*In GUI, if the second row in the table is vanished, then ppp() failed,…. Why does such bug occur?? ha. I am tired. 2020 March 8
FPF and TPF plot by mean and CI inteval, the scatter plot is hard to see.
Bayes Factor
SBC
Mean and Conf. Interval representation for synthesized datasets in the scatter plot of ppp()
Reduce dependencies
Applying the central limit theorem,
\[d \log \Phi \in \text{Exponential family}?\] If not how we can approximate it by exponential family
summary cannot use, I regret, in my package my initial periods, I use summary for extract estimates from stanfit, which does not allow me to make generic function summary for stanfitExtended, since the code is overlapped and cause error.If x1(t),…,xn(t) are curves into plane, then we can define its mean curve
by x(t):= mean(x1,…,xn). Or use mean parameter over all readers to get modaitywise one.
I think, if number of readers are very large, then I guess such pooling will be required. 2020 Jan
Check Packgae –R CMD check additional options should be specified as following
--as-cran --run-donttest
the author noticed that he should use
`if (interactive()) { }`BayesianFROC.Rcheck / BayesianFROC-Ex.R shows the example codes designated in #'@examples.
uses \dontrun instead \donttest
improves prior to get more uniformly distributed rank statistics of SBC
the following roxygen is not allowed and causes error on R CMD check.
#' @examples
# \dontrun{ <- as comment, not code
#' \donttest{
#'
#'
#'}#donttest
#'
#}#dontrun <- as comment, not codeIn case of a single reader and multple modaity case, an array of type, e.g., [3,1] is reduced to a vector of dimension 3 and it caused some error. So, the author fixed it.
The author had forgotten to adjust the number of lesions denoted by NL for the function ppp_srsc such that it reflects the number of hits. It caused the true positive fractions of fake datasets to calculates ppp are greater than 1. So, in this update, the author has fixed this.
2020 Jan
GUI for MRMC
Non-hierarchical MRMC Model is introduced as a new model to avoid the divergent transition issues
2019 Oct 21
In roxygen comments, the following multiple line does not be allowed.
\code{
ssssss
ssss
sss
}Moreover such multiple line cannot be detected by the R CMD check in my computer but in R CMD check in CRAN detects it. So the debug or find such multiple line is very hard to find because the error message never specify the information about such a location.
In .Rd files I should not use
or or any other. The reason is it cause unknown errors. The author struggled these unknown issues in several days. Because, the error is not appear in R CMD check in my computer but in CRAN auto check says the error that
Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64 Check: PDF version of manual, Result: WARNING LaTeX errors when creating PDF version. This typically indicates Rd problems. LaTeX errors found: ! Paragraph ended before was complete.
l.16983
This error is very heavy to debug.
The statistical model and theory is significantly changed. The previous models are not generate models. To ensure the sum of hits is less than the number of lesions, we have to change the model and the author has changed so that the summation condition satisfies and hence we obtain the generative model so that the model generates the dataset of FROC trial.
The posterior predictive p values (ppp) is wrong in the previous release. Thus, in the current release, I ensure the ppp and fixed.
ppp() very correctly works!Made a ppp() for Predictive Posterior P value and implement on the Shiny GUI in fit_GUI_Shiny()
For the only one modality case, I made a model to pool AUCs among readers.
I attempted to use rstantools::rstan_create_package("name") but I failed. I am not so young, I do not want to waste a time to fix errors. head ache. no. ital.
2019 August 2
Revise the GUI of BayesianFROC::fit_GUI() so that it is faster, and add more buttons in it.
Shiny based Graphical User Interface for fitting and estimates and drawing curve;
fit_GUI()
fit_GUI_simple()
fit_GUI_dashboard() .css file is used
Develop theory, in particular, the author find some latent variable to determine the false alarm rate,
SBC for SRSC
Provides a GUI via Shiny for single reader and single modality.
BayesianFROC::fit_GUI() Provides posterior mean of chi square goodness of fit for MRMC case.
Fix the following inconsistent
model <- stan_model(
model_code = "parameters { real<lower = 0> y; }
transformed parameters { real<upper = -1> z = y; }"
)
fit <- sampling(model)which cause the error
[1] "Error in sampler$call_sampler(args_list[[i]]) : Initialization failed."Some Stan developer taught this in stack over flows, His answer is very plain, I appreciate him. He helps me many times, thank you.
2019.Jun
In statistical perspective,
I use proper priors instead of improper priors which does not be shown yet in vignettes.
I export the null hypothesis test via Bayes factor. (The result is converse, why???)
Stan file had been changed from improper priors to proper priors.
Proper priors decrease WAIC for some dataset.
Fix English or Grammar in documents of manual and vignettes.
Fix errors.
2019.05.22 Revised.
Core R scripts is changed but Stan file is not changed essentially.
The aim of update is fix English or Grammar in documents of manual and vignettes.
I found [F7] key is useful for spell check of Rmd file.
CRAN.