## 2: https://doi.org/10.5281/zenodo.3874805
## 3: https://doi.org/10.5281/zenodo.3886638
## 4: https://doi.org/10.5281/zenodo.3886590
## 5: https://doi.org/10.5281/zenodo.3874808
## 6: https://doi.org/10.5281/zenodo.3874802

By default, the survey data from list_surveys() is effectively cached, so it will run very quickly the next time you run it. See ?list_surveys() for more detail.

Downloading surveys

Surveys can be downloaded using download_survey(). This will get the relevant data of a survey given its Zenodo DOI (as returned by list_surveys()).

polymod_doi <- "https://doi.org/10.5281/zenodo.3874557"
polymod_survey_files <- download_survey(polymod_doi, verbose = FALSE)
polymod_survey_files

## [1] "/Users/runner/Library/Application Support/org.R-project.R/R/contactsurveys/zenodo.3874557/2008_Mossong_POLYMOD_contact_common.csv"    
## [2] "/Users/runner/Library/Application Support/org.R-project.R/R/contactsurveys/zenodo.3874557/2008_Mossong_POLYMOD_dictionary.xls"        
## [3] "/Users/runner/Library/Application Support/org.R-project.R/R/contactsurveys/zenodo.3874557/2008_Mossong_POLYMOD_hh_common.csv"         
## [4] "/Users/runner/Library/Application Support/org.R-project.R/R/contactsurveys/zenodo.3874557/2008_Mossong_POLYMOD_hh_extra.csv"          
## [5] "/Users/runner/Library/Application Support/org.R-project.R/R/contactsurveys/zenodo.3874557/2008_Mossong_POLYMOD_participant_common.csv"
## [6] "/Users/runner/Library/Application Support/org.R-project.R/R/contactsurveys/zenodo.3874557/2008_Mossong_POLYMOD_participant_extra.csv" 
## [7] "/Users/runner/Library/Application Support/org.R-project.R/R/contactsurveys/zenodo.3874557/2008_Mossong_POLYMOD_sday.csv"

Getting citations

A reference for any given survey can be obtained by passing a DOI to get_citation():

get_citation(polymod_doi, verbose = FALSE)

## @dataset{joel_mossong_2020_3874557,
##   author       = {Joël Mossong and
##                   Niel Hens and
##                   Mark Jit and
##                   Philippe Beutels and
##                   Kari Auranen and
##                   Rafael Mikolajczyk and
##                   Marco Massari and
##                   Stefania Salmaso and
##                   Gianpaolo Scalia Tomba and
##                   Jacco Wallinga and
##                   Janneke Heijne and
##                   Malgorzata Sadkowska-Todys and
##                   Magdalena Rosinska and
##                   W. John Edmunds},
##   title        = {POLYMOD social contact data},
##   month        = jun,
##   year         = 2020,
##   publisher    = {Zenodo},
##   version      = 2,
##   doi          = {10.5281/zenodo.3874557},
##   url          = {https://doi.org/10.5281/zenodo.3874557},
## }

Using contact matrices with socialmixr

You can then use the survey files downloaded with functions from socialmixr, load_survey() and contact_matrix().

library(socialmixr)

## 
## Attaching package: 'socialmixr'

## The following objects are masked from 'package:contactsurveys':
## 
##     download_survey, get_citation, list_surveys

polymod_loaded <- load_survey(polymod_survey_files)

## Warning: No reference provided.

uk_contact_matrix <- contact_matrix(
      polymod_loaded,
      countries = "United Kingdom",
      age_limits = c(0, 18, 65)
    )

uk_contact_matrix

## $matrix
##          contact.age.group
## age.group   [0,18)  [18,65)       65+
##   [0,18)  7.813187 5.505495 0.2664835
##   [18,65) 2.103215 8.174281 0.6463621
##   65+     1.160714 5.464286 1.7142857
## 
## $participants
##    age.group participants proportion
##       <char>        <int>      <num>
## 1:    [0,18)          364  0.3600396
## 2:   [18,65)          591  0.5845697
## 3:       65+           56  0.0553907

Contributors

All contributions to this project are gratefully acknowledged using the allcontributors package following the allcontributors specification. Contributions of any kind are welcome!

Code

sbfnk, Bisaloo, njtierney, lwillem, Degoot-AM, jarvisc1, alxsrobert

Issues

avallecam