fit {cystiSim}

Fit cystiSim parameters

Description

This function simulates random cystiSim parameters, and return those scenarios that result in a baseline prevalence close to the specified target.

Usage

fit(n.sim, n.update, target, limit,
    man, pig, ph2m, pl2m, m2p, e2p, age.coef = c(0, 0),
    slaughter = slaughter_nbinom,
    slaughter.args = list(min = 6,  max = 36, size = 0.70, mu = 80))

Arguments

n.sim

Desired number of retained scenarios.

n.update

Number of updates of the baseline model.

target

Named list of target prevalences for ht, pc and/or pi

limit

Maximum tolerated deviance.

man

Human population dataframe.

pig

Pig population dataframe.

ph2m

Pig (Heavy infection) to Man transmission probability.

pl2m

Pig (Light infection) to Man transmission probability.

m2p

Man to Pig transmission probability.

e2p

Environment to Pig transmission probability.

age.coef

Optional intercept and slope for the association between age and taeniosis.

slaughter

Function that defines the slaughter probability of pigs.

slaughter.args

Arguments to be passed to the slaughter function.

Details

The abbreviations used:

• ht....Human Taeniosis prevalence

• pc....Porcine Cysticercosis prevalence

• pi....Pig Intensity proportion (i.e., proportion heavily infection pigs)

Note

For more details and examples, please visit the cystiSim Wiki pages on https://github.com/brechtdv/cystiSim/wiki.

Author(s)

[e-mail]