Flatten a multi-grouping contact matrix to its T x T form

Returns the contact matrix in the flattened representation of Manna et al. — a T x T matrix where each axis enumerates the Cartesian product of grouping levels. For a single-grouping matrix this is the matrix itself.

Row/column names join the grouping levels with a colon, e.g. "[0,5):F" for the age group [0,5) combined with gender level F. The participant axes vary fastest in the first grouping (column-major reshape).

Usage

flatten(x)

Arguments

x

a contact_matrix object as returned by compute_matrix()

Value

a numeric T x T matrix

References

Manna A, Dall'Amico L, Tizzoni M, Karsai M, Perra N (2024). Generalized contact matrices allow integrating socioeconomic variables into epidemic models. Science Advances 10(41), eadk4606. doi:10.1126/sciadv.adk4606

Examples

data(polymod)
polymod |>
  (\(s) s[country == "United Kingdom"])() |>
  assign_age_groups(age_limits = c(0, 5, 15)) |>
  compute_matrix(by = c("age", "gender")) |>
  flatten()
#>                 [0,5):    [5,15):  [15,Inf):   [0,5):F  [5,15):F [15,Inf):F
#> [0,5):F    0.020408163 0.02040816 0.00000000 1.3673469 1.1428571   3.755102
#> [5,15):F   0.009523810 0.12380952 0.13333333 0.3523810 5.4000000   4.190476
#> [15,Inf):F 0.008130081 0.01897019 0.05420054 0.2520325 0.8590786   5.669377
#> [0,5):M    0.065217391 0.06521739 0.10869565 0.8260870 0.5217391   3.413043
#> [5,15):M   0.000000000 0.08080808 0.01010101 0.2222222 2.5858586   3.262626
#> [15,Inf):M 0.002915452 0.01457726 0.16618076 0.1166181 0.4139942   4.192420
#>              [0,5):M  [5,15):M [15,Inf):M
#> [0,5):F    0.8979592 0.6122449   1.795918
#> [5,15):F   0.2666667 2.7904762   2.371429
#> [15,Inf):F 0.2547425 0.6639566   4.000000
#> [0,5):M    0.6304348 0.4782609   1.978261
#> [5,15):M   0.2020202 4.8888889   2.434343
#> [15,Inf):M 0.1370262 0.5918367   5.096210