BayesianFROC (version 0.4.0)

stanfitExtended: stanfitExtended, an S4 class inherited from the S4 class stanfit

Description

Inherits from the class stanfit which is an S4 class defined in the package rstan :

Slots

plotdataMRMC

Plot data for MRMC case.

plotdata

This is a data frame with four components which is used to draw curves such as FROC curves and AFROC curves. So, this slot includes the component:

fit@plotdata$x.AFROC,

fit@plotdata$y.AFROC,

fit@plotdata$x.FROC,

fit@plotdata$y.FROC

where fit is an object of class stanfitExtended.

For example, we can use this slot

# E.g.

plot(f@plotdata$x.FROC,f@plotdata$y.FROC,xlim=c(0,1),type="l")

#Or

plot(f@plotdata$x.AFROC, f@plotdata$y.AFROC, type="l" )

The author think this slot is not good because it increases the object size.

dataList

An FROC dataset, to which a model is fitted.

dataList.Name

whose class is "character", indicating the name of data object. This data object is fitted a model.

multinomial

A logical, if true, then the classical, traditional model is fitted, which is not the author's model.

studyDesign

A character, e.g., "srsc.per.image", "srsc.per.lesion", according to False Positive Fraction (FPF) is per image or per lesion.

metadata

An additional data calculated from dataList, such as cumulative hits and false alarms,...,etc.

WAIC

A WAIC calculated by the function waic .

convergence

A logical R object TRUE or FALSE. If TRUE, then the model is good in the R hat criterion.

PreciseLogLikelihood

A logical. If TRUE, then target formulation is used. In the past, the author made a target and non-target model, but now the model is declared by target only, so, this slot is now, redandunt.

chisquare

This is a chi square at the posterior mean estimates. Chi square statistic is \(\chi^2 (Data|\theta)\), there are three simple ways to get it.

(1) \( \int \chi^2(Data|\theta ) \pi(\theta|Data)d\theta \)

(2) \( \chi^2(Data|\int \theta \pi(\theta|Data)d\theta) \)

(3) \( \int \chi^2(Data|\theta ) f(Data|\theta)\pi(\theta|Data)d\theta \)

where, \(f( Data|\theta )\) denotes a likelihood and \(\pi(\theta| Data )\) is a posterior. This slot retains the (2)

See also ppp()

index

An object of numeric class. This is for programming phase.

Divergences

This is the number of the divergence transitions in the MCMC simulation.

MCMC.Iterations

A MCMC iterations which does not count the burn-in period.

Divergence.rate

A divergence rate, calculated by dividing the number of the divergence iterations by total MCMC iterations except Burn-in period is not included.

model_name

A slot of the stanfit which is an S4 class defined in the rstan package.

model_pars

A slot of the stanfit which is an S4 class in the package rstan.

par_dims

A slot of the stanfit which is an S4 class in the package rstan.

mode

A slot of the stanfit which is an S4 class in the package rstan.

sim

A slot of the stanfit which is an S4 class in the package rstan.

inits

A slot of the stanfit which is an S4 class in the package rstan.

stan_args

A slot of the stanfit which is an S4 class in the package rstan.

stanmodel

A slot of the stanfit which is an S4 class in the package rstan.

date

A slot of the stanfit which is an S4 class in the package rstan.

.MISC

A slot of the stanfit which is an S4 class in the package rstan.

Details

Revised in 2019.Jun 5 Revised in 2019 Oct 19 Revised in 2019 Nov 25

-------- To read the table of R object of class stanfit in case of MRMC ----------------------------

* The AUC denoted by AA[modalityID , readerID] are shown.

For example, AA[2,3] means the AUC of the 2 nd modality and the 3 rd reader.

* The column of 2.5% and 97.5% means the lower and upper bounds of the 95