
stanfitExtended
, an S4 class inherited
from the S4 class stanfit
Inherits from the class stanfit
which
is an S4 class defined in the package rstan :
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.AFROC
where fit
is an
object of class stanfitExtended
.
For example, we can use this slot
such as plot(fit@plotdata$x.AFROC, fit@plotdata$y.AFROC )
,
where fit
is a fitted model object of class stanfitExtended
.
The author think this slot is not so good since it increase the object size.
dataList
An FROC dataset. Using the dataset, the fitting has done.
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 it means your model is good in the R hat criterion.
PreciseLogLikelihood
This is TRUE or FALSE. If TRUE,
then target formulation is used in the stan file. However,
non-target formulation has warning for non-linear Jacobian
issue. So, the author use target formulations
for all .stan
files, and thus this slot is now, redandunt.
chisquare
This is a chi square calculated with
Expected A Posterior estimates, i.e.,
the posterior mean estimates.
Chi square statistic is
(1)
(2)
(3)
where,
Note that this is not calculated by integrating
the posterior predictive measure. Do not confuse
with the p value calculated with the posterior
predicitive measure implemented
in the function ppp()
index
This is for programming phase.
Divergences
This is a 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, that is the number of the divergence iterations over total MCMC iterations. Burn-in period is not included.
model_name
A slot from the stanfit
which is an S4 class defined in the rstan package.
model_pars
A slot from the stanfit
which is an S4 class in the package rstan.
par_dims
A slot from the stanfit
which is an S4 class in the package rstan.
mode
A slot from the stanfit
which is an S4 class in the package rstan.
sim
A slot from the stanfit
which is an S4 class in the package rstan.
inits
A slot from the stanfit
which is an S4 class in the package rstan.
stan_args
A slot from the stanfit
which is an S4 class in the package rstan.
stanmodel
A slot from the stanfit
which is an S4 class in the package rstan.
date
A slot from the stanfit
which is an S4 class in the package rstan.
.MISC
A slot from the stanfit
which is an S4 class in the package rstan.
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