computeDistanceAbc: Compute the distance between a model and data for ABC

In sbfnk/fitR: Tool box for fitting dynamic infectious disease models to time series

Compute the distance between a model and data for ABC

Description

Compute the distance (using distanceAbc) between the observed time series and a simulated time series of observations obtained by running the model with parameters theta.

Usage

computeDistanceAbc(sumStats, distanceAbc, fitmodel, theta, initState, data)

Arguments

sumStats	a list of functions to calculate summary statistics. Each of these takes one argument (a trajectory with an "obs" column) and returns a number (the summary statistic given the trajectory)
distanceAbc	a function that take three arguments: sumStats, a list of summary statistics, dataObs (the data trajectory of observations) and modelObs (a model trajectory of observations), and returns the distance between the model run and the data in terms of the summary statistics
fitmodel	a fitmodel object
theta	named numeric vector. Values of the parameters. Names should match fitmodel$thetaNames.
initState	named numeric vector. Initial values of the state variables. Names should match fitmodel$stateNames.
data	data frame. Observation times and observed data. The time column must be named "time" and the observation column must be named "obs".

Value

a sampled distance between

sbfnk/fitR documentation built on July 18, 2023, 3:28 p.m.