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Compute surveillance quality metrics

Source: R/13-infrastructure.R
surv_quality.Rd

Returns a single-row tibble of design quality indicators suitable for inclusion in manuscripts. Analogous to broom::glance() but for the surveillance design itself.

Usage

surv_quality(design, target_lineage = NULL, target_prevalence = 0.01)

Arguments

design

A surv_design object.

target_lineage

Character or NULL. Default NULL auto-selects.

target_prevalence

Numeric. For detection calculation. Default 0.01.

Value

A single-row tibble with columns: n_obs, n_strata, gini, rate_ratio, effective_n, deff, detection_prob, mean_bias.

See also

surv_report(), surv_design()

Examples

sim <- surv_simulate(n_regions = 3, n_weeks = 10, seed = 1)
d <- surv_design(sim$sequences, ~ region,
                 sim$population[c("region", "seq_rate")], sim$population)
surv_quality(d)
#> # A tibble: 1 × 12
#>   n_obs n_strata n_lineages  gini rate_min rate_max rate_ratio effective_n  deff
#>   <int>    <int>      <int> <dbl>    <dbl>    <dbl>      <dbl>       <dbl> <dbl>
#> 1   759        3          4 0.356   0.0395    0.220        5.6         573  1.33
#> # ℹ 3 more variables: detection_at_1pct <dbl>, mean_abs_bias_pp <dbl>,
#> #   target_lineage <chr>