inst/doc/allocation-optimization.R

In survinger: Design-Adjusted Inference for Pathogen Lineage Surveillance

## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(collapse = TRUE, comment = "#>",
                      fig.width = 7, fig.height = 4, dev = "png")

## ----example------------------------------------------------------------------
library(survinger)
data(sarscov2_surveillance)

design <- surv_design(
  data = sarscov2_surveillance$sequences,
  strata = ~ region,
  sequencing_rate = sarscov2_surveillance$population[c("region", "seq_rate")],
  population = sarscov2_surveillance$population,
  source_type = "source_type"
)

## ----min-mse------------------------------------------------------------------
alloc_mse <- surv_optimize_allocation(design, "min_mse", total_capacity = 500)
print(alloc_mse)
plot(alloc_mse)

## ----compare------------------------------------------------------------------
comparison <- surv_compare_allocations(design, total_capacity = 500)
print(comparison)

## ----floor--------------------------------------------------------------------
alloc_floor <- surv_optimize_allocation(
  design, "min_mse", total_capacity = 500, min_per_stratum = 20
)
print(alloc_floor)