surv_estimate_delay: Estimate reporting delay distribution

In survinger: Design-Adjusted Inference for Pathogen Lineage Surveillance

Estimate reporting delay distribution

Description

Fits a parametric distribution to the delay between sample collection and sequence reporting, accounting for right-truncation.

Usage

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

surv_estimate_delay(
  design,
  distribution = c("negbin", "poisson", "lognormal", "nonparametric"),
  strata = NULL,
  max_delay = 60L,
  ref_date = NULL
)

Arguments

x	Object to print.
...	Additional arguments (unused).
design	A surv_design object with both collection and report dates.
distribution	Character: "negbin" (default), "poisson", "lognormal", or "nonparametric".
strata	Optional one-sided formula for delay stratification.
max_delay	Integer. Maximum plausible delay in days. Default 60.
ref_date	Date. Reference date for right-truncation. Default is max report date in data.

Value

Invisibly returns the input object.

A surv_delay_fit object.

Examples

sim <- surv_simulate(n_regions = 3, n_weeks = 12, seed = 1)
d <- surv_design(sim$sequences, ~ region,
                 sim$population[c("region", "seq_rate")], sim$population)
fit <- surv_estimate_delay(d)
print(fit)

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