Checks that a survey fulfills all the requirements to work with the 'contact_matrix' function
Usage
as_contact_survey(
x,
id_column = "part_id",
country_column = NULL,
year_column = NULL,
...,
id.column = deprecated(),
country.column = deprecated(),
year.column = deprecated()
)Arguments
- x
list containing
an element named 'participants', a data frame containing participant information
an element named 'contacts', a data frame containing contact information
(optionally) an element named 'reference, a list containing information information needed to reference the survey, in particular it can contain$a "title", "bibtype", "author", "doi", "publisher", "note", "year"
- id_column
the column in both the
participantsandcontactsdata frames that links contacts to participants- country_column
the column in the
participantsdata frame containing the country in which the participant was queried; if NULL (default), will use "country" column if present- year_column
the column in the
participantsdata frame containing the year in which the participant was queried; if NULL (default), will use "year" column if present- ...
additional arguments (currently ignored)
- id.column, country.column, year.column
![[Deprecated]](figures/lifecycle-deprecated.svg)
Use the underscore versions
(e.g., id_column) instead.
Examples
data(polymod)
as_contact_survey(polymod)
#> $participants
#> Key: <hh_id>
#> hh_id part_id part_gender part_occupation part_occupation_detail
#> <char> <int> <char> <int> <int>
#> 1: Mo08HH1 1 F 5 7
#> 2: Mo08HH10 10 F 6 7
#> 3: Mo08HH100 100 M 5 NA
#> 4: Mo08HH1000 1000 F 1 8
#> 5: Mo08HH1001 1001 M 1 8
#> ---
#> 7286: Mo08HH995 995 M 4 8
#> 7287: Mo08HH996 996 F 3 6
#> 7288: Mo08HH997 997 F 5 NA
#> 7289: Mo08HH998 998 M 4 7
#> 7290: Mo08HH999 999 M 1 7
#> part_education part_education_length participant_school_year
#> <int> <int> <int>
#> 1: 3 13 NA
#> 2: 5 16 NA
#> 3: 6 18 NA
#> 4: 2 12 NA
#> 5: 2 12 NA
#> ---
#> 7286: 2 12 NA
#> 7287: 2 12 NA
#> 7288: 1 10 NA
#> 7289: 2 12 NA
#> 7290: 2 12 NA
#> participant_nationality child_care child_care_detail child_relationship
#> <char> <char> <int> <int>
#> 1: IT Y NA 2
#> 2: IT N NA 1
#> 3: IT Y NA 1
#> 4: Y NA NA
#> 5: Y NA 2
#> ---
#> 7286: Y NA 1
#> 7287: Y NA 1
#> 7288: Y NA 1
#> 7289: Y NA 1
#> 7290: Y NA 2
#> child_nationality problems diary_how diary_missed_unsp diary_missed_skin
#> <char> <char> <int> <int> <int>
#> 1: IT N 2 2 NA
#> 2: IT N 1 1 NA
#> 3: IT N 2 1 NA
#> 4: 1 NA NA
#> 5: NA NA NA
#> ---
#> 7286: NA NA NA
#> 7287: 1 NA NA
#> 7288: 1 NA NA
#> 7289: 1 NA NA
#> 7290: 1 NA NA
#> diary_missed_noskin sday_id type day month year dayofweek hh_age_1
#> <int> <int> <int> <int> <int> <int> <int> <int>
#> 1: NA 20060525 3 25 5 2006 4 8
#> 2: NA 20060525 3 25 5 2006 4 0
#> 3: NA 20060526 3 26 5 2006 5 2
#> 4: NA 20060612 3 12 6 2006 1 7
#> 5: NA 20060522 3 22 5 2006 1 7
#> ---
#> 7286: NA 20060618 3 18 6 2006 0 8
#> 7287: NA 20060117 3 17 1 2006 2 7
#> 7288: NA 20060618 3 18 6 2006 0 7
#> 7289: NA 20060706 3 6 7 2006 4 7
#> 7290: NA 20060612 3 12 6 2006 1 1
#> hh_age_2 hh_age_3 hh_age_4 hh_age_5 hh_age_6 hh_age_7 hh_age_8 hh_age_9
#> <int> <int> <int> <int> <int> <int> <int> <int>
#> 1: 42 NA NA NA NA NA NA NA
#> 2: 3 40 NA NA NA NA NA NA
#> 3: 5 8 44 NA NA NA NA NA
#> 4: 32 NA NA NA NA NA NA NA
#> 5: 14 37 41 NA NA NA NA NA
#> ---
#> 7286: 14 15 44 NA NA NA NA NA
#> 7287: 16 40 NA NA NA NA NA NA
#> 7288: 11 15 40 44 NA NA NA NA
#> 7289: 22 48 50 NA NA NA NA NA
#> 7290: 7 25 29 NA NA NA NA NA
#> hh_age_10 hh_age_11 hh_age_12 hh_age_13 hh_age_14 hh_age_15 hh_age_16
#> <int> <int> <int> <int> <int> <int> <lgcl>
#> 1: NA NA NA NA NA NA NA
#> 2: NA NA NA NA NA NA NA
#> 3: NA NA NA NA NA NA NA
#> 4: NA NA NA NA NA NA NA
#> 5: NA NA NA NA NA NA NA
#> ---
#> 7286: NA NA NA NA NA NA NA
#> 7287: NA NA NA NA NA NA NA
#> 7288: NA NA NA NA NA NA NA
#> 7289: NA NA NA NA NA NA NA
#> 7290: NA NA NA NA NA NA NA
#> hh_age_17 hh_age_18 hh_age_19 hh_age_20 class_size country hh_size
#> <lgcl> <lgcl> <lgcl> <lgcl> <int> <fctr> <int>
#> 1: NA NA NA NA NA Italy 3
#> 2: NA NA NA NA NA Italy 4
#> 3: NA NA NA NA NA Italy 5
#> 4: NA NA NA NA 22 Germany 2
#> 5: NA NA NA NA 22 Germany 4
#> ---
#> 7286: NA NA NA NA 15 Germany 4
#> 7287: NA NA NA NA 9 Germany 3
#> 7288: NA NA NA NA 28 Germany 5
#> 7289: NA NA NA NA 21 Germany 4
#> 7290: NA NA NA NA 30 Germany 4
#> part_age_exact
#> <int>
#> 1: 8
#> 2: 3
#> 3: 5
#> 4: 7
#> 5: 7
#> ---
#> 7286: 7
#> 7287: 7
#> 7288: 7
#> 7289: 7
#> 7290: 7
#>
#> $contacts
#> cont_id part_id cnt_age_exact cnt_age_est_min cnt_age_est_max cnt_gender
#> <int> <int> <int> <int> <int> <char>
#> 1: 1 1 42 NA NA F
#> 2: 2 1 9 NA NA F
#> 3: 3 1 NA 40 45 F
#> 4: 4 1 8 NA NA F
#> 5: 5 1 NA 28 30 F
#> ---
#> 97900: 97900 8001 11 NA NA F
#> 97901: 97901 8001 3 NA NA M
#> 97902: 97902 8001 43 NA NA F
#> 97903: 97903 8001 33 NA NA F
#> 97904: 97904 8001 15 NA NA F
#> cnt_home cnt_work cnt_school cnt_transport cnt_leisure cnt_otherplace
#> <int> <int> <int> <int> <int> <int>
#> 1: 1 0 0 0 0 0
#> 2: 0 0 1 0 0 0
#> 3: 0 0 0 0 1 0
#> 4: 0 0 1 0 0 0
#> 5: 0 0 1 0 0 0
#> ---
#> 97900: 1 0 0 0 0 0
#> 97901: 1 0 0 0 0 0
#> 97902: 1 0 0 0 0 0
#> 97903: 0 0 0 0 0 1
#> 97904: 0 0 0 0 1 0
#> frequency_multi phys_contact duration_multi
#> <int> <int> <int>
#> 1: 1 1 4
#> 2: 1 1 5
#> 3: 3 1 4
#> 4: 1 1 5
#> 5: 2 1 3
#> ---
#> 97900: 1 1 5
#> 97901: 1 1 5
#> 97902: 1 1 5
#> 97903: 4 1 3
#> 97904: 3 1 4
#>
#> $reference
#> $reference$title
#> [1] "POLYMOD social contact data"
#>
#> $reference$bibtype
#> [1] "Misc"
#>
#> $reference$author
#> [1] "Joël Mossong" "Niel Hens"
#> [3] "Mark Jit" "Philippe Beutels"
#> [5] "Kari Auranen" "Rafael Mikolajczyk"
#> [7] "Marco Massari" "Stefania Salmaso"
#> [9] "Gianpaolo Scalia Tomba" "Jacco Wallinga"
#> [11] "Janneke Heijne" "Malgorzata Sadkowska-Todys"
#> [13] "Magdalena Rosinska" "W. John Edmunds"
#>
#> $reference$year
#> [1] 2017
#>
#> $reference$note
#> [1] "Version 1.1"
#>
#> $reference$doi
#> [1] "10.5281/zenodo.1157934"
#>
#>
#> attr(,"class")
#> [1] "contact_survey"