Nothing
tests/testthat/_snaps/matrix.md
In socialmixr: Social Mixing Matrices for Infectious Disease Modelling
contact matrices look as expected
Code
contacts
Output
$test1
$test1$matrix
contact.age.group
age.group [0,5) [5,10) [10,15) [15,20) [20,25) [25,30)
[0,5) 178.966087 88.880184 45.354727 30.972284 42.6051270 74.733934
[5,10) 66.232016 668.044656 134.274185 35.203096 31.4355346 66.434003
[10,15) 42.023723 111.436616 688.396514 103.714503 22.1280347 44.956109
[15,20) 24.673006 78.346794 158.510591 700.280260 97.5761783 77.930858
[20,25) 26.973497 35.707872 15.991597 93.248381 152.7117404 76.040717
[25,30) 43.200207 43.480995 18.063760 42.873620 88.9892562 107.950930
[30,35) 40.425052 56.416277 28.910736 24.861596 45.4570091 57.681248
[35,40) 57.413396 96.817442 53.334831 39.057969 44.1828453 49.687374
[40,45) 14.841394 55.860697 61.956371 53.157270 47.6076053 45.907692
[45,50) 12.023640 8.993476 37.232448 63.569833 48.1737784 46.208130
[50,55) 24.897017 19.732155 21.398703 46.303262 58.2690366 58.172490
[55,60) 11.463500 12.454714 24.118950 16.234386 33.0913231 46.499652
[60,65) 13.095699 32.832242 17.740504 13.131377 35.0665384 43.906001
[65,70) 7.009383 13.174960 11.319417 13.157194 10.0526235 19.717793
[70,75) 3.046779 2.949233 8.945245 15.924334 9.6280647 9.140336
[75,80) 0.000000 2.137842 1.068921 3.110274 0.9724316 1.068921
[80,Inf) 0.000000 0.000000 0.000000 0.000000 0.0000000 0.000000
contact.age.group
age.group [30,35) [35,40) [40,45) [45,50) [50,55) [55,60)
[0,5) 91.708976 95.882802 51.956159 27.5221001 30.779454 29.361522
[5,10) 108.803439 100.314642 102.291590 54.9530408 38.811919 20.808874
[10,15) 63.258912 127.846712 115.751398 58.3753992 40.509099 25.514605
[15,20) 52.068678 113.778963 98.589173 81.3480282 42.672234 34.694509
[20,25) 51.094350 44.650806 43.261966 57.6368055 25.722105 23.020902
[25,30) 69.506069 55.360694 51.309724 54.4364839 49.972141 30.754586
[30,35) 99.809224 91.659424 48.732356 34.1893655 35.866531 40.608316
[35,40) 61.866181 104.774182 86.462595 55.7946573 42.695162 37.111034
[40,45) 61.971992 81.658609 84.170188 82.6206655 43.740523 33.866735
[45,50) 49.432321 59.367926 69.586529 102.0096136 51.387754 27.667104
[50,55) 61.170361 55.261460 58.258871 39.5785652 48.739562 54.806600
[55,60) 33.424551 36.774400 36.345039 42.6153774 56.419796 62.962663
[60,65) 49.981599 66.335051 61.743763 40.0468592 38.810582 55.694066
[65,70) 17.141104 26.737375 22.039887 15.8129795 14.819010 22.646402
[70,75) 4.029856 2.949233 20.149282 15.9243343 10.025868 7.962167
[75,80) 3.206763 3.110274 4.082705 0.9724316 7.096489 2.041353
[80,Inf) 0.000000 0.000000 0.000000 0.0000000 0.000000 0.000000
contact.age.group
age.group [60,65) [65,70) [70,75) [75,80) [80,Inf)
[0,5) 24.677783 8.727480 9.909679 2.993785 0.000000
[5,10) 25.803873 11.048926 6.071756 4.959343 4.094807
[10,15) 18.924121 11.851619 10.258733 7.282992 3.982674
[15,20) 24.902552 21.186852 4.887084 4.966279 1.074401
[20,25) 11.156829 11.025208 4.056875 8.113749 2.037269
[25,30) 20.230725 13.096621 5.962517 0.000000 4.007345
[30,35) 23.553124 7.798386 5.067440 3.117843 1.071522
[35,40) 27.499796 20.825517 15.028551 8.346657 6.186883
[40,45) 29.207953 14.039942 12.903832 7.134775 10.833673
[45,50) 29.816565 6.941030 12.314681 15.053803 12.314681
[50,55) 26.754035 13.911797 17.707294 5.995743 10.975055
[55,60) 41.949384 15.278607 10.217936 7.007663 23.503946
[60,65) 43.217595 23.798264 13.034119 6.958521 10.976500
[65,70) 22.812626 19.057977 9.023120 3.025473 8.003353
[70,75) 11.876586 17.988035 12.780010 13.958179 4.915388
[75,80) 5.151626 0.000000 1.068921 3.986216 1.944863
[80,Inf) 0.000000 0.000000 0.000000 0.000000 0.000000
$test1$participants
age.group participants proportion
<char> <int> <num>
1: [0,5) 95 0.093966370
2: [5,10) 102 0.100890208
3: [10,15) 102 0.100890208
4: [15,20) 105 0.103857567
5: [20,25) 59 0.058358061
6: [25,30) 59 0.058358061
7: [30,35) 60 0.059347181
8: [35,40) 70 0.069238378
9: [40,45) 62 0.061325420
10: [45,50) 55 0.054401583
11: [50,55) 66 0.065281899
12: [55,60) 54 0.053412463
13: [60,65) 66 0.065281899
14: [65,70) 27 0.026706231
15: [70,75) 22 0.021760633
16: [75,80) 7 0.006923838
17: [80,Inf) 0 0.000000000
$test2
$test2$matrix
contact.age.group
age.group [0,5) [5,Inf)
[0,5) 1.5429448 7.027931
[5,Inf) 0.3673316 13.474102
$test2$demography
age.group population proportion year
<char> <num> <num> <int>
1: [0,5) 13498647 0.04967121 2005
2: [5,Inf) 258261321 0.95032879 2005
$test2$participants
age.group participants proportion
<char> <int> <num>
1: [0,5) 654 0.0908712
2: [5,Inf) 6543 0.9091288
$test3
$test3$mean.contacts
[1] 3.887154
$test3$normalisation
[1] 1.021167
$test3$contacts
[1] 1.0973166 1.4632281 0.9342813
$test3$matrix
contact.age.group
age.group [0,5) [5,10) [10,Inf)
[0,5) 1.769367 1.836114 0.8815070
[5,10) 1.376954 2.441012 0.8642004
[10,Inf) 1.035333 1.353471 0.9708081
$test3$demography
age.group population proportion year
<char> <num> <num> <int>
1: [0,5) 1271578 0.06282841 2005
2: [5,10) 1329536 0.06569210 2005
3: [10,Inf) 17637787 0.87147948 2005
$test3$participants
age.group participants proportion
<char> <int> <num>
1: [0,5) 95 0.09396637
2: [5,10) 102 0.10089021
3: [10,Inf) 814 0.80514342
$test4
$test4$matrix
contact.age.group
age.group [0,5) [5,15) [15,Inf)
[0,5) 0.0000000 2.019697 3.087121
[5,15) 0.9217259 7.579330 27.392285
[15,Inf) 0.1822259 3.542984 7.130996
$test4$demography
age.group population proportion year
<char> <num> <num> <int>
1: [0,5) 13498647 0.04967121 2005
2: [5,15) 29578398 0.10884016 2005
3: [15,Inf) 228682923 0.84148863 2005
$test4$participants
age.group participants proportion
<char> <int> <num>
1: [0,5) 660 0.09134948
2: [5,15) 1374 0.19017301
3: [15,Inf) 5191 0.71847751
survey argument is validated
Code
contact_matrix(survey = "bogus")
Condition
Error in `contact_matrix()`:
! `survey` must be a survey object (created using `survey()` or `get_survey()`).
error is thrown if age limits are non-numeric
Code
contact_matrix(survey = polymod, age_limits = c(0, 5, "fifteen"))
Condition
Warning in `check_age_limits_increasing()`:
NAs introduced by coercion
Error in `contact_matrix()`:
! `<int>` must be an increasing integer vector of lower age limits.
i We see: 0, 5, and NA
error is thrown if country is not found
Code
contact_matrix(survey = polymod, countries = c("Italy", "Zamonia"))
Condition
Error in `flexible_countrycode()`:
! Survey data not found for: "Zamonia".
warning is thrown if filter column is not found
Filter column: "test" not found.
warning is thrown if missing data exist
Automatic country population lookup in `contact_matrix()` was deprecated in socialmixr 0.6.0.
When `countries` is given (or a `country` column is present) without `survey_pop`, contact_matrix() currently calls the soft-deprecated `wpp_age()` to look up population data. This automatic lookup will be removed in a future release: callers will then have to supply `survey_pop` whenever `symmetric`, `split`, `per_capita`, `weigh_age`, or `return_demography` is TRUE.
i Pass `survey_pop` explicitly to silence this warning, e.g. `survey_pop = survey_country_population(survey, countries)` or a data frame from the wpp2024 package.
error is thrown if an unknown argument is passed
Code
contact_matrix(dummy = "test")
Condition
Error in `check_arg_dots_in()`:
! Unknown argument: "dummy".
error is thrown if invalid age limits are passed
Code
contact_matrix(survey = polymod, age_limits = c(13, 11))
Condition
Error in `contact_matrix()`:
! `<int>` must be an increasing integer vector of lower age limits.
i We see: 13 and 11
error if no participants after selecting the country
Code
contact_matrix(survey = polymod, countries = "Romania")
Condition
Error in `filter_countries()`:
! No participants left after selecting countries: "Romania"
warning if population needed but no 'year' column
Automatic country population lookup in `contact_matrix()` was deprecated in socialmixr 0.6.0.
When `countries` is given (or a `country` column is present) without `survey_pop`, contact_matrix() currently calls the soft-deprecated `wpp_age()` to look up population data. This automatic lookup will be removed in a future release: callers will then have to supply `survey_pop` whenever `symmetric`, `split`, `per_capita`, `weigh_age`, or `return_demography` is TRUE.
i Pass `survey_pop` explicitly to silence this warning, e.g. `survey_pop = survey_country_population(survey, countries)` or a data frame from the wpp2024 package.
warning if day of week weigh requested but not present
`weigh_dayofweek` is "TRUE", but no `dayofweek` column in the data.
i Will ignore.
warning is thrown if country has no survey population
Code
contact_matrix(survey = polymod5, symmetric = TRUE)
Condition
Warning:
Automatic country population lookup in `contact_matrix()` was deprecated in socialmixr 0.6.0.
When `countries` is given (or a `country` column is present) without `survey_pop`, contact_matrix() currently calls the soft-deprecated `wpp_age()` to look up population data. This automatic lookup will be removed in a future release: callers will then have to supply `survey_pop` whenever `symmetric`, `split`, `per_capita`, `weigh_age`, or `return_demography` is TRUE.
i Pass `survey_pop` explicitly to silence this warning, e.g. `survey_pop = survey_country_population(survey, countries)` or a data frame from the wpp2024 package.
Warning:
`wpp_age()` was deprecated in socialmixr 0.6.0.
Pass population data directly via the {.arg survey_pop} argument instead.
i The underlying {.pkg wpp2017} data is also outdated; use {.pkg wpp2024} from GitHub for more recent data.
Error in `survey_pop_from_countries()`:
! Could not find population data for: "Zamonia".
i Pass population data directly via the `survey_pop` argument.
warning is thrown if contact survey has no age information
Contact age column `cnt_age` or columns to estimate contact age (`cnt_age_exact` or `cnt_age_est_min` and `cnt_age_est_max`) do not exist in the contact data frame.
warning is thrown if participant data has no country
Country column `country` does not exist in the participant data frame.
check result is reported back
Code
check(x = polymod2)
Message
> Check OK.
good suggestions are made
Automatic country population lookup in `contact_matrix()` was deprecated in socialmixr 0.6.0.
When `countries` is given (or a `country` column is present) without `survey_pop`, contact_matrix() currently calls the soft-deprecated `wpp_age()` to look up population data. This automatic lookup will be removed in a future release: callers will then have to supply `survey_pop` whenever `symmetric`, `split`, `per_capita`, `weigh_age`, or `return_demography` is TRUE.
i Pass `survey_pop` explicitly to silence this warning, e.g. `survey_pop = survey_country_population(survey, countries)` or a data frame from the wpp2024 package.
Automatic country population lookup in `contact_matrix()` was deprecated in socialmixr 0.6.0.
When `countries` is given (or a `country` column is present) without `survey_pop`, contact_matrix() currently calls the soft-deprecated `wpp_age()` to look up population data. This automatic lookup will be removed in a future release: callers will then have to supply `survey_pop` whenever `symmetric`, `split`, `per_capita`, `weigh_age`, or `return_demography` is TRUE.
i Pass `survey_pop` explicitly to silence this warning, e.g. `survey_pop = survey_country_population(survey, countries)` or a data frame from the wpp2024 package.
Automatic country population lookup in `contact_matrix()` was deprecated in socialmixr 0.6.0.
When `countries` is given (or a `country` column is present) without `survey_pop`, contact_matrix() currently calls the soft-deprecated `wpp_age()` to look up population data. This automatic lookup will be removed in a future release: callers will then have to supply `survey_pop` whenever `symmetric`, `split`, `per_capita`, `weigh_age`, or `return_demography` is TRUE.
i Pass `survey_pop` explicitly to silence this warning, e.g. `survey_pop = survey_country_population(survey, countries)` or a data frame from the wpp2024 package.
nonsensical operations are warned about
Automatic country population lookup in `contact_matrix()` was deprecated in socialmixr 0.6.0.
When `countries` is given (or a `country` column is present) without `survey_pop`, contact_matrix() currently calls the soft-deprecated `wpp_age()` to look up population data. This automatic lookup will be removed in a future release: callers will then have to supply `survey_pop` whenever `symmetric`, `split`, `per_capita`, `weigh_age`, or `return_demography` is TRUE.
i Pass `survey_pop` explicitly to silence this warning, e.g. `survey_pop = survey_country_population(survey, countries)` or a data frame from the wpp2024 package.
Code
contact_matrix(survey = polymod, counts = TRUE, symmetric = TRUE, age_limits = c(
0, 5))
Condition
Warning:
Automatic country population lookup in `contact_matrix()` was deprecated in socialmixr 0.6.0.
When `countries` is given (or a `country` column is present) without `survey_pop`, contact_matrix() currently calls the soft-deprecated `wpp_age()` to look up population data. This automatic lookup will be removed in a future release: callers will then have to supply `survey_pop` whenever `symmetric`, `split`, `per_capita`, `weigh_age`, or `return_demography` is TRUE.
i Pass `survey_pop` explicitly to silence this warning, e.g. `survey_pop = survey_country_population(survey, countries)` or a data frame from the wpp2024 package.
Warning:
`wpp_age()` was deprecated in socialmixr 0.6.0.
Pass population data directly via the {.arg survey_pop} argument instead.
i The underlying {.pkg wpp2017} data is also outdated; use {.pkg wpp2024} from GitHub for more recent data.
Warning in `contact_matrix()`:
`symmetric = TRUE` does not make sense with `counts = TRUE`; will not make matrix symmetric.
Warning in `normalise_weighted_matrix()`:
Large differences in the size of the sub-populations with the current age breaks are likely to result in artefacts after making the matrix symmetric.
! Please reconsider the age breaks to obtain more equally sized sub-populations.
i Normalization factors: [0.2 and 5.1]
Output
$matrix
contact.age.group
age.group [0,5) [5,Inf)
[0,5) 1463.000 26710.24
[5,Inf) 1396.075 87824.00
$demography
age.group population proportion year
<char> <num> <num> <int>
1: [0,5) 13498647 0.04967121 2005
2: [5,Inf) 258261321 0.95032879 2005
$participants
age.group participants proportion
<char> <int> <num>
1: [0,5) 654 0.09085857
2: [5,Inf) 6544 0.90914143
Automatic country population lookup in `contact_matrix()` was deprecated in socialmixr 0.6.0.
When `countries` is given (or a `country` column is present) without `survey_pop`, contact_matrix() currently calls the soft-deprecated `wpp_age()` to look up population data. This automatic lookup will be removed in a future release: callers will then have to supply `survey_pop` whenever `symmetric`, `split`, `per_capita`, `weigh_age`, or `return_demography` is TRUE.
i Pass `survey_pop` explicitly to silence this warning, e.g. `survey_pop = survey_country_population(survey, countries)` or a data frame from the wpp2024 package.
warning if survey is assumed to be representative
No `survey.pop` or `countries` given, and no `country` column found in the data.
i I don't know which population this is from (assuming the survey is representative).
user-defined reference populations with open age groups
Code
contact_matrix(polymod_nocountry, age_limits = c(0, 18, 60), symmetric = TRUE,
survey_pop = "dummy")
Condition
Warning:
`wpp_age()` was deprecated in socialmixr 0.6.0.
Pass population data directly via the {.arg survey_pop} argument instead.
i The underlying {.pkg wpp2017} data is also outdated; use {.pkg wpp2024} from GitHub for more recent data.
Error in `survey_pop_from_countries()`:
! Could not find population data for: "dummy".
i Pass population data directly via the `survey_pop` argument.
symmetric matrices with large norm weights warn
Automatic country population lookup in `contact_matrix()` was deprecated in socialmixr 0.6.0.
When `countries` is given (or a `country` column is present) without `survey_pop`, contact_matrix() currently calls the soft-deprecated `wpp_age()` to look up population data. This automatic lookup will be removed in a future release: callers will then have to supply `survey_pop` whenever `symmetric`, `split`, `per_capita`, `weigh_age`, or `return_demography` is TRUE.
i Pass `survey_pop` explicitly to silence this warning, e.g. `survey_pop = survey_country_population(survey, countries)` or a data frame from the wpp2024 package.
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contact matrices look as expected
Code
contacts
Output
$test1
$test1$matrix
contact.age.group
age.group [0,5) [5,10) [10,15) [15,20) [20,25) [25,30)
[0,5) 178.966087 88.880184 45.354727 30.972284 42.6051270 74.733934
[5,10) 66.232016 668.044656 134.274185 35.203096 31.4355346 66.434003
[10,15) 42.023723 111.436616 688.396514 103.714503 22.1280347 44.956109
[15,20) 24.673006 78.346794 158.510591 700.280260 97.5761783 77.930858
[20,25) 26.973497 35.707872 15.991597 93.248381 152.7117404 76.040717
[25,30) 43.200207 43.480995 18.063760 42.873620 88.9892562 107.950930
[30,35) 40.425052 56.416277 28.910736 24.861596 45.4570091 57.681248
[35,40) 57.413396 96.817442 53.334831 39.057969 44.1828453 49.687374
[40,45) 14.841394 55.860697 61.956371 53.157270 47.6076053 45.907692
[45,50) 12.023640 8.993476 37.232448 63.569833 48.1737784 46.208130
[50,55) 24.897017 19.732155 21.398703 46.303262 58.2690366 58.172490
[55,60) 11.463500 12.454714 24.118950 16.234386 33.0913231 46.499652
[60,65) 13.095699 32.832242 17.740504 13.131377 35.0665384 43.906001
[65,70) 7.009383 13.174960 11.319417 13.157194 10.0526235 19.717793
[70,75) 3.046779 2.949233 8.945245 15.924334 9.6280647 9.140336
[75,80) 0.000000 2.137842 1.068921 3.110274 0.9724316 1.068921
[80,Inf) 0.000000 0.000000 0.000000 0.000000 0.0000000 0.000000
contact.age.group
age.group [30,35) [35,40) [40,45) [45,50) [50,55) [55,60)
[0,5) 91.708976 95.882802 51.956159 27.5221001 30.779454 29.361522
[5,10) 108.803439 100.314642 102.291590 54.9530408 38.811919 20.808874
[10,15) 63.258912 127.846712 115.751398 58.3753992 40.509099 25.514605
[15,20) 52.068678 113.778963 98.589173 81.3480282 42.672234 34.694509
[20,25) 51.094350 44.650806 43.261966 57.6368055 25.722105 23.020902
[25,30) 69.506069 55.360694 51.309724 54.4364839 49.972141 30.754586
[30,35) 99.809224 91.659424 48.732356 34.1893655 35.866531 40.608316
[35,40) 61.866181 104.774182 86.462595 55.7946573 42.695162 37.111034
[40,45) 61.971992 81.658609 84.170188 82.6206655 43.740523 33.866735
[45,50) 49.432321 59.367926 69.586529 102.0096136 51.387754 27.667104
[50,55) 61.170361 55.261460 58.258871 39.5785652 48.739562 54.806600
[55,60) 33.424551 36.774400 36.345039 42.6153774 56.419796 62.962663
[60,65) 49.981599 66.335051 61.743763 40.0468592 38.810582 55.694066
[65,70) 17.141104 26.737375 22.039887 15.8129795 14.819010 22.646402
[70,75) 4.029856 2.949233 20.149282 15.9243343 10.025868 7.962167
[75,80) 3.206763 3.110274 4.082705 0.9724316 7.096489 2.041353
[80,Inf) 0.000000 0.000000 0.000000 0.0000000 0.000000 0.000000
contact.age.group
age.group [60,65) [65,70) [70,75) [75,80) [80,Inf)
[0,5) 24.677783 8.727480 9.909679 2.993785 0.000000
[5,10) 25.803873 11.048926 6.071756 4.959343 4.094807
[10,15) 18.924121 11.851619 10.258733 7.282992 3.982674
[15,20) 24.902552 21.186852 4.887084 4.966279 1.074401
[20,25) 11.156829 11.025208 4.056875 8.113749 2.037269
[25,30) 20.230725 13.096621 5.962517 0.000000 4.007345
[30,35) 23.553124 7.798386 5.067440 3.117843 1.071522
[35,40) 27.499796 20.825517 15.028551 8.346657 6.186883
[40,45) 29.207953 14.039942 12.903832 7.134775 10.833673
[45,50) 29.816565 6.941030 12.314681 15.053803 12.314681
[50,55) 26.754035 13.911797 17.707294 5.995743 10.975055
[55,60) 41.949384 15.278607 10.217936 7.007663 23.503946
[60,65) 43.217595 23.798264 13.034119 6.958521 10.976500
[65,70) 22.812626 19.057977 9.023120 3.025473 8.003353
[70,75) 11.876586 17.988035 12.780010 13.958179 4.915388
[75,80) 5.151626 0.000000 1.068921 3.986216 1.944863
[80,Inf) 0.000000 0.000000 0.000000 0.000000 0.000000
$test1$participants
age.group participants proportion
<char> <int> <num>
1: [0,5) 95 0.093966370
2: [5,10) 102 0.100890208
3: [10,15) 102 0.100890208
4: [15,20) 105 0.103857567
5: [20,25) 59 0.058358061
6: [25,30) 59 0.058358061
7: [30,35) 60 0.059347181
8: [35,40) 70 0.069238378
9: [40,45) 62 0.061325420
10: [45,50) 55 0.054401583
11: [50,55) 66 0.065281899
12: [55,60) 54 0.053412463
13: [60,65) 66 0.065281899
14: [65,70) 27 0.026706231
15: [70,75) 22 0.021760633
16: [75,80) 7 0.006923838
17: [80,Inf) 0 0.000000000
$test2
$test2$matrix
contact.age.group
age.group [0,5) [5,Inf)
[0,5) 1.5429448 7.027931
[5,Inf) 0.3673316 13.474102
$test2$demography
age.group population proportion year
<char> <num> <num> <int>
1: [0,5) 13498647 0.04967121 2005
2: [5,Inf) 258261321 0.95032879 2005
$test2$participants
age.group participants proportion
<char> <int> <num>
1: [0,5) 654 0.0908712
2: [5,Inf) 6543 0.9091288
$test3
$test3$mean.contacts
[1] 3.887154
$test3$normalisation
[1] 1.021167
$test3$contacts
[1] 1.0973166 1.4632281 0.9342813
$test3$matrix
contact.age.group
age.group [0,5) [5,10) [10,Inf)
[0,5) 1.769367 1.836114 0.8815070
[5,10) 1.376954 2.441012 0.8642004
[10,Inf) 1.035333 1.353471 0.9708081
$test3$demography
age.group population proportion year
<char> <num> <num> <int>
1: [0,5) 1271578 0.06282841 2005
2: [5,10) 1329536 0.06569210 2005
3: [10,Inf) 17637787 0.87147948 2005
$test3$participants
age.group participants proportion
<char> <int> <num>
1: [0,5) 95 0.09396637
2: [5,10) 102 0.10089021
3: [10,Inf) 814 0.80514342
$test4
$test4$matrix
contact.age.group
age.group [0,5) [5,15) [15,Inf)
[0,5) 0.0000000 2.019697 3.087121
[5,15) 0.9217259 7.579330 27.392285
[15,Inf) 0.1822259 3.542984 7.130996
$test4$demography
age.group population proportion year
<char> <num> <num> <int>
1: [0,5) 13498647 0.04967121 2005
2: [5,15) 29578398 0.10884016 2005
3: [15,Inf) 228682923 0.84148863 2005
$test4$participants
age.group participants proportion
<char> <int> <num>
1: [0,5) 660 0.09134948
2: [5,15) 1374 0.19017301
3: [15,Inf) 5191 0.71847751
survey argument is validated
Code
contact_matrix(survey = "bogus")
Condition
Error in `contact_matrix()`:
! `survey` must be a survey object (created using `survey()` or `get_survey()`).
error is thrown if age limits are non-numeric
Code
contact_matrix(survey = polymod, age_limits = c(0, 5, "fifteen"))
Condition
Warning in `check_age_limits_increasing()`:
NAs introduced by coercion
Error in `contact_matrix()`:
! `<int>` must be an increasing integer vector of lower age limits.
i We see: 0, 5, and NA
error is thrown if country is not found
Code
contact_matrix(survey = polymod, countries = c("Italy", "Zamonia"))
Condition
Error in `flexible_countrycode()`:
! Survey data not found for: "Zamonia".
warning is thrown if filter column is not found
Filter column: "test" not found.
warning is thrown if missing data exist
Automatic country population lookup in `contact_matrix()` was deprecated in socialmixr 0.6.0.
When `countries` is given (or a `country` column is present) without `survey_pop`, contact_matrix() currently calls the soft-deprecated `wpp_age()` to look up population data. This automatic lookup will be removed in a future release: callers will then have to supply `survey_pop` whenever `symmetric`, `split`, `per_capita`, `weigh_age`, or `return_demography` is TRUE.
i Pass `survey_pop` explicitly to silence this warning, e.g. `survey_pop = survey_country_population(survey, countries)` or a data frame from the wpp2024 package.
error is thrown if an unknown argument is passed
Code
contact_matrix(dummy = "test")
Condition
Error in `check_arg_dots_in()`:
! Unknown argument: "dummy".
error is thrown if invalid age limits are passed
Code
contact_matrix(survey = polymod, age_limits = c(13, 11))
Condition
Error in `contact_matrix()`:
! `<int>` must be an increasing integer vector of lower age limits.
i We see: 13 and 11
error if no participants after selecting the country
Code
contact_matrix(survey = polymod, countries = "Romania")
Condition
Error in `filter_countries()`:
! No participants left after selecting countries: "Romania"
warning if population needed but no 'year' column
Automatic country population lookup in `contact_matrix()` was deprecated in socialmixr 0.6.0.
When `countries` is given (or a `country` column is present) without `survey_pop`, contact_matrix() currently calls the soft-deprecated `wpp_age()` to look up population data. This automatic lookup will be removed in a future release: callers will then have to supply `survey_pop` whenever `symmetric`, `split`, `per_capita`, `weigh_age`, or `return_demography` is TRUE.
i Pass `survey_pop` explicitly to silence this warning, e.g. `survey_pop = survey_country_population(survey, countries)` or a data frame from the wpp2024 package.
warning if day of week weigh requested but not present
`weigh_dayofweek` is "TRUE", but no `dayofweek` column in the data.
i Will ignore.
warning is thrown if country has no survey population
Code
contact_matrix(survey = polymod5, symmetric = TRUE)
Condition
Warning:
Automatic country population lookup in `contact_matrix()` was deprecated in socialmixr 0.6.0.
When `countries` is given (or a `country` column is present) without `survey_pop`, contact_matrix() currently calls the soft-deprecated `wpp_age()` to look up population data. This automatic lookup will be removed in a future release: callers will then have to supply `survey_pop` whenever `symmetric`, `split`, `per_capita`, `weigh_age`, or `return_demography` is TRUE.
i Pass `survey_pop` explicitly to silence this warning, e.g. `survey_pop = survey_country_population(survey, countries)` or a data frame from the wpp2024 package.
Warning:
`wpp_age()` was deprecated in socialmixr 0.6.0.
Pass population data directly via the {.arg survey_pop} argument instead.
i The underlying {.pkg wpp2017} data is also outdated; use {.pkg wpp2024} from GitHub for more recent data.
Error in `survey_pop_from_countries()`:
! Could not find population data for: "Zamonia".
i Pass population data directly via the `survey_pop` argument.
warning is thrown if contact survey has no age information
Contact age column `cnt_age` or columns to estimate contact age (`cnt_age_exact` or `cnt_age_est_min` and `cnt_age_est_max`) do not exist in the contact data frame.
warning is thrown if participant data has no country
Country column `country` does not exist in the participant data frame.
check result is reported back
Code
check(x = polymod2)
Message
> Check OK.
good suggestions are made
Automatic country population lookup in `contact_matrix()` was deprecated in socialmixr 0.6.0.
When `countries` is given (or a `country` column is present) without `survey_pop`, contact_matrix() currently calls the soft-deprecated `wpp_age()` to look up population data. This automatic lookup will be removed in a future release: callers will then have to supply `survey_pop` whenever `symmetric`, `split`, `per_capita`, `weigh_age`, or `return_demography` is TRUE.
i Pass `survey_pop` explicitly to silence this warning, e.g. `survey_pop = survey_country_population(survey, countries)` or a data frame from the wpp2024 package.
Automatic country population lookup in `contact_matrix()` was deprecated in socialmixr 0.6.0.
When `countries` is given (or a `country` column is present) without `survey_pop`, contact_matrix() currently calls the soft-deprecated `wpp_age()` to look up population data. This automatic lookup will be removed in a future release: callers will then have to supply `survey_pop` whenever `symmetric`, `split`, `per_capita`, `weigh_age`, or `return_demography` is TRUE.
i Pass `survey_pop` explicitly to silence this warning, e.g. `survey_pop = survey_country_population(survey, countries)` or a data frame from the wpp2024 package.
Automatic country population lookup in `contact_matrix()` was deprecated in socialmixr 0.6.0.
When `countries` is given (or a `country` column is present) without `survey_pop`, contact_matrix() currently calls the soft-deprecated `wpp_age()` to look up population data. This automatic lookup will be removed in a future release: callers will then have to supply `survey_pop` whenever `symmetric`, `split`, `per_capita`, `weigh_age`, or `return_demography` is TRUE.
i Pass `survey_pop` explicitly to silence this warning, e.g. `survey_pop = survey_country_population(survey, countries)` or a data frame from the wpp2024 package.
nonsensical operations are warned about
Automatic country population lookup in `contact_matrix()` was deprecated in socialmixr 0.6.0.
When `countries` is given (or a `country` column is present) without `survey_pop`, contact_matrix() currently calls the soft-deprecated `wpp_age()` to look up population data. This automatic lookup will be removed in a future release: callers will then have to supply `survey_pop` whenever `symmetric`, `split`, `per_capita`, `weigh_age`, or `return_demography` is TRUE.
i Pass `survey_pop` explicitly to silence this warning, e.g. `survey_pop = survey_country_population(survey, countries)` or a data frame from the wpp2024 package.
Code
contact_matrix(survey = polymod, counts = TRUE, symmetric = TRUE, age_limits = c(
0, 5))
Condition
Warning:
Automatic country population lookup in `contact_matrix()` was deprecated in socialmixr 0.6.0.
When `countries` is given (or a `country` column is present) without `survey_pop`, contact_matrix() currently calls the soft-deprecated `wpp_age()` to look up population data. This automatic lookup will be removed in a future release: callers will then have to supply `survey_pop` whenever `symmetric`, `split`, `per_capita`, `weigh_age`, or `return_demography` is TRUE.
i Pass `survey_pop` explicitly to silence this warning, e.g. `survey_pop = survey_country_population(survey, countries)` or a data frame from the wpp2024 package.
Warning:
`wpp_age()` was deprecated in socialmixr 0.6.0.
Pass population data directly via the {.arg survey_pop} argument instead.
i The underlying {.pkg wpp2017} data is also outdated; use {.pkg wpp2024} from GitHub for more recent data.
Warning in `contact_matrix()`:
`symmetric = TRUE` does not make sense with `counts = TRUE`; will not make matrix symmetric.
Warning in `normalise_weighted_matrix()`:
Large differences in the size of the sub-populations with the current age breaks are likely to result in artefacts after making the matrix symmetric.
! Please reconsider the age breaks to obtain more equally sized sub-populations.
i Normalization factors: [0.2 and 5.1]
Output
$matrix
contact.age.group
age.group [0,5) [5,Inf)
[0,5) 1463.000 26710.24
[5,Inf) 1396.075 87824.00
$demography
age.group population proportion year
<char> <num> <num> <int>
1: [0,5) 13498647 0.04967121 2005
2: [5,Inf) 258261321 0.95032879 2005
$participants
age.group participants proportion
<char> <int> <num>
1: [0,5) 654 0.09085857
2: [5,Inf) 6544 0.90914143
Automatic country population lookup in `contact_matrix()` was deprecated in socialmixr 0.6.0.
When `countries` is given (or a `country` column is present) without `survey_pop`, contact_matrix() currently calls the soft-deprecated `wpp_age()` to look up population data. This automatic lookup will be removed in a future release: callers will then have to supply `survey_pop` whenever `symmetric`, `split`, `per_capita`, `weigh_age`, or `return_demography` is TRUE.
i Pass `survey_pop` explicitly to silence this warning, e.g. `survey_pop = survey_country_population(survey, countries)` or a data frame from the wpp2024 package.
warning if survey is assumed to be representative
No `survey.pop` or `countries` given, and no `country` column found in the data.
i I don't know which population this is from (assuming the survey is representative).
user-defined reference populations with open age groups
Code
contact_matrix(polymod_nocountry, age_limits = c(0, 18, 60), symmetric = TRUE,
survey_pop = "dummy")
Condition
Warning:
`wpp_age()` was deprecated in socialmixr 0.6.0.
Pass population data directly via the {.arg survey_pop} argument instead.
i The underlying {.pkg wpp2017} data is also outdated; use {.pkg wpp2024} from GitHub for more recent data.
Error in `survey_pop_from_countries()`:
! Could not find population data for: "dummy".
i Pass population data directly via the `survey_pop` argument.
symmetric matrices with large norm weights warn
Automatic country population lookup in `contact_matrix()` was deprecated in socialmixr 0.6.0.
When `countries` is given (or a `country` column is present) without `survey_pop`, contact_matrix() currently calls the soft-deprecated `wpp_age()` to look up population data. This automatic lookup will be removed in a future release: callers will then have to supply `survey_pop` whenever `symmetric`, `split`, `per_capita`, `weigh_age`, or `return_demography` is TRUE.
i Pass `survey_pop` explicitly to silence this warning, e.g. `survey_pop = survey_country_population(survey, countries)` or a data frame from the wpp2024 package.
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