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

Description Objects from the Class Slots Extends Methods Author(s) See Also Examples

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

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  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.