surv_design: Create a genomic surveillance design object

In survinger: Design-Adjusted Inference for Pathogen Lineage Surveillance

Create a genomic surveillance design object

Description

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)

survinger documentation built on April 27, 2026, 9:10 a.m.