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
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)
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.3874802By 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)## [zen4R][INFO] ZenodoRecord - Download in sequential mode
## [zen4R][INFO] ZenodoRecord - Will download 7 files from record '3874557' (doi: '10.5281/zenodo.3874557') - total size: 7.4 MiB
## [zen4R][INFO] Downloading file '2008_Mossong_POLYMOD_hh_common.csv' - size: 120 KiB
## [zen4R][INFO] Downloading file '2008_Mossong_POLYMOD_contact_common.csv' - size: 6.2 MiB
## [zen4R][INFO] Downloading file '2008_Mossong_POLYMOD_dictionary.xls' - size: 41 KiB
## [zen4R][INFO] Downloading file '2008_Mossong_POLYMOD_hh_extra.csv' - size: 523 KiB
## [zen4R][INFO] Downloading file '2008_Mossong_POLYMOD_participant_common.csv' - size: 153.1 KiB
## [zen4R][INFO] Downloading file '2008_Mossong_POLYMOD_participant_extra.csv' - size: 221.8 KiB
## [zen4R][INFO] Downloading file '2008_Mossong_POLYMOD_sday.csv' - size: 188.7 KiB
## [zen4R][INFO] Files downloaded at '/Users/runner/Library/Application Support/org.R-project.R/R/contactsurveys'.
## [zen4R][INFO] ZenodoRecord - Verifying file integrity...
## [zen4R][INFO] File '2008_Mossong_POLYMOD_hh_common.csv': integrity verified (md5sum: d7fb1359ad84dba8cce4c444063940aa)
## [zen4R][INFO] File '2008_Mossong_POLYMOD_contact_common.csv': integrity verified (md5sum: 52baf32033bf780786fae6604043ec00)
## [zen4R][INFO] File '2008_Mossong_POLYMOD_dictionary.xls': integrity verified (md5sum: 06415516c91b52dedfaa53622e352647)
## [zen4R][INFO] File '2008_Mossong_POLYMOD_hh_extra.csv': integrity verified (md5sum: b0063f8d1a4f391d919495493611b3f1)
## [zen4R][INFO] File '2008_Mossong_POLYMOD_participant_common.csv': integrity verified (md5sum: ac784c281a71e15c7e64eaf2d6365709)
## [zen4R][INFO] File '2008_Mossong_POLYMOD_participant_extra.csv': integrity verified (md5sum: 4e2dd8d6ba2d23bb5b1f236be215b936)
## [zen4R][INFO] File '2008_Mossong_POLYMOD_sday.csv': integrity verified (md5sum: 148c5fc86ca10d385e3d047014e14a09)
## [zen4R][INFO] ZenodoRecord - End of download
polymod_survey_files## [1] "/Users/runner/Library/Application Support/org.R-project.R/R/contactsurveys/2008_Mossong_POLYMOD_hh_common.csv"
## [2] "/Users/runner/Library/Application Support/org.R-project.R/R/contactsurveys/2008_Mossong_POLYMOD_contact_common.csv"
## [3] "/Users/runner/Library/Application Support/org.R-project.R/R/contactsurveys/2008_Mossong_POLYMOD_dictionary.xls"
## [4] "/Users/runner/Library/Application Support/org.R-project.R/R/contactsurveys/2008_Mossong_POLYMOD_hh_extra.csv"
## [5] "/Users/runner/Library/Application Support/org.R-project.R/R/contactsurveys/2008_Mossong_POLYMOD_participant_common.csv"
## [6] "/Users/runner/Library/Application Support/org.R-project.R/R/contactsurveys/2008_Mossong_POLYMOD_participant_extra.csv"
## [7] "/Users/runner/Library/Application Support/org.R-project.R/R/contactsurveys/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().
##
## Attaching package: 'socialmixr'
## The following objects are masked from 'package:contactsurveys':
##
## download_survey, get_citation, list_surveys
polymod_loaded <- load_survey(polymod_survey_files)
uk_contact_matrix <- contact_matrix(
polymod_loaded,
countries = "United Kingdom",
age.limits = c(0, 18, 65)
)## Removing participants that have contacts without age information.
## ℹ To change this behaviour, set the 'missing.contact.age' option.
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 0.0553907Contributors
All contributions to this project are gratefully acknowledged using the allcontributors package following the allcontributors specification. Contributions of any kind are welcome!