Downloads survey data. Uses a caching mechanism via the default
argument for directory.
Usage
download_survey(
survey,
directory = contactsurveys_dir(),
verbose = TRUE,
overwrite = FALSE,
timeout = 3600,
rate = purrr::rate_backoff(pause_base = 5, max_times = 4)
)Arguments
- survey
A DOI of a survey, (see
list_surveys()). If a HTML link is given, the DOI will be isolated and used.- directory
Directory of where to save survey files. The default value is to use the directory for your system using
contactsurveys_dir(), which usestools::R_user_dir(), and appends the survey URL/DOI basename as a new directory. E.g., if you provide in thesurveyargument, "10.5281/zenodo.1095664", it will save the surveys into a directoryzenodo.1095664undercontactsurveys_dir()This effectively caches the data. You can specify your own directory, or set an environment variable,CONTACTSURVEYS_HOME, seeSys.setenv()or Renviron for more detail. If this argument is set to something other thancontactsurveys_dir(), a warning is issued to discourage unnecessary downloads outside the persistent cache. Note that identical content accessed via different identifiers (e.g., DOI vs. a resolved record URL) will be cached in separate directories by design.- verbose
Whether downloads should be echoed to output. Default TRUE.
- overwrite
If files should be overwritten if they already exist. Default FALSE
- timeout
A numeric value specifying timeout in seconds. Default 3600 seconds.
- rate
a purrr rate object, to facilitate downloading if the download fails. Defaults to an exponential backoff of 5 seconds (up to 4 attempts: 1 initial + 3 retries) changed by specifying your own rate object, see
?purrr::rate_backoff()for details.
Examples
# \donttest{
list_surveys()
#> ℹ Downloading survey list from zenodo
#> ✔ Downloading survey list from zenodo [5.4s]
#>
#> Key: <date_added>
#> date_added
#> <char>
#> 1: 2017-11-07
#> 2: 2017-12-07
#> 3: 2017-12-22
#> 4: 2018-01-23
#> 5: 2018-02-05
#> 6: 2018-06-14
#> 7: 2018-09-05
#> 8: 2019-01-24
#> 9: 2019-08-13
#> 10: 2019-09-16
#> 11: 2020-08-06
#> 12: 2020-09-30
#> 13: 2020-09-30
#> 14: 2020-10-12
#> 15: 2020-10-16
#> 16: 2021-05-06
#> 17: 2021-05-20
#> 18: 2021-05-25
#> 19: 2021-06-07
#> 20: 2021-06-29
#> 21: 2021-06-29
#> 22: 2021-06-29
#> 23: 2021-06-29
#> 24: 2021-06-29
#> 25: 2021-06-29
#> 26: 2021-07-03
#> 27: 2021-07-26
#> 28: 2021-07-26
#> 29: 2021-08-20
#> 30: 2022-04-11
#> 31: 2022-05-10
#> 32: 2022-05-10
#> 33: 2022-05-10
#> 34: 2022-05-10
#> 35: 2022-05-12
#> 36: 2022-05-12
#> 37: 2022-05-12
#> 38: 2022-08-22
#> 39: 2023-03-13
#> 40: 2023-05-24
#> 41: 2023-07-07
#> 42: 2024-03-05
#> 43: 2024-05-08
#> 44: 2024-07-27
#> 45: 2025-01-30
#> date_added
#> title
#> <char>
#> 1: POLYMOD social contact data
#> 2: Social contact data for Peru
#> 3: Social contact data for Zimbabwe
#> 4: Social contact data for France
#> 5: Social contact data for Hong Kong
#> 6: Social contact data for Vietnam
#> 7: Social contact data for UK
#> 8: Social contact data for Zambia and South Africa (CODA dataset)
#> 9: Social contact data for China mainland
#> 10: Social contact data for Russia
#> 11: CoMix social contact data (Belgium )
#> 12: Social contact data for Belgium (2010-2011)
#> 13: Social contact data for Belgium (2006)
#> 14: Social contact data before and during COVID-19 in China
#> 15: Social contact data for Thailand
#> 16: Social contact data for Thailand (2015)
#> 17: CoMix social contact data (Austria)
#> 18: CoMix social contact data (Netherlands)
#> 19: CoMix social contact data (UK)
#> 20: CoMix social contact data (Denmark)
#> 21: CoMix social contact data (Spain)
#> 22: CoMix social contact data (France)
#> 23: CoMix social contact data (Italy)
#> 24: CoMix social contact data (Portugal)
#> 25: CoMix social contact data (Poland)
#> 26: Social contact data for the Netherlands
#> 27: CoMix social contact data (Greece)
#> 28: CoMix social contact data (Slovenia)
#> 29: Social contact data for IDPs in Somaliland (2019)
#> 30: Social contact data for Taiwan
#> 31: CoMix social contact data (Croatia)
#> 32: CoMix social contact data (Slovakia)
#> 33: CoMix social contact data (Hungary)
#> 34: CoMix social contact data (Estonia)
#> 35: CoMix social contact data (Lithuania)
#> 36: CoMix social contact data (Finland)
#> 37: CoMix social contact data (Switzerland)
#> 38: CoMix 2.0 social contact data
#> 39: Contact data of older adults (70+) in the Netherlands in 2021
#> 40: Household contact survey (Belgium)
#> 41: Contact data of Children in Belgium, Italy and Poland
#> 42: Contact data of Pienter3 (2016-2017) and PiCo (2020-2023) studies in the Netherlands
#> 43: CoMix data (last round in BE, CH, NL and UK)
#> 44: Social contact data for the BHDSS and FWHDSS in the Gambia (2022)
#> 45: Social mixing patterns of United States health care personnel at a quaternary health center
#> title
#> creator url
#> <char> <char>
#> 1: Joël Mossong https://doi.org/10.5281/zenodo.3874557
#> 2: Carlos G. Grijalva https://doi.org/10.5281/zenodo.3874805
#> 3: Alessia Melegaro https://doi.org/10.5281/zenodo.3886638
#> 4: Guillaume Béraud https://doi.org/10.5281/zenodo.3886590
#> 5: Kathy Leung https://doi.org/10.5281/zenodo.3874808
#> 6: Horby Peter https://doi.org/10.5281/zenodo.3874802
#> 7: Albert Jan van Hoek https://doi.org/10.5281/zenodo.3874717
#> 8: Peter J. Dodd https://doi.org/10.5281/zenodo.3874675
#> 9: Zhang, Juanjuan https://doi.org/10.5281/zenodo.3878754
#> 10: Maria Litvinova https://doi.org/10.5281/zenodo.3874674
#> 11: Pietro Coletti https://doi.org/10.5281/zenodo.10549953
#> 12: Willem Lander https://doi.org/10.5281/zenodo.4302055
#> 13: Hens Niel https://doi.org/10.5281/zenodo.4059864
#> 14: Zhang Juanjuan https://doi.org/10.5281/zenodo.7326686
#> 15: Mahikul Wiriya https://doi.org/10.5281/zenodo.4086739
#> 16: Weerasak Putthasri https://doi.org/10.5281/zenodo.4739777
#> 17: Gimma, Amy https://doi.org/10.5281/zenodo.6362906
#> 18: Backer, Jantien https://doi.org/10.5281/zenodo.7276465
#> 19: Gimma, Amy https://doi.org/10.5281/zenodo.13684044
#> 20: Gimma, Amy https://doi.org/10.5281/zenodo.6362899
#> 21: Gimma, Amy https://doi.org/10.5281/zenodo.6362898
#> 22: Gimma, Amy https://doi.org/10.5281/zenodo.6362893
#> 23: Gimma, Amy https://doi.org/10.5281/zenodo.6362888
#> 24: Gimma, Amy https://doi.org/10.5281/zenodo.6362887
#> 25: Gimma, Amy https://doi.org/10.5281/zenodo.6362879
#> 26: van de Kassteele, Jan https://doi.org/10.5281/zenodo.5062244
#> 27: Gimma, Amy https://doi.org/10.5281/zenodo.6362870
#> 28: Gimma, Amy https://doi.org/10.5281/zenodo.6362865
#> 29: van Zandvoort, Kevin https://doi.org/10.5281/zenodo.7071876
#> 30: Fu, Yang-Chih https://doi.org/10.5281/zenodo.6385759
#> 31: Gimma, Amy https://doi.org/10.5281/zenodo.7257433
#> 32: Gimma, Amy https://doi.org/10.5281/zenodo.6535357
#> 33: Gimma, Amy https://doi.org/10.5281/zenodo.6535344
#> 34: Gimma, Amy https://doi.org/10.5281/zenodo.6535313
#> 35: Gimma, Amy https://doi.org/10.5281/zenodo.6542668
#> 36: Gimma, Amy https://doi.org/10.5281/zenodo.6542664
#> 37: Gimma, Amy https://doi.org/10.5281/zenodo.6542657
#> 38: Coletti, Pietro https://doi.org/10.5281/zenodo.7331926
#> 39: Jantien A. Backer https://doi.org/10.5281/zenodo.7751724
#> 40: Goeyvaerts, Nele https://doi.org/10.5281/zenodo.7965594
#> 41: Coletti,Pietro https://doi.org/10.5281/zenodo.8123632
#> 42: Backer, Jantien https://doi.org/10.5281/zenodo.10370353
#> 43: Jarvis, Christopher https://doi.org/10.5281/zenodo.11154066
#> 44: Osei, Isaac https://doi.org/10.5281/zenodo.13101862
#> 45: Pischel, Lauren https://doi.org/10.5281/zenodo.14156576
#> creator url
peru_survey <- download_survey("https://doi.org/10.5281/zenodo.1095664")
#> Fetching contact survey filenames from: https://doi.org/10.5281/zenodo.1095664.
#> ✔ Successfully fetched list of published records!
#> ! No record for DOI '10.5281/zenodo.1095664'!
#> ℹ Try to get deposition by Zenodo specific record id '1095664'
#> ✔ Successfully fetched list of published records!
#> ! No record for id '1095664'!
#> ℹ Successfully fetched list of published records - page 1
#> ✔ Successfully fetched list of published records!
#> ✔ Successfully fetched published record for concept DOI '10.5281/zenodo.1095664'!
#> Downloading from https://doi.org/10.5281/zenodo.1095664.
#> ! Overwrite is 'false', aborting download of existing files
#> ℹ Download in sequential mode
#> [zen4R][INFO] ZenodoRecord - Download in sequential mode
#> ℹ Will download 7 files from record '3874805' (doi: '10.5281/zenodo.3874805') - total size: 760.6 KiB
#> [zen4R][INFO] ZenodoRecord - Will download 7 files from record '3874805' (doi: '10.5281/zenodo.3874805') - total size: 760.6 KiB
#> ℹ Downloading file '2015_Grijalva_Peru_sday.csv' - size: 16 KiB
#> [zen4R][INFO] Downloading file '2015_Grijalva_Peru_sday.csv' - size: 16 KiB
#> ℹ Downloading file '2015_Grijalva_Peru_participant_common.csv' - size: 11.3 KiB
#> [zen4R][INFO] Downloading file '2015_Grijalva_Peru_participant_common.csv' - size: 11.3 KiB
#> ℹ Downloading file '2015_Grijalva_Peru_hh_extra.csv' - size: 27 KiB
#> [zen4R][INFO] Downloading file '2015_Grijalva_Peru_hh_extra.csv' - size: 27 KiB
#> ℹ Downloading file '2015_Grijalva_Peru_hh_common.csv' - size: 1.5 KiB
#> [zen4R][INFO] Downloading file '2015_Grijalva_Peru_hh_common.csv' - size: 1.5 KiB
#> ℹ Downloading file '2015_Grijalva_Peru_dictionary.xls' - size: 32.5 KiB
#> [zen4R][INFO] Downloading file '2015_Grijalva_Peru_dictionary.xls' - size: 32.5 KiB
#> ℹ Downloading file '2015_Grijalva_Peru_contact_common.csv' - size: 617.3 KiB
#> [zen4R][INFO] Downloading file '2015_Grijalva_Peru_contact_common.csv' - size: 617.3 KiB
#> ℹ Downloading file '2015_Grijalva_Peru_participant_extra.csv' - size: 55 KiB
#> [zen4R][INFO] Downloading file '2015_Grijalva_Peru_participant_extra.csv' - size: 55 KiB
#> ℹ Files downloaded at '/home/runner/.local/share/R/contactsurveys/zenodo.1095664'.
#> [zen4R][INFO] Files downloaded at '/home/runner/.local/share/R/contactsurveys/zenodo.1095664'.
#> ℹ Verifying file integrity...
#> [zen4R][INFO] ZenodoRecord - Verifying file integrity...
#> ℹ File '2015_Grijalva_Peru_sday.csv': integrity verified (md5sum: b43c28fa6cce8d7bd6ec6b0621aa5b02)
#> [zen4R][INFO] File '2015_Grijalva_Peru_sday.csv': integrity verified (md5sum: b43c28fa6cce8d7bd6ec6b0621aa5b02)
#> ℹ File '2015_Grijalva_Peru_participant_common.csv': integrity verified (md5sum: dada729474938c5ed593fc824f98fff9)
#> [zen4R][INFO] File '2015_Grijalva_Peru_participant_common.csv': integrity verified (md5sum: dada729474938c5ed593fc824f98fff9)
#> ℹ File '2015_Grijalva_Peru_hh_extra.csv': integrity verified (md5sum: ad68e9171a547a0634998f413c02464d)
#> [zen4R][INFO] File '2015_Grijalva_Peru_hh_extra.csv': integrity verified (md5sum: ad68e9171a547a0634998f413c02464d)
#> ℹ File '2015_Grijalva_Peru_hh_common.csv': integrity verified (md5sum: a86d50476a603f7633de8f30959b6b03)
#> [zen4R][INFO] File '2015_Grijalva_Peru_hh_common.csv': integrity verified (md5sum: a86d50476a603f7633de8f30959b6b03)
#> ℹ File '2015_Grijalva_Peru_dictionary.xls': integrity verified (md5sum: 4c43fb5e299090740663db093823fdd9)
#> [zen4R][INFO] File '2015_Grijalva_Peru_dictionary.xls': integrity verified (md5sum: 4c43fb5e299090740663db093823fdd9)
#> ℹ File '2015_Grijalva_Peru_contact_common.csv': integrity verified (md5sum: 50dcb17f306aa7c62846351c5019bdad)
#> [zen4R][INFO] File '2015_Grijalva_Peru_contact_common.csv': integrity verified (md5sum: 50dcb17f306aa7c62846351c5019bdad)
#> ℹ File '2015_Grijalva_Peru_participant_extra.csv': integrity verified (md5sum: 4d7044f954db6a83ee1b9bcc95b24cfa)
#> [zen4R][INFO] File '2015_Grijalva_Peru_participant_extra.csv': integrity verified (md5sum: 4d7044f954db6a83ee1b9bcc95b24cfa)
#> ✔ End of download
#> [zen4R][INFO] ZenodoRecord - End of download
# }