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 :

Arguments

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)

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