surv_estimate: Pipe-friendly surveillance analysis

In survinger: Design-Adjusted Inference for Pathogen Lineage Surveillance

Pipe-friendly surveillance analysis

Description

Convenience wrapper that creates a design, estimates prevalence, and optionally applies delay correction in a single pipe-friendly call. Designed for rapid exploratory analysis in interactive sessions.

Usage

surv_estimate(
  data,
  strata,
  sequencing_rate,
  population,
  lineage,
  correct_delay = FALSE,
  method = "hajek",
  ...
)

Arguments

data	Data frame of sequence records.
strata	One-sided formula for stratification.
sequencing_rate	Sequencing rate specification (see surv_design()).
population	Population data frame.
lineage	Character. Target lineage to estimate.
correct_delay	Logical. Apply delay correction? Default FALSE.
method	Character. Prevalence method. Default "hajek".
...	Additional arguments passed to surv_design().

Value

A surv_prevalence or surv_adjusted object.

See Also

surv_design(), surv_lineage_prevalence()

Examples

sim <- surv_simulate(n_regions = 3, n_weeks = 10, seed = 1)
# One-liner analysis:
result <- surv_estimate(
  data = sim$sequences, strata = ~ region,
  sequencing_rate = sim$population[c("region", "seq_rate")],
  population = sim$population,
  lineage = "BA.2.86"
)
print(result)

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