Example of using EPPASM with leapfrog model engine

2026-01-28

EPPASM can use the leapfrog model during simulation and fitting. This vignette shows an example of using leapfrog with EPPASM.

Firstly we need to read the data

pjnz <- system.file("extdata/testpjnz", "Mozambique_Maputo_Cidade2018.PJNZ", package="eppasm.lf")

Simulate with direct incidence input

fp <- eppasm.lf::prepare_directincid(pjnz)
mod <- eppasm.lf::simmod(fp, VERSION = "leapfrog")

Simulate with transmission input

theta_rhybrid <- c(-0.407503322169364, -2.76794181367538, -1.26018073624346, 1995.96447776502,
                   -0.00307437171215574, 0.0114118307148102, 0.00760958379603691, 0.02,
                   2.24103194827232, -0.0792123921862689, -5.01917961803606, 0.359444135205712,
                   -6.10051517060137)

inputs <- eppasm.lf::prepare_spec_fit(pjnz, 2018.5)

prep <- eppasm.lf::prep_fp_fitmod(inputs[["Maputo Cidade"]], eppmod = "rhybrid")
fp <- stats::update(prep$fp, list=eppasm.lf::fnCreateParam(theta_rhybrid, prep$fp))

mod <- eppasm.lf::simmod(fp, VERSION = "leapfrog")

Fit model

eppasm.lf::fitmod(
  inputs[["Maputo Cidade"]],
  eppmod = "rhybrid",
  rw_start = 2005,
  B0=1e3,
  B=1e2,
  opt_iter = 1,
  number_k=50
)