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Create a genomic surveillance design object

Source: R/00-classes.R, R/01-design.R
surv_design.Rd

Constructs a survey design object tailored for pathogen genomic surveillance, encoding stratification structure, sequencing rates, and population information needed for design-weighted inference.

Usage

# S3 method for class 'surv_design'
print(x, ...)

# S3 method for class 'surv_design'
summary(object, ...)

# S3 method for class 'summary.surv_design'
print(x, ...)

surv_design(
  data,
  strata,
  sequencing_rate,
  population,
  date_collected = "collection_date",
  date_reported = "report_date",
  lineage = "lineage",
  source_type = NULL,
  source_config = NULL
)

Arguments

x

Object to print or summarize.

...

Additional arguments (unused).

object

A surv_design object to summarize.

data

Data frame of individual sequence records.

strata

One-sided formula specifying stratification variables (e.g., ~ region or ~ region + source_type).

sequencing_rate

Either a one-sided formula (~ n_sequenced / n_positive), a named numeric vector, or a data frame with strata columns and seq_rate.

population

Data frame with one row per stratum, containing stratification variables and population-level denominators.

date_collected

Column name for collection date. Default "collection_date".

date_reported

Column name for report date. Default "report_date". Set NULL if unavailable.

lineage

Column name for lineage. Default "lineage".

source_type

Column name for sample source. Default NULL.

source_config

Optional tibble of per-source characteristics.

Value

Invisibly returns the input object.

A summary list of class summary.surv_design.

Invisibly returns the input object.

An object of class surv_design.

See also

surv_simulate(), surv_lineage_prevalence(), surv_optimize_allocation()

Examples

sim <- surv_simulate(n_regions = 3, n_weeks = 8, seed = 42)
design <- surv_design(
  data = sim$sequences,
  strata = ~ region,
  sequencing_rate = sim$population[c("region", "seq_rate")],
  population = sim$population
)
print(design)
#> ── Genomic Surveillance Design ─────────────────────────────────────────────────
#> Observations: 775
#> Strata: 3 (region)
#> Date range: 2024-01-01 to 2024-02-25
#> Lineages: 4
#> Weight range: [3.716, 18.053]