surv_nowcast_lineage: Nowcast lineage counts correcting for reporting delays

In survinger: Design-Adjusted Inference for Pathogen Lineage Surveillance

Nowcast lineage counts correcting for reporting delays

Description

Nowcast lineage counts correcting for reporting delays

Usage

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

## S3 method for class 'surv_nowcast'
as.data.frame(x, ...)

surv_nowcast_lineage(
  design,
  delay_fit,
  lineage = NULL,
  time = "epiweek",
  horizon = 4L,
  ref_date = NULL,
  method = c("direct", "em")
)

Arguments

x	Object to print.
...	Additional arguments (unused).
design	A surv_design object.
delay_fit	A surv_delay_fit object.
lineage	Character or NULL. Target lineage.
time	Character. Default "epiweek".
horizon	Integer. Recent periods to nowcast. Default 4.
ref_date	Date or NULL. Default max report date.
method	Character: "direct" (default) or "em".

Value

Invisibly returns the input object.

A surv_nowcast 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)
nc <- surv_nowcast_lineage(d, fit, "BA.2.86")
print(nc)

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