DrawCurves_MRMC_pairwise_BlackWhite

An S4 object of class <code> <a rd-options="" href="/link/stanfitExtended?package=BayesianFROC&version=0.2.1" data-mini-rdoc="BayesianFROC::stanfitExtended">stanfitExtended</a></code> which is an inherited class from the S4 class <code><a rd-options="rstan" href="/link/stanfit?package=BayesianFROC&version=0.2.1&to=rstan" data-mini-rdoc="rstan::stanfit">stanfit</a></code>. This R object can be passed to the <code><a rd-options="" href="/link/DrawCurves?package=BayesianFROC&version=0.2.1" data-mini-rdoc="BayesianFROC::DrawCurves">DrawCurves</a>()</code>, <code><a rd-options="" href="/link/ppp?package=BayesianFROC&version=0.2.1" data-mini-rdoc="BayesianFROC::ppp">ppp</a>()</code> and ... etc

StanS4class

This is a vector indicating modalityID whose component is natural namber.

modalityID

This is a vector indicating readerID whose component is natural namber.

readerID

Logical: <code>TRUE</code> of <code>FALSE</code>. If TRUE (default), then open a new device to draw curve.
Using this we can draw curves in same plain by new.imaging.device=FALSE.

new.imaging.device

Logical: <code>TRUE</code> of <code>FALSE</code>. Whether the FROC curve is to be drawn.

DrawFROCcurve

Logical: <code>TRUE</code> of <code>FALSE</code>. Whether the AFROC curve is to be drawn.

DrawAFROCcurve

Logical: <code>TRUE</code> of <code>FALSE</code>. Whether the CFP and CTP points are to be drawn. CFP: Cumulative false positive per lesion (or image) which is also called False Positive Fraction (FPF). CTP Cumulative True Positive per lesion which is also called True Positive Fraction (TPF)..

DrawCFPCTP

Logical, that is <code>TRUE</code> or <code>FALSE</code>. Whether or not the upper bounds of vertical axis are determined automatically.

Draw.Flexible.upper_y

Logical, that is <code>TRUE</code> or <code>FALSE</code>. Whether or not the lower bounds of vertical axis are determined automatically.

Draw.Flexible.lower_y

Logical: <code>TRUE</code> of <code>FALSE</code>. Whether to print the verbose summary, i.e., logical; If <code>TRUE</code> then verbose summary is printed in the R console. If <code>FALSE</code>, the output is minimal. I regret, this variable name should be verbose.

summary

An integer, for the color of background and etc.

type

Plot curves without any color (dark theme), that is, black and white (white backgroud with black curves). Draw FROC curves and AFROC curves for user's specified modality and user's specified reader.
Using this function repeatedly, we can draw or compare the different reader and modality in a same plane simultaneously.
So, we can visualize the difference of modality (reader).

Execute BayesianFROC::fit_GUI_Shiny() (or fit_GUI_Shiny_MRMC()) for a graphical user interface via Shiny. The free-response receiver operating characteristic (FROC) method developed by Chakraborty is a generalization of receiver operating characteristic analysis, but Chakraborty used a non-Bayesian approach. This package aims to reconstruct Chakraborty's technique using a Bayesian approach and to verify that our models fit practical datasets. We also develop hierarchical Bayesian models for comparing modalities with new methods. The ultimate aim of FROC analysis is to compare observer performances, which means comparing characteristics, such as area under the curve (AUC) or figure of merit (FOM). In this package, we only use the notion of AUC for modality comparison, where by "modality", we mean imaging methods such as Magnetic Resonance Imaging (MRI), Computed Tomography (CT), Positron Emission Tomography (PET), ..., etc. So there is a problem that which imaging method is better to detect lesions from shadows in radiographs. To solve modality comparison issues, this package provides new methods using hierarchical Bayesian models proposed by the author of this package. Using this package, one can obtain at least one conclusion that which imaging methods are better for finding lesions in radiographs with the case of your data. Fitting FROC statistical models is sometimes not so good, it can easily confirm by drawing FROC curves and comparing these curves and the points constructed by False Positive fractions (FPFs) and True Positive Fractions (TPFs), we can validate the goodness of fit intuitively. Such validation is also implemented by the Chi square goodness of fit statistics in the Bayesian context which means that the parameter is not deterministic, thus by integrating it with the posterior predictive measure, we get a desired value. To compare modalities (imaging methods: MRI, CT, PET, ... , etc), we evaluate AUCs for each modality. FROC is developed by Dev Chakraborty, his FROC model in his 1989 paper relies on the maximal likelihood methodology. The author modified and provided the alternative Bayesian FROC model. Strictly speaking, his model does not coincide with models in this package. In FROC context, we means by multiple reader and multiple case (MRMC) the case of the number of reader or modality is two or more. The MRMC data is available for functions of this package. I hope that medical researchers use not only the frequentist method but also alternative Bayesian methods. In medical research, many problems are considered under only frequentist methods, such as the notion of p-values. But p-value is sometimes misunderstood. Bayesian methods provide very simple, direct, intuitive answer for research questions. Combining frequentist methods with Bayesian methods, we can obtain more reliable answer for research questions. Please execute the following R scripts from the R (R studio) console, demo(demo_MRMC, package = "BayesianFROC"); demo(demo_srsc, package = "BayesianFROC"); demo(demo_stan, package = "BayesianFROC"); demo(demo_drawcurves_srsc, package = "BayesianFROC"); demo_Bayesian_FROC(); demo_Bayesian_FROC_without_pause(). References: Dev Chakraborty (1989) <doi:10.1118/1.596358> Maximum likelihood analysis of free - response receiver operating characteristic (FROC) data. Pre-print: Issei Tsunoda; Bayesian Models for free-response receiver operating characteristic analysis. See the vignettes for more details.

Issei Tsunoda

BayesianFROC

FROC Analysis by Bayesian Approaches

DrawCurves_MRMC_pairwise_BlackWhite function

An S4 object of class <code> <a rd-options='' href='stanfitExtended'>stanfitExtended</a></code> which is an inherited class from the S4 class <code><a rd-options='rstan' href='stanfit'>stanfit</a></code>. This R object can be passed to the <code><a rd-options='' href='DrawCurves'>DrawCurves</a>()</code>, <code><a rd-options='' href='ppp'>ppp</a>()</code> and ... etc

DrawCurves_MRMC_pairwise_BlackWhite: Draw the FROC curves without colour

Description

Usage

Arguments