fit_dynamic_model: Fit a dynamic model to the measles outbreak in Katanga

In sbfnk/measles.katanga: Code accompanying the manuscript "The impact of reactive mass vaccination campaigns on measles outbreaks in the Katanga region, Democratic Republic of Congo" (doi:10.1101/201574).

Description

Uses the LibBi interface provided by the rbi package

Usage

fit_dynamic_model(model, year = 2015, end = 5, start_threshold = 10,
  vaccine_delay = 0, nbdata, particles, under_5_multiplier = 0.169)

Arguments

model	a 'bi_model'
year	the year to which to fit
end	how many weeks to retain after the last data point
start_threshold	when this number is exceeded over a two-week period, start fitting
vaccine_delay	delay in vaccine protection; default: 0 (instantaneous protection)
nbdata	number of data points to require; if fewer data points are available in a health zone, the health zone will be discarded
particles	number of particles, if given; otherwise will be determined from the variance of the log-likelihood estimate
under_5_multiplier	multiplier for population size to get under-5 population size; default: 0.169

Value

libbi object containing the posterior samples

Author(s)

Sebastian Funk

sbfnk/measles.katanga documentation built on Nov. 11, 2019, 4:27 a.m.