LBOptionsML-class: Class "LBOptionsML" - maximum likelihood inference in SEIR...

In RLadyBug: Analysis of Infectious Diseases using Stochastic Epidemic Models

Description

Specification of LadyBug SEIR models using maximum likelihood inference

Objects from the Class

Objects can be created by calls of the form new("LBOptionsML", seed, LBmodel, ignoreData, initBeta, initBetaN, initIncu, initInf, initDia, algo, randomWalk).

Slots

seed:

Object of class "numeric" The seed value to use when calling the Java program

LBmodel:

Object of class "vector" Contains a specification of the SEIR model, i.e. a vector with names

incuTimePDF	distribution of incubation time
infTimePDF	distribution of the infectious time
diagTimePDF	distribution of the seroconversion time
meanVar	mean variance representation of periods (TRUE/FALSE)

ignoreData:

Object of class "vector" Booleans

ignoreE	Ignore the specified exposure (E) event times
ignoreI	Ignore the specified infective (I) event times
ignoreD	Ignore the specified diagnose (D) event time

initBeta:

Object of class "list" Inital values:

init	for β
gamma	for the priori parameter γ
delta	for the priori parameter δ

initBetaN:

Object of class "list" Inital values:

init	for β_n
gamma	for the priori parameter γ
delta	for the priori parameter δ

initIncu:

Object of class "list" Initial values:

g	for parameter γ of the gamma distribution of the incubation time
g.gamma	for the parameter gamma of the distribution of g
g.delta	for the parameter delta of the distribution of g
d	for parameter δ of the gamma distribution of the incubation time
d.gamma	for the parameter gamma of the distribution of d
d.delta	for the parameter delta of the distribution of d

or choose asis or constant:

asis	TRUE/FALSE
const	TRUE/FALSE
const.val	value of constant if const == TRUE

initInf:

Object of class "list" Initial values:

g	for parameter γ of the gamma distribution of the infectious time
g.gamma	for the parameter gamma of the distribution of g
g.delta	for the parameter delta of the distribution of g
d	for parameter δ of the gamma distribution of the infectious time
d.gamma	for the parameter gamma of the distribution of d
d.delta	for the parameter delta of the distribution of d

initDia:

Object of class "list" Initial values:

g	for parameter γ of the gamma distribution of the seroconversion time
g.gamma	for the parameter gamma of the distribution of g
g.delta	for the parameter delta of the distribution of g
d	for parameter δ of the gamma distribution of the seroconversion time
d.gamma	for the parameter gamma of the distribution of d
d.delta	for the parameter delta of the distribution of d

Extends

Class "LBOptions", directly.

Methods

show

signature(object = "LBOptionsML"):
shows the object

summary

signature(object = "LBOptionsML"):
gives a summary of the object (at the moment no difference to show )

writeOptionFile

signature(object = "LBOptionsML", filename = "vector" ):
writes a file containing all options as input for java

Author(s)

M. Hoehle and U. Feldmann

See Also

See also LBOptions-class and LBOptionsMCMC-class

Examples

  opts <- new( "LBOptionsML", seed=2003,
                              LBmodel=c( "constant", "gamma", "none", FALSE ),
                              ignoreData=c( FALSE, FALSE, FALSE ),
                              initBeta=list( 0.4, 0.001, 0.001 ),
                              initBetaN=list( init=0.005, gamma=0.001, delta=0.001 ),
                              initIncu=list( asis=TRUE ),
                              initInf=list( 1, 0.001, 0.001, 0.11, 0.001, 0.001 ),
                              initDia=list( 8, 0.001, 0.001, 0.8, 0.001, 0.001 ) )

RLadyBug documentation built on May 2, 2019, 5:50 p.m.