Compute contact matrix from prepared survey data — compute

Computes a contact matrix from a contact_survey that has been processed by assign_age_groups() and optionally weigh(). This is the final step in the pipeline workflow.

For post-processing, pipe the result into symmetrise(), split_matrix(), or per_capita().

Usage

compute_matrix(survey, counts = FALSE, weight_threshold = NULL)

Arguments

survey: a survey() object with age groups assigned (via assign_age_groups())
counts: whether to return counts instead of means
weight_threshold: numeric; if provided, weights above this threshold are capped to the threshold value and then re-normalised (default NULL)

Value

a list with elements matrix and participants

Examples

data(polymod)
polymod |>
  assign_age_groups(age_limits = c(0, 5, 15)) |>
  compute_matrix()
#> 
#> ── Contact matrix (3 age groups) ──
#> 
#> Ages: "[0,5)", "[5,15)", and "[15,Inf)"
#> Participants: 7198
#> 
#>           contact.age.group
#> age.group      [0,5)   [5,15)  [15,Inf)
#>   [0,5)    2.2370031 1.556575  6.434251
#>   [5,15)   0.5252009 8.948137  7.100804
#>   [15,Inf) 0.3478261 1.019710 11.705507