Wave 1 CoMix yields all NA matrix

[sbfnk]

          A follow up question I had was how to stratify on survey wave, e.g. subset on wave 1 participants in CoMix, and generate the corresponding social contact matrix -  at the moment it's returning NA entries (see below), but there's probably something simple I'm not getting.

Full draft walkthrough is here.

# get UK CoMix data from 2020-22 - note this is slow to load
comix_uk <- get_survey("https://zenodo.org/doi/10.5281/zenodo.4905745")

# subset on 1st wave of surveys in April/May 2020
comix_uk_wave_1 <- comix_uk
comix_uk_wave_1$participants <- comix_uk$participants |> filter(wave==1)

contact_data_comix <- socialmixr::contact_matrix(
  comix_uk_wave_1,
  countries = "United Kingdom",
  age.limits = c(0, 5, 18, 40, 65),
  symmetric = TRUE
)

> contact_data_comix
$matrix
      contact.age.group
       [0,5) [5,18) [18,40) [40,65) 65+
  [1,]    NA     NA      NA      NA  NA
  [2,]    NA     NA      NA      NA  NA
  [3,]    NA     NA      NA      NA  NA
  [4,]    NA     NA      NA      NA  NA
  [5,]    NA     NA      NA      NA  NA

$demography
   age.group population proportion  year
      <char>      <num>      <num> <int>
1:     [0,5)    4370647         NA  1950
2:    [5,18)    8910009         NA  1950
3:   [18,40)   15997248         NA  1950
4:   [40,65)   15855240         NA  1950
5:       65+         NA         NA  1950

$participants
   age.group participants   proportion
      <char>        <int>        <num>
1:     [0,5)          192 0.1594684385
2:    [5,18)          998 0.8289036545
3:   [18,40)            1 0.0008305648
4:   [40,65)           11 0.0091362126
5:       65+            2 0.0016611296

Originally posted by @adamkucharski in #108 (comment)

[sbfnk]

This is caused by a combination of issues:

1. the COMIX data has the year column set to 20. The package takes the nearest population data which is from 1950.
2. wpp_age returns some age groups as having NA population size if they were not represented in a given census.

We can fix (2) but (1) would have to be fixed by updating the raw data, I think.