Description Objects from the Class Slots Methods Author(s) See Also Examples
Specification of LadyBug SEIR models
Objects can be created by calls of the form new("LBOptions",
seed, LBmodel, ignoreData, initBeta, initBetaN, initIncu, initInf,
initDia, algo, randomWalk)
.
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 |
signature(object = "LBOptions")
:
returns value of slot ignoreData
signature(object = "LBOptions", value = "vector")
:
assigns value
to slot ignoreData
signature(object = "LBOptions")
:
returns value of slot initBeta
signature(object = "LBOptions", value = "list")
:
assigns value
to slot initBeta
signature(object = "LBOptions")
:
returns value of slot initBetaN
signature(object = "LBOptions", value = "list")
:
assigns value
to slot initBetaN
signature(object = "LBOptions")
:
returns value of slot initDia
signature(object = "LBOptions", value = "list")
:
assigns value
to slot initDia
signature(.Object = "LBOptions")
:
does initializing of the slots when new( "LBOptions", ... )
is called
signature(object = "LBOptions")
:
returns value of slot initIncu
signature(object = "LBOptions", value = "list")
:
assigns value
to slot initIncu
signature(object = "LBOptions")
:
returns value of slot initInf
signature(object = "LBOptions", value = "list")
:
assigns value
to slot initInf
signature(object = "LBOptions")
:
returns initial values in a dataframe format
signature(object = "LBOptions")
:
returns all initial values (as there are initBeta
, initBetaN
, initIncu
, initInf
, initDia
)
signature(object = "LBOptions", value = "list")
:
assigns value
to all initial value slots (as there are initBeta
, initBetaN
, initIncu
, initInf
, initDia
)
signature(object = "LBOptions")
:
returns value of slot LBModel
signature(object = "LBOptions", value = "vector")
:
assigns value
to slot LBModel
signature(object = "LBOptions")
:
returns values of real option slots (as there are seed
, LBModel
, ignoreData
)
signature(object = "LBOptions", value = "list")
:
assigns value to real option slots (as there are seed
, LBModel
, ignoreData
)
signature(object = "LBOptions")
:
returns real option values in a dataframe format
signature(object = "LBOptions")
:
returns value of slot seed
signature(object = "LBOptions", value = "numeric")
:
assigns value
to slot seed
signature(object = "LBOptions")
:
shows the object
signature(object = "LBOptions", layout = "Layout")
:
simulates data according to the specified model and init values and the given layout structure
signature(object = "LBOptions")
:
gives a summary of the object (at the moment no difference to show
)
M. Hoehle and U. Feldmann
See also LBOptionsMCMC-class
and LBOptionsML-class
1 2 3 4 5 6 7 8 9 10 11 12 13 | 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 )
|
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