LBOptions-class: Class "LBOptions"

In RLadyBug: Analysis of Infectious Diseases using Stochastic Epidemic Models

Description

Specification of LadyBug SEIR models

Objects from the Class

Objects can be created by calls of the form new("LBOptions", 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

Methods

ignoreData

signature(object = "LBOptions"):
returns value of slot ignoreData

ignoreData<-

signature(object = "LBOptions", value = "vector"):
assigns value to slot ignoreData

initBeta

signature(object = "LBOptions"):
returns value of slot initBeta

initBeta<-

signature(object = "LBOptions", value = "list"):
assigns value to slot initBeta

initBetaN

signature(object = "LBOptions"):
returns value of slot initBetaN

initBetaN<-

signature(object = "LBOptions", value = "list"):
assigns value to slot initBetaN

initDia

signature(object = "LBOptions"):
returns value of slot initDia

initDia<-

signature(object = "LBOptions", value = "list"):
assigns value to slot initDia

initialize

signature(.Object = "LBOptions"):
does initializing of the slots when new( "LBOptions", ... ) is called

initIncu

signature(object = "LBOptions"):
returns value of slot initIncu

initIncu<-

signature(object = "LBOptions", value = "list"):
assigns value to slot initIncu

initInf

signature(object = "LBOptions"):
returns value of slot initInf

initInf<-

signature(object = "LBOptions", value = "list"):
assigns value to slot initInf

initsAsDataFrame

signature(object = "LBOptions"):
returns initial values in a dataframe format

LBInits

signature(object = "LBOptions"):
returns all initial values (as there are initBeta, initBetaN, initIncu, initInf, initDia )

LBInits<-

signature(object = "LBOptions", value = "list"):
assigns value to all initial value slots (as there are initBeta, initBetaN, initIncu, initInf, initDia )

LBModel

signature(object = "LBOptions"):
returns value of slot LBModel

LBModel<-

signature(object = "LBOptions", value = "vector"):
assigns value to slot LBModel

LBOptions

signature(object = "LBOptions"):
returns values of real option slots (as there are seed, LBModel, ignoreData )

LBOptions<-

signature(object = "LBOptions", value = "list"):
assigns value to real option slots (as there are seed, LBModel, ignoreData )

optionsAsDataFrame

signature(object = "LBOptions"):
returns real option values in a dataframe format

seed

signature(object = "LBOptions"):
returns value of slot seed

seed<-

signature(object = "LBOptions", value = "numeric"):
assigns value to slot seed

show

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

simulate

signature(object = "LBOptions", layout = "Layout"):
simulates data according to the specified model and init values and the given layout structure

summary

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

Author(s)

M. Hoehle and U. Feldmann

See Also

See also LBOptionsMCMC-class and LBOptionsML-class

Examples

  opts <- new( "LBOptions", seed=2003,
                            LBmodel=c( "gamma", "gamma", "gamma", FALSE ),
                            ignoreData=c( TRUE, FALSE, FALSE ),
                            initBeta=list( 0.125, 0.001, 0.001 ),
                            initBetaN=list( init=0.018, gamma=0.001, delta=0.001 ),
                            initIncu=list( g=6.697, g.gamma=0.001, g.delta=0.001,
                                           d=0.840, d.gamma=0.001, d.delta=0.001 ),
                            initInf=list( 1.772, 0.001, 0.001, 0.123, 0.001, 0.001 ),
                            initDia=list( 149.126, 0.001, 0.001, 8.737, 0.001, 0.001 ) )
 layout <- new( "LBLayout", S0=matrix( c( 14, 14 ), ncol=2 ),
                            E0=matrix( c( 0, 1 ), ncol=2 ) )

 exp <- simulate( opts, layout=layout )

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